# Comparative Genomics of Ten Solanaceous Plastomes

Authors: Harpreet Kaur; Bhupinder Pal Singh; Harpreet Singh; Avinash Kaur Nagpal
Journal: Advances in Bioinformatics
 (2014)

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## Abstract

Availability of complete plastid genomes of ten solanaceous species,Atropa belladonna, Capsicum annuum, Datura stramonium, Nicotiana sylvestris, Nicotiana tabacum, Nicotiana tomentosiformis, Nicotiana undulata, Solanum bulbocastanum, Solanum lycopersicum, and Solanum tuberosum provided us with an opportunity to conduct their in silico comparative analysis in depth. The size of complete chloroplast genomes and LSC and SSC regions of three species of Solanum is comparatively smaller than that of any other species studied till date (exception: SSC region of A. belladonna). AT content of coding regions was found to be less than noncoding regions. A duplicate copy of trnH gene in C. annuum and two alternative tRNA genes for proline in D. stramonium were observed for the first time in this analysis. Further, homology search revealed the presence of rps19 pseudogene and infA genes in A. belladonna and D. stramonium, a region identical to rps19 pseudogene in C. annum and orthologues of sprA gene in another six species. Among the eighteen intron-containing genes, 3 genes have two introns and 15 genes have one intron. The longest insertion was found in accD gene in C. annuum. Phylogenetic analysis using concatenated protein coding sequences gave two clades, one for Nicotiana species and another for Solanum, Capsicum, Atropa, and Datura.


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## Body

## 1. Introduction

Chloroplasts are essential cellular organelles within plant cells possessing the enzymatic machinery for the process of photosynthesis which provides essential energy to plants. Besides photosynthesis, chloroplasts are also involved in biosynthesis of fatty acids, amino acids, pigments, and vitamins [1, 2]. Despite enormous divergence in whole plant form and habitat, chloroplast structure and function have remained remarkably conserved which might be due to intense evolutionary selection pressures associated with the functional requirements of photosynthesis [3–7]. The chloroplast genome is actually a reduced genome derived from a cyanobacterial ancestor that was captured early in the evolution of the eukaryotic cell [8, 9]. Among the three genomes of the plant cell, the plastome is the most gene dense with more than 100 genes in a genome of only 120 to 210 kb [10]. In the last two decades, the nucleotide sequences of large number of plastid genomes have been published leading to better understanding of their organization and evolution [2, 11, 12]. Currently, about 470 eukaryotic chloroplast genomes have been sequenced completely (http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=2759&hopt=html) with the best representation from flowering plants.Most land plant chloroplast genomes are composed of a single circular chromosome with a quadripartite structure which includes two copies of an inverted repeat (IR) region that separates the large and small single copy regions (LSC and SSC). Genes of chloroplast genomes of higher plants can be divided into three broad categories [13, 14]. In the first, there are genetic system genes encoding for rRNAs, tRNAs, ribosomal proteins, and RNA polymerase subunits. The second category is comprised of genes for photosynthesis which encode subunits of the two photosystems, the cytochrome b6f complex and the ATP synthase. Open reading frames (orfs) of unknown function constitute the third category. Besides, there are some other genes coding for different kinds of proteins including infA, matK, clpP, cemA, accD, and ccsA. Although overall chloroplast genome organization is highly conserved among taxa, structural rearrangements due to inversions have been reported in different taxa like Campanulaceae [15], Cyatheaceae [16], Fabaceae [17], Funariaceae [18], Geraniaceae [19], Onagraceae [20], and Poaceae [21, 22]. Besides structural rearrangements, sequence polymorphisms have also been reported in some cereals [23, 24] andOenothera species [20]. These studies revealed that highly divergent sequences were concentrated in specific regions called “hotspots.” Such sequence polymorphisms have been used to derive phylogenetic relationships among species.Solanaceae is an important family of dicots comprising more than 3000 species placed within about 90 genera. It is an ethnobotanical family and is extensively utilized by humans and has recently become a model of comparative and evolutionary genomics research. Few efforts have been made to study the variations in chloroplast genomes of Solanaceae family by usingin silico tools. Most of these attempts have been concentrated on comparison of newly sequenced chloroplast genome with the available complete chloroplast genomes from some members of this family [25–29]. The availability of complete nucleotide sequences of plastid genomes of ten solanaceous species,Atropa belladonna (NC_004561.1; [30]),Capsicum annuum (NC_018552.1; [29]),Datura stramonium (NC_018117.1; Li et al. (unpublished)),Nicotiana sylvestris (NC_007500.1; [28]),Nicotiana tabacum (NC_001879.2; [31]),Nicotiana tomentosiformis (NC_007602.1; [28]),Nicotiana undulata (NC_016068.1; [32]),Solanum bulbocastanum (NC_007943.1; [26]),Solanum lycopersicum (NC_007898.2; [27]), andSolanum tuberosum (NC_008096.2; [33]), provided us with an opportunity to conduct theirin silico comparative analysis in depth. Hence, the present study is an attempt to compare the genome organization, structure, and coding capacity of chloroplast genomes of ten solanaceous species. The study focuses on length mutations, intron-containing genes, grouping of genes in different identity classes based on pairwise comparison of individual genes, and InDel analysis of divergent genes.


## 2. Materials and Methods

### 2.1. Sequence Analysis

Whole chloroplast genome sequences as well as individual gene and protein sequences of ten solanaceous species were obtained from “Organelle Genome Resources” section of NCBI in Genbank as well as in Fasta format. Sequence regions corresponding to various genomic features including genes, exons, introns, and cds were specifically extracted from the Genbank files using Extractfeat, Extractseq, and Featcopy programs from Jemboss package. AT percentage for different genomic regions was calculated using Wordcount and Union programs from Jemboss package. Pairwise comparison of gene sequences was done by using NCBI BLAST program and multiple sequence alignment of nucleotide as well as protein sequences was done by using ClustalW. Alignments of protein sequences for some of the genes were manually edited in correspondence to InDels observed in alignments of their nucleotide sequences.


### 2.2. Phylogenetic Analysis of Concatenated Protein-Coding Genes

75 protein-coding genes of plastomes of ten solanaceous species and two outgroup species (Daucus carota andCoffea arabica) were selected for phylogenetic analysis from the total of 79 classified protein-coding genes excluding accD, rpl20, ycf1, and ycf15. Ycf15 was excluded due to its absence on the plastome of both outgroup species chosen while the other three were not included in the phylogenetic analysis due to their high levels of variation. Multiple sequence alignment of each gene was obtained using ClustalW (https://www.ebi.ac.uk/Tools/msa/clustalw2/). These alignments were then concatenated using standalone BIOEDIT version 7.25 (http://www.mbio.ncsu.edu/bioedit/bioedit.html) and maximum likelihood phylogenetic tree with 500 bootstrap iterations was constructed using PhyMLv3.0 (http://www.atgc-montpellier.fr/phyml/). A graphical view of tree was generated using Archaeopteryx 0.988 SR (https://sites.google.com/site/cmzmasek/home/software/archaeopteryx).


## 2.1. Sequence Analysis

Whole chloroplast genome sequences as well as individual gene and protein sequences of ten solanaceous species were obtained from “Organelle Genome Resources” section of NCBI in Genbank as well as in Fasta format. Sequence regions corresponding to various genomic features including genes, exons, introns, and cds were specifically extracted from the Genbank files using Extractfeat, Extractseq, and Featcopy programs from Jemboss package. AT percentage for different genomic regions was calculated using Wordcount and Union programs from Jemboss package. Pairwise comparison of gene sequences was done by using NCBI BLAST program and multiple sequence alignment of nucleotide as well as protein sequences was done by using ClustalW. Alignments of protein sequences for some of the genes were manually edited in correspondence to InDels observed in alignments of their nucleotide sequences.


## 2.2. Phylogenetic Analysis of Concatenated Protein-Coding Genes

75 protein-coding genes of plastomes of ten solanaceous species and two outgroup species (Daucus carota andCoffea arabica) were selected for phylogenetic analysis from the total of 79 classified protein-coding genes excluding accD, rpl20, ycf1, and ycf15. Ycf15 was excluded due to its absence on the plastome of both outgroup species chosen while the other three were not included in the phylogenetic analysis due to their high levels of variation. Multiple sequence alignment of each gene was obtained using ClustalW (https://www.ebi.ac.uk/Tools/msa/clustalw2/). These alignments were then concatenated using standalone BIOEDIT version 7.25 (http://www.mbio.ncsu.edu/bioedit/bioedit.html) and maximum likelihood phylogenetic tree with 500 bootstrap iterations was constructed using PhyMLv3.0 (http://www.atgc-montpellier.fr/phyml/). A graphical view of tree was generated using Archaeopteryx 0.988 SR (https://sites.google.com/site/cmzmasek/home/software/archaeopteryx).


## 3. Results and Discussion

### 3.1. Comparison of Properties of Chloroplast Genomes

Comparison of the properties of plastid genomes of ten solanaceous species with respect to their genome size (size of complete plastid genome and LSC, SSC, and IR regions); percent coding regions, introns, and intergenic regions; AT content of overall plastid genomes as well as coding and noncoding regions is presented in Table1. The total plastid genome size ranged from 155296 bp (S. tuberosum) to 156781 bp (C. annuum). The large size of plastome ofC. annuum can be attributed to large LSC region as compared to other species. On the contrary, size of SSC region inC. annuum was the least as compared to other species. The largest size of IR region was inA. belladonna. Among fourNicotiana species studied,N. sylvestris andN. tabacum were almost identical to each other with respect to size of complete genome (difference of only 2 bps) or LSC, SSC, or IR regions compared with plastome of any other species studied. However the percent coding region was slightly more forN. sylvestris (61.49%) than inN. tabacum (61.12%). The size of complete chloroplast genome and LSC and SSC regions of three species ofSolanum is comparatively smaller than that of any other species studied except forA. belladonna where size of SSC region was the smallest (18008 bp). However the size of IR region ofSolanum species is larger as compared toNicotiana species. Coding region percentage was found to be higher inNicotiana species as compared to all other species with maximum forN. undulata (63.12%) and minimum forS. tuberosum (58.45%). Maximum of 12.8% of the plastome was shown to be introns forS. bulbocastanum whereas minimum intron percentage (11.62%) was observed forD. stramonium. Maximum percentage (29.19%) of intergenic region was observed inD. stramonium and minimum (24.19%) was observed inN. undulata. The AT content of noncoding regions was found to be higher as compared to coding regions for all the ten species studied. Similarly, protein-coding regions have shown higher content of AT base pairs as compared to RNA coding genes which can be explained by the requirement of more GC base pairs for proper folding of highly structured ribosomal RNAs and tRNAs [13–27]. Comparison of AT content in LSC, SSC, and IR regions reveals that AT content was the highest in SSC regions and the lowest in IR regions. Some earlier studies have also shown similar distribution of AT content in LSC, SSC, and IR regions with the lowest AT content in IR region and the highest AT content in SSC region [2, 27, 34, 35]. The low AT content of IR regions reflects low AT content in the four ribosomal RNA genes in this region.Table 1
Properties of the solanaceous chloroplast genomes.
Property
Name of species
ABE
CAN
DST
NSY
NTA
NTO
NUN
SBU
SLY
STU
Genome size (bp)
156687
156781
155871
155941
155943
155745
155863
155371
155461
155296
LSC (bp) (coordinates)*
86,869 (1–86869)
87366 (1–87366)
86297 (1–86297)
86684 (1–86684)
86,686 (1–86686)
86392 (1–86392)
86633 (1–86633)
85785 (1–85785)
85,882 (1–85882)
85737 (1–85737)
IRB (bp) (coordinates)*
25,905 (86870–112774)
25783 (87367–113149)
25563 (86298–111860)
25342 (86685–112026)
25,343 (86687–112029)
25429 (86393–111821)
25331 (86634–111964)
25588 (85786–111373)
25,608 (85883–111490)
25593 (85738–111330)
SSC (bp) (coordinates)*
18,008 (112775–130782)
17849 (113150–130998)
18448 (111861–130308)
18573 (112027–130599)
18,571 (112030–130600)
18495 (111822–130316)
18568 (111965–130532)
18381 (111374–129754)
18,363 (111491–129853)
18373 (111331–129703)
IRA (bp) (coordinates)*
25,905 (130783–156687)
25783 (130999–156781)
25563 (130309–155871)
25342 (130600–155941)
25,343 (130601–155943)
25429 (130317–155745)
25331 (130533–155863)
25588 (129755–155342)
25,608 (129854–155461)
25593 (129704–155296)
Coding regions (%)
58.89
58.50
59.19
61.49
61.12
61.58
63.12
58.52
58.91
58.45
Introns (%)
12.51
12.71
11.62
12.70
12.70
12.68
12.69
12.82
12.47
12.49
Intergenic regions (%)
28.60
28.79
29.19
25.81
26.18
25.73
24.19
28.66
28.62
29.06
AT content (%)
Overall
62.44
62.27
62.12
62.15
62.15
62.21
62.12
62.12
62.14
62.12
Coding regions
59.86
59.68
59.65
59.85
59.79
59.79
59.70
59.61
59.65
59.59
Noncoding regions
66.13
65.93
65.72
65.84
65.87
66.09
66.27
65.66
65.71
65.68
tRNAs
47.70
47.38
47.08
47.06
47.05
47.10
47.08
47.12
47.01
47.06
rRNAs
44.64
44.73
44.63
44.64
44.64
44.64
44.64
44.66
44.66
44.65
Protein-coding genes
62.01
61.83
61.79
61.91
61.86
61.84
61.68
61.76
61.80
61.74
LSC
64.37
64.25
64.04
64.05
64.05
64.12
64.01
63.99
64.01
63.99
SSC
68.35
67.99
67.72
67.94
67.93
68.03
67.87
67.87
67.97
67.91
IR
57.14
56.94
56.87
56.78
56.78
56.84
56.78
56.93
56.91
56.90
ABE:Atropa belladonna, CAN: Capsicum annuum, DST: Datura stramonium, NSY: Nicotiana sylvestris, NTA: Nicotiana tabacum, NTO: Nicotiana tomentosiformis, NUN: Nicotiana undulata, SBU: Solanum bulbocastanum, SLY: Solanum lycopersicum, STU: Solanum tuberosum, LSC: large single copy region, SSC: small single copy region, and IR: inverted repeat region.
*Start and end position of nucleotide in the genome.


### 3.2. Gene Content of Solanaceous Chloroplast Genomes

The genes present in different regions of the plastid genomes are highly conserved except for several open reading frames [6, 26, 36]. There are typically 111 genes, 5 hypothetical chloroplast reading frames (ycfs), and few open reading frames (orfs). Some of our unique findings have been discussed below.(i)
The trnP-GGG which codes for tRNA for proline was annotated only inD. stramonium whereas its alternative code trnP-UGG was annotated in all other species includingD. stramonium (NC_018117.1; Li et al. (unpublished)). We mined all the species for similar sequence by BLAST search but no similar sequence was found in any other species. Gene trnH was only reported to be trnH coding gene inC. annuum. In all other species, this region was reported to be part of ycf2 gene as inC. annuum also. These observations indicate the presence of duplicate copy of trnH gene sequence inC. annuum and twoalternative tRNA genes coding for proline amino acid inD. stramonium. However, no other evidence was found in databases about this particular region coding for trnH.
(ii)
Rps19 pseudogene was reported in three species, namely,N. tomentosiformis,S. bulbocastanum, andS. tuberosum. All other species were mined for similar pseudogene using BLAST pairwise algorithm which confirmed the presence of rps19 pseudogene in other species, namely,A. belladonna,C. annuum, andD. stramonium. The presence of pseudogene may be attributed to the expansion of IRB into the LSC region. In three species, namely,N. sylvestris,N. tabacum, andN. undulata, rps19 pseudogene was found to be absent.
(iii)
infA, a pseudogene for all species exceptA. belladonna,D. stramonium, andS. Lycopercicum, is a protein-coding gene forS. bulbocastanum. Homology search with infA sequence fromS. bulbocastanum against plastomes ofA. belladonna andD. stramonium revealed identical sequence in both species.
(iv)
sprA gene has been annotated forN. sylvestris,N. tomentosiformis,S. lycopersicum, andS. tuberosum. Its identical orthologous gene sequences were found inA. belladonna,C. annuum,D. stramonium,N. tabacum,N. undulata, andS. bulbocastanum using BLAST search.


### 3.3. Split Genes

A total of eighteen split genes have been reported. The sizes of exons and introns for these genes in all the solanaceous species studied are summarized in Table2. The rps12 gene is divided such that its 5′ end exon is located in the LSC region whereas second and third exons are located in the IR region. Maturation of RNA transcript requires a trans-splicing mechanism between exon 1 and exon 2 [34, 37]. Among the eighteen intron-containing genes, ycf3, clpP, and rps12 contained two introns whereas the other 15 genes contain only one intron. As per Kim and Lee [34] trnL-UAA gene intron belongs to the self-splicing group I intron whereas all other introns belong to group II. Generally, the size of exons was shown to be conserved and variability was observed in the intron regions; however, ndhB was found to be highly conserved for both exons and introns.Table 2
The lengths of introns and exons for the split genes of ten solanaceous species.
Gene (region)
Exon/intron
ABE
CAN
DST
NSY
NTA
NTO
NUN
SBU
SLY
STU
trnK-UUU (LSC)
Exon I
37
37
37
37
37
37
37
37
37
37
Intron I
2519
2500
2506
2526
2526
2526
2521
2501
2514
2512
Exon II
36
35
35
35
35
35
35
35
35
35
rps16 (LSC)
Exon I
40
40
40
40
40
40
40
40
40
40
Intron I
822
865
866
860
860
860
859
855
864
855
Exon II
227
227
227
218
218
218
218
227
227
227
trnG-UCC (LSC)
Exon I
23
23
23
23
23
23
23
23
23
23
Intron I
692
692
694
692
692
690
691
701
695
692
Exon II
48
48
48
48
48
48
48
37
48
48
atpF (LSC)
Exon I
145
145
145
145
145
145
145
144
144
145
Intron I
715
693
700
695
695
692
692
693
686
693
Exon II
410
410
410
410
410
410
410
411
411
410
rpoC1 (LSC)
Exon I
432
453
453
453
453
432
453
453
453
453
Intron I
737
742
737
737
737
709
733
737
737
737
Exon II
1614
1614
1614
1614
1614
1614
1623
1614
1614
1614
ycf3 (LSC)
Exon I
124
124
124
124
124
124
124
124
124
124
Intron I
739
742
740
739
738
731
735
730
729
727
Exon II
230
230
230
230
230
230
230
230
230
230
Intron II
763
744
753
783
783
779
781
750
750
750
Exon III
153
153
159
153
153
153
153
153
153
153
trnL-UAA (LSC)
Exon I
35
35
35
35
35
35
35
37
35
35
Intron I
497
426
501
503
503
497
498
502
497
497
Exon II
50
50
50
50
50
50
50
50
50
50
trnV-UAC (LSC)
Exon I
38
38
38
38
38
38
38
38
38
38
Intron I
572
575
569
571
571
572
573
569
571
571
Exon II
35
35
37
35
35
35
35
37
35
35
rps12*
Exon I
114
114
114
114
114
114
114
114
114
114
Intron I
—
—
—
—
—
—
—
—
—
—
Exon II
232
232
232
232
232
232
232
232
232
232
Intron II
535
536
536
536
536
536
536
536
536
536
Exon III
26
26
26
26
26
26
26
26
26
26
clpP (LSC)
Exon I
71
71
71
71
71
71
71
71
71
71
Intron I
799
811
792
807
807
789
789
789
798
789
Exon II
292
292
292
292
292
292
292
292
292
292
Intron II
622
626
624
637
637
634
631
625
617
620
Exon III
228
228
234
228
228
228
228
234
258
234
petB (LSC)
Exon I
6
6
6
6
6
6
6
6
6
6
Intron I
759
755
746
753
753
753
753
747
747
747
Exon II
642
642
642
642
642
642
642
642
642
642
petD (LSC)
Exon I
8
8
9
8
8
8
8
6
8
8
Intron I
742
742
748
742
742
742
742
739
738
739
Exon II
475
475
474
475
475
475
475
477
475
475
rpl16 (LSC)
Exon I
9
9
9
9
9
9
9
9
9
9
Intron I
1019
1026
1025
1020
1020
1021
1020
1014
1018
1014
Exon II
396
396
396
396
396
396
396
396
396
396
rpl2 (IR)
Exon I
391
391
393
391
391
391
391
390
391
391
Intron I
664
665
669
666
666
666
666
666
666
666
Exon II
434
434
429
434
434
434
434
435
434
434
ndhB (IR)
Exon I
777
777
777
777
777
777
777
777
777
777
Intron I
679
679
679
679
679
679
679
679
679
679
Exon II
756
756
756
756
756
756
756
756
756
756
trnI-GAU (IR)
Exon I
37
37
42
37
37
37
37
42
37
37
Intron I
717
722
717
707
707
716
716
717
722
722
Exon II
34
35
35
35
35
35
35
35
35
35
trnA-UGC (IR)
Exon I
38
38
38
38
38
38
38
38
38
38
Intron I
681
811
811
709
709
709
709
811
811
811
Exon II
35
35
35
35
35
35
35
35
35
35
ndhA (SSC)
Exon I
553
553
552
553
553
553
553
552
553
553
Intron I
1150
1157
1154
1148
1148
1149
1148
1158
1133
1158
Exon II
539
539
537
539
539
539
539
540
539
539
*rps12 gene is dividing gene. The 3′-rps12 locates on the IR-region, while the 5′-rps12 locates on the LSC region.
ABE:Atropa belladonna, CAN: Capsicum annuum, DST: Datura stramonium, NSY: Nicotiana sylvestris, NTA: Nicotiana tabacum, NTO: Nicotiana tomentosiformis, NUN: Nicotiana undulata, SBU: Solanum bulbocastanum, SLY: Solanum lycopersicum, and STU: Solanum tuberosum.


### 3.4. Pairwise Comparison of Plastid Genes of Solanaceae and InDel Analyses

Pairwise comparison of nucleotide sequences of individual gene sequences (45 combinations) for 116 genes was also performed to classify genes based on percent identity. Supplementary Table 1 (Supplementary Material available online athttp://dx.doi.org/10.1155/2014/424873) shows grouping of genes in different clusters based on percent identity in pairwise comparison. Genes which showed 100% identity in comparison were considered as highly conserved and the genes showing less than 95% identity at least once in the comparison were considered as highly divergent. These highly divergent genes were further explored at nucleotide as well as at protein level to probe the variations in detail. A total of 11 highly divergent genes were found whereas the number of highly conserved genes varied from 26 (for species pair:N. tomentosiformis andS. lycopersicum) to 107 (for species pair:N. sylvestris andN. tabacum). Most of the tRNA genes were found to be highly conserved. Genes accD, cemA, clpP, ndhA, rpl32, rpl36, rps16, sprA, trnA-UGC, trnL-UAA, and ycf1 were found to be highly diverged.Tables3 and 4 describe the summary of InDels observed in nucleotide and amino acid sequences, respectively. Partial multiple sequence alignment of 9 genes and 5 proteins is shown in Figures 1 and 2, respectively. The longest insertion of 141 bp was observed in accD gene sequence ofC. annuum. Since genes clpP, ndhA, rps16, and trnL-UAA contained introns, it was important to examine whether these InDels were present in exon or intron region. It was found that all the InDels reported in ndhA and trnL-UAA were present in introns whereas, in case of clpP, InDel 24 was located in exon of the gene. Similarly, the first and last InDels of gene rps16 were present in exons of the gene. Keeping in view the observations in number and length of InDels in nucleotide and protein sequences of genes under consideration, the variation for individual genes is discussed below.Table 3
InDels in nucleotide sequences of 9 genes of ten solanaceous plastid genomes.
S. number
Geneabc
Total number of InDels
InDel length (bp)
1
accDa
4
24, 9, 141, 6
2
clpPa
24
8(I), 14(I), 13(I), 7(I), 1(I), 2-3(I), 7(I), 1–7(I), 3(I), 2(I), 3(I), 1–7(I), 1–3(I), 1(I), 1(I), 1(I), 1–5(I), 4–7(I), 1(I), 9(I), 1-2(I), 3(I), 5(I), 24–30
3
ndhAb
14
9(I), 5-6(I), 3(I), 1(I), 9(I), 3(I), 4(I), 1–4(I), 1-2(I), 1–23(I), 1-2(I), 2(I), 1(I), 3(I)
4
rpl32b
2
2-3, 4
5
rps16a
11
1–38, 9(I), 1(I), 1(I), 5(I), 1-2(I), 5(I), 4(I), 6(I), 1(I), 9
6
sprAb
2
109, 7
7
trnA-UGCc
1
102–130
8
trnL-UAAa
4
1, 6, 71, 4
9
ycf1b
31
3, 18, 18, 21, 6, 6, 48, 9, 6, 6, 42, 3, 6, 30, 3, 15, 12–39, 18, 6, 9–36, 6, 6, 6, 9, 9, 12, 6, 6, 6, 57, 6
abcLocation in different regions; aLSC, bSSC, and cIR; I: InDels present in introns.Table 4
InDels in amino acid sequences of 5 proteins of ten solanaceous plastid genomes.
S. number
Protein
Total number of InDels
InDel length (bp)
1
accD
4
8, 3, 47, 2
2
clpP
2
2, 10
3
rpl32
1
1-2
4
rps16
1
3
5
ycf1
29
1, 6, 6, 7, 2, 2, 7, 3, 2, 2, 14, 1–10, 1, 5, 4–13, 6, 2, 3–12, 2, 2, 2, 3, 3, 4, 2, 2, 2, 19, 2Partial multiple sequence alignment of accD, clpP, ndhA, rpl32, rps16, sprA, tRNA-Ala (UGC), tRNA-Leu(UAA), and ycf1 gene sequences of ten solanaceous species showing location of InDels indicated by hyphens.Figure 2
Partial multiple sequence alignment of amino acid sequences of genes, namely, accD, clpP, ndhA, rpl32, rps16, sprA, tRNA-Ala(UGC), tRNA-Leu(UAA), and ycf1, of ten solanaceous species showing location of InDels indicated by hyphens.(1) accD. A total of four InDels were observed in accD gene as depicted in Figure 1. Insertion of 24 bp was present interestingly in allNicotiana species andD. stramonium followed by insertion of 9 bp in allSolanum species indicating stronger sequence conservation at genus level. These insertions were also reported by Chung et al. [25]. A 141 bp insertion was observed specifically inC. annuum which has also been reported by Jo et al. [29] and confirmed by RT-PCR. Similarly a species specific deletion of 6 bp was found inD. stramonium. All these InDels were also reflected in the corresponding protein sequences as shown in Figure 2. The accD gene has been reported to be one of the most variable plastid genes and is probably under diversifying selection [26].(2) clpP. In clpP gene InDels were found both in intron and in exon regions. Two major consequences were observed in the InDels in the exon regions. An insertion of 6 bp inS. bulbocastanum andS. tuberosum and 30 bp inS. lycopersicum at 3′ end (exon 3) of the clpP gene resulted in shifting of stop codon by 6, 6, and 30 bp downstream in respective species compared to other species of Solanaceae family, increasing the length of the coding sequence and the protein product (Figures 1 and 2). An interesting feature was observed as InDel 1 in protein sequence corresponding to insertion of a repeat of “I” amino acids inD. stramonium making exon 3 region longer by 6 bp. This region however corresponds to the end of intron 2 in clpP gene in all other species. SinceD. stramonium chloroplast genome has been sequenced recently, this observation needs to be experimentally validated.(3) ndhA. All the InDels found in ndhA were present in introns while the protein-coding regions (exons) were highly conserved. This indicates high diversifying selection on intronic region of this gene. Out of the total 14 InDels most of the InDels were observed with respect toC. annuum (InDels 1, 2, 5, 7, and 10). InDel 10 was observed to be shared byC. annuum andS. lycopersicum in full and byC. annuum andA. belladonna in part.(4) rpl32. In rpl32 insertion of 1 bp inD. stramonium and 3 bp inC. annuum was found in the 3′ region of gene while a deletion of 4 bp was observed inD. stramonium. The insertion of 3 bp inC. annuum only altered the length of the protein by making it longer by 1 amino acid. However, the small insertion of 1 bp inD. stramonium proved to be a frameshift mutation resulting in three changes in the amino acid sequence near the C-terminus. Moreover, deletion of 4 bp at the 3′ end resulted in premature termination of protein synthesis. The frameshift mutation and the 3′ end deletion finally reduced the gene product length by 1 amino acid. As the C-terminal of amino acid chain is well conserved in all the other species, the effect of above mentioned variations needs to be validated experimentally.(5) rps16. In rps16 also InDels were observed in introns as well as exons. Five of the major insertions in the intron regions were species specific. Insertion of 38 bp (InDel 1), 9 bp (InDel 2), 5 bp (InDel 7), 4 bp (InDel 8), and 6 bp (InDel 9) was observed inA. belladonna,S. lycopersicum,D. stramonium, andC. annuum. A deletion of 5 bp was observed in all the threeSolanum species andC. annuum. A deletion of 9 bp was observed in allNicotiana species resulting in an amino acid change (P to S) and shortening of protein by three amino acids in the C-terminal region. Similar deletion has also been observed by Kahlau et al. [27] and was suggested to be functionally neutral.(6) sprA. sprA gene has been reported as stable noncoding RNA of unknown function. This gene has been suggested to influence 16S rRNA maturation [38, 39]. In many species this gene seems to be present as remnant and shows large variations in its 5′ region. The largest deletion of 109 bp was observed inC. annuum. The rest of this gene appears to be more conserved with a deletion towards the 3′ end in allNicotiana species andA. belladonna. The manner in which this gene functions and the consequences of the above mentioned variations are yet to be investigated experimentally.(7) trnA-UGC. In this particular gene a long deletion of 102 bp was observed in allNicotiana species. Interestingly, this deletion was further extended to 130 bp in both directions inA. belladonna. These deletions were found in the intron region and so are unlikely to have any negative impact on gene product function.(8) trnL-UAA. The trend of variation in trnL-UAA was similar to that in ndhA as all InDels were observed in introns. The longest species specific deletion (InDel 3) was observed inC. annuum whereas short insertion of four nucleotides, a repeat of “T,” was observed specifically inD. stramonium. Another insertion of 6 bp was observed in twoNicotiana species, that is,N. sylvestris andN. tabacum.(9) ycf1. Many InDels (3′ region) were found in the fastest evolving gene, that is, ycf1 gene. Most of the InDels were found to be species specific. Maximum InDels (InDels 2, 3, 5, 7, 9, 16, 17, 19, 23, 24, 25, and 30) were observed inC. annuum followed byD. stramonium (InDels 4, 6, 20, 26, and 31), byN. tomentosiformis (InDels 8, 17, and 18), and byS. lycopersicum (InDels 16, 22, and 28). Two genus specific InDels (InDels 14 and 21) were observed in all the fourNicotiana species. However, InDel 19 was also present inD. stramonium. Another genus specific InDel (InDel 29) was observed inSolanum species. Most of the InDels altered the length of the gene product with maximum length of 1906 amino acids (aa) observed inC. annuum and the minimum of 1873 aa observed inD. stramonium. Among theSolanum species the length of protein (1887 aa) was conserved amongS. bulbocastanum andS. tuberosum. However,S. lycopersicum was having the amino acid sequence of 1891 aa, larger by 4 aa as compared to the other two species of the same genus. Among the fourNicotiana species the ycf1 gene product length was conserved amongN. sylvestris,N. tabacum, andN. undulata having protein lengths of 1901 aa, 1902 aa, and 1901 aa, respectively. However,N. tomentosiformis was observed to be the most variable member of the genusNicotiana having protein length of 1892 aa.


### 3.5. Phylogenetic Analysis of Solanaceous Plastomes

Evolutionary relationships between diverse plant species have been analyzed using several plastome markers including matK and rbcL (genes) or trnH-psbA and trnL-trnF (intergenic regions) due to sequence conservation among plant taxa blended with suitable variation [40, 41]. However, determination of phylogeny based on single gene sequences may be inaccurate [42]. Availability of complete chloroplast sequences for many species has made it possible to use many individual genes or concatenated gene sequences to deduce phylogenetic relationships among taxa [42–44].Efforts have been made to carry out phylogenetic analysis of solanaceous species using complete plastome sequences by Moore et al. [44] and Jansen et al. [45]. Evolutionary positions ofCapsicum andDatura in Solanaceae have been determined using a single or a few plastid genes [46, 47]. Recently, concatenated protein-coding gene sequences from completely sequenced plastomes were used to obtain reasonable phylogenetic relationships for solanaceous species [29]. In the present investigation we also used a similar approach to analyze the phylogenetic relationship for ten solanaceous species with completely sequenced plastomes. Individual multiple sequence alignments were concatenated for maximum likelihood phylogenetic tree generation. As depicted in Figure 3, taxa were divided into two clades with 100% bootstrap value of 500. The first clade consisted of fourNicotiana species while the species inSolanum,Capsicum,Atropa, andDatura were included in the second clade. These results are in line with previous phylogenetic analyses using concatenated protein-coding gene sequences as well as phylogenetic analyses using plastid ndhF and trnL-F sequences [29, 47]. However, in an analysis of 13 orfs of solanaceous plastomes, a different arrangement was shown in whichAtropa was shown to be separated fromSolanum and was grouped together withNicotiana [25].Figure 3
Maximum likelihood phylogenetic tree derived using concatenated nucleotide sequences of 75 protein-coding genes of ten solanaceous species and two outgroup species.


## 3.1. Comparison of Properties of Chloroplast Genomes

Comparison of the properties of plastid genomes of ten solanaceous species with respect to their genome size (size of complete plastid genome and LSC, SSC, and IR regions); percent coding regions, introns, and intergenic regions; AT content of overall plastid genomes as well as coding and noncoding regions is presented in Table1. The total plastid genome size ranged from 155296 bp (S. tuberosum) to 156781 bp (C. annuum). The large size of plastome ofC. annuum can be attributed to large LSC region as compared to other species. On the contrary, size of SSC region inC. annuum was the least as compared to other species. The largest size of IR region was inA. belladonna. Among fourNicotiana species studied,N. sylvestris andN. tabacum were almost identical to each other with respect to size of complete genome (difference of only 2 bps) or LSC, SSC, or IR regions compared with plastome of any other species studied. However the percent coding region was slightly more forN. sylvestris (61.49%) than inN. tabacum (61.12%). The size of complete chloroplast genome and LSC and SSC regions of three species ofSolanum is comparatively smaller than that of any other species studied except forA. belladonna where size of SSC region was the smallest (18008 bp). However the size of IR region ofSolanum species is larger as compared toNicotiana species. Coding region percentage was found to be higher inNicotiana species as compared to all other species with maximum forN. undulata (63.12%) and minimum forS. tuberosum (58.45%). Maximum of 12.8% of the plastome was shown to be introns forS. bulbocastanum whereas minimum intron percentage (11.62%) was observed forD. stramonium. Maximum percentage (29.19%) of intergenic region was observed inD. stramonium and minimum (24.19%) was observed inN. undulata. The AT content of noncoding regions was found to be higher as compared to coding regions for all the ten species studied. Similarly, protein-coding regions have shown higher content of AT base pairs as compared to RNA coding genes which can be explained by the requirement of more GC base pairs for proper folding of highly structured ribosomal RNAs and tRNAs [13–27]. Comparison of AT content in LSC, SSC, and IR regions reveals that AT content was the highest in SSC regions and the lowest in IR regions. Some earlier studies have also shown similar distribution of AT content in LSC, SSC, and IR regions with the lowest AT content in IR region and the highest AT content in SSC region [2, 27, 34, 35]. The low AT content of IR regions reflects low AT content in the four ribosomal RNA genes in this region.Table 1
Properties of the solanaceous chloroplast genomes.
Property
Name of species
ABE
CAN
DST
NSY
NTA
NTO
NUN
SBU
SLY
STU
Genome size (bp)
156687
156781
155871
155941
155943
155745
155863
155371
155461
155296
LSC (bp) (coordinates)*
86,869 (1–86869)
87366 (1–87366)
86297 (1–86297)
86684 (1–86684)
86,686 (1–86686)
86392 (1–86392)
86633 (1–86633)
85785 (1–85785)
85,882 (1–85882)
85737 (1–85737)
IRB (bp) (coordinates)*
25,905 (86870–112774)
25783 (87367–113149)
25563 (86298–111860)
25342 (86685–112026)
25,343 (86687–112029)
25429 (86393–111821)
25331 (86634–111964)
25588 (85786–111373)
25,608 (85883–111490)
25593 (85738–111330)
SSC (bp) (coordinates)*
18,008 (112775–130782)
17849 (113150–130998)
18448 (111861–130308)
18573 (112027–130599)
18,571 (112030–130600)
18495 (111822–130316)
18568 (111965–130532)
18381 (111374–129754)
18,363 (111491–129853)
18373 (111331–129703)
IRA (bp) (coordinates)*
25,905 (130783–156687)
25783 (130999–156781)
25563 (130309–155871)
25342 (130600–155941)
25,343 (130601–155943)
25429 (130317–155745)
25331 (130533–155863)
25588 (129755–155342)
25,608 (129854–155461)
25593 (129704–155296)
Coding regions (%)
58.89
58.50
59.19
61.49
61.12
61.58
63.12
58.52
58.91
58.45
Introns (%)
12.51
12.71
11.62
12.70
12.70
12.68
12.69
12.82
12.47
12.49
Intergenic regions (%)
28.60
28.79
29.19
25.81
26.18
25.73
24.19
28.66
28.62
29.06
AT content (%)
Overall
62.44
62.27
62.12
62.15
62.15
62.21
62.12
62.12
62.14
62.12
Coding regions
59.86
59.68
59.65
59.85
59.79
59.79
59.70
59.61
59.65
59.59
Noncoding regions
66.13
65.93
65.72
65.84
65.87
66.09
66.27
65.66
65.71
65.68
tRNAs
47.70
47.38
47.08
47.06
47.05
47.10
47.08
47.12
47.01
47.06
rRNAs
44.64
44.73
44.63
44.64
44.64
44.64
44.64
44.66
44.66
44.65
Protein-coding genes
62.01
61.83
61.79
61.91
61.86
61.84
61.68
61.76
61.80
61.74
LSC
64.37
64.25
64.04
64.05
64.05
64.12
64.01
63.99
64.01
63.99
SSC
68.35
67.99
67.72
67.94
67.93
68.03
67.87
67.87
67.97
67.91
IR
57.14
56.94
56.87
56.78
56.78
56.84
56.78
56.93
56.91
56.90
ABE:Atropa belladonna, CAN: Capsicum annuum, DST: Datura stramonium, NSY: Nicotiana sylvestris, NTA: Nicotiana tabacum, NTO: Nicotiana tomentosiformis, NUN: Nicotiana undulata, SBU: Solanum bulbocastanum, SLY: Solanum lycopersicum, STU: Solanum tuberosum, LSC: large single copy region, SSC: small single copy region, and IR: inverted repeat region.
*Start and end position of nucleotide in the genome.


## 3.2. Gene Content of Solanaceous Chloroplast Genomes

The genes present in different regions of the plastid genomes are highly conserved except for several open reading frames [6, 26, 36]. There are typically 111 genes, 5 hypothetical chloroplast reading frames (ycfs), and few open reading frames (orfs). Some of our unique findings have been discussed below.(i)
The trnP-GGG which codes for tRNA for proline was annotated only inD. stramonium whereas its alternative code trnP-UGG was annotated in all other species includingD. stramonium (NC_018117.1; Li et al. (unpublished)). We mined all the species for similar sequence by BLAST search but no similar sequence was found in any other species. Gene trnH was only reported to be trnH coding gene inC. annuum. In all other species, this region was reported to be part of ycf2 gene as inC. annuum also. These observations indicate the presence of duplicate copy of trnH gene sequence inC. annuum and twoalternative tRNA genes coding for proline amino acid inD. stramonium. However, no other evidence was found in databases about this particular region coding for trnH.
(ii)
Rps19 pseudogene was reported in three species, namely,N. tomentosiformis,S. bulbocastanum, andS. tuberosum. All other species were mined for similar pseudogene using BLAST pairwise algorithm which confirmed the presence of rps19 pseudogene in other species, namely,A. belladonna,C. annuum, andD. stramonium. The presence of pseudogene may be attributed to the expansion of IRB into the LSC region. In three species, namely,N. sylvestris,N. tabacum, andN. undulata, rps19 pseudogene was found to be absent.
(iii)
infA, a pseudogene for all species exceptA. belladonna,D. stramonium, andS. Lycopercicum, is a protein-coding gene forS. bulbocastanum. Homology search with infA sequence fromS. bulbocastanum against plastomes ofA. belladonna andD. stramonium revealed identical sequence in both species.
(iv)
sprA gene has been annotated forN. sylvestris,N. tomentosiformis,S. lycopersicum, andS. tuberosum. Its identical orthologous gene sequences were found inA. belladonna,C. annuum,D. stramonium,N. tabacum,N. undulata, andS. bulbocastanum using BLAST search.


## 3.3. Split Genes

A total of eighteen split genes have been reported. The sizes of exons and introns for these genes in all the solanaceous species studied are summarized in Table2. The rps12 gene is divided such that its 5′ end exon is located in the LSC region whereas second and third exons are located in the IR region. Maturation of RNA transcript requires a trans-splicing mechanism between exon 1 and exon 2 [34, 37]. Among the eighteen intron-containing genes, ycf3, clpP, and rps12 contained two introns whereas the other 15 genes contain only one intron. As per Kim and Lee [34] trnL-UAA gene intron belongs to the self-splicing group I intron whereas all other introns belong to group II. Generally, the size of exons was shown to be conserved and variability was observed in the intron regions; however, ndhB was found to be highly conserved for both exons and introns.Table 2
The lengths of introns and exons for the split genes of ten solanaceous species.
Gene (region)
Exon/intron
ABE
CAN
DST
NSY
NTA
NTO
NUN
SBU
SLY
STU
trnK-UUU (LSC)
Exon I
37
37
37
37
37
37
37
37
37
37
Intron I
2519
2500
2506
2526
2526
2526
2521
2501
2514
2512
Exon II
36
35
35
35
35
35
35
35
35
35
rps16 (LSC)
Exon I
40
40
40
40
40
40
40
40
40
40
Intron I
822
865
866
860
860
860
859
855
864
855
Exon II
227
227
227
218
218
218
218
227
227
227
trnG-UCC (LSC)
Exon I
23
23
23
23
23
23
23
23
23
23
Intron I
692
692
694
692
692
690
691
701
695
692
Exon II
48
48
48
48
48
48
48
37
48
48
atpF (LSC)
Exon I
145
145
145
145
145
145
145
144
144
145
Intron I
715
693
700
695
695
692
692
693
686
693
Exon II
410
410
410
410
410
410
410
411
411
410
rpoC1 (LSC)
Exon I
432
453
453
453
453
432
453
453
453
453
Intron I
737
742
737
737
737
709
733
737
737
737
Exon II
1614
1614
1614
1614
1614
1614
1623
1614
1614
1614
ycf3 (LSC)
Exon I
124
124
124
124
124
124
124
124
124
124
Intron I
739
742
740
739
738
731
735
730
729
727
Exon II
230
230
230
230
230
230
230
230
230
230
Intron II
763
744
753
783
783
779
781
750
750
750
Exon III
153
153
159
153
153
153
153
153
153
153
trnL-UAA (LSC)
Exon I
35
35
35
35
35
35
35
37
35
35
Intron I
497
426
501
503
503
497
498
502
497
497
Exon II
50
50
50
50
50
50
50
50
50
50
trnV-UAC (LSC)
Exon I
38
38
38
38
38
38
38
38
38
38
Intron I
572
575
569
571
571
572
573
569
571
571
Exon II
35
35
37
35
35
35
35
37
35
35
rps12*
Exon I
114
114
114
114
114
114
114
114
114
114
Intron I
—
—
—
—
—
—
—
—
—
—
Exon II
232
232
232
232
232
232
232
232
232
232
Intron II
535
536
536
536
536
536
536
536
536
536
Exon III
26
26
26
26
26
26
26
26
26
26
clpP (LSC)
Exon I
71
71
71
71
71
71
71
71
71
71
Intron I
799
811
792
807
807
789
789
789
798
789
Exon II
292
292
292
292
292
292
292
292
292
292
Intron II
622
626
624
637
637
634
631
625
617
620
Exon III
228
228
234
228
228
228
228
234
258
234
petB (LSC)
Exon I
6
6
6
6
6
6
6
6
6
6
Intron I
759
755
746
753
753
753
753
747
747
747
Exon II
642
642
642
642
642
642
642
642
642
642
petD (LSC)
Exon I
8
8
9
8
8
8
8
6
8
8
Intron I
742
742
748
742
742
742
742
739
738
739
Exon II
475
475
474
475
475
475
475
477
475
475
rpl16 (LSC)
Exon I
9
9
9
9
9
9
9
9
9
9
Intron I
1019
1026
1025
1020
1020
1021
1020
1014
1018
1014
Exon II
396
396
396
396
396
396
396
396
396
396
rpl2 (IR)
Exon I
391
391
393
391
391
391
391
390
391
391
Intron I
664
665
669
666
666
666
666
666
666
666
Exon II
434
434
429
434
434
434
434
435
434
434
ndhB (IR)
Exon I
777
777
777
777
777
777
777
777
777
777
Intron I
679
679
679
679
679
679
679
679
679
679
Exon II
756
756
756
756
756
756
756
756
756
756
trnI-GAU (IR)
Exon I
37
37
42
37
37
37
37
42
37
37
Intron I
717
722
717
707
707
716
716
717
722
722
Exon II
34
35
35
35
35
35
35
35
35
35
trnA-UGC (IR)
Exon I
38
38
38
38
38
38
38
38
38
38
Intron I
681
811
811
709
709
709
709
811
811
811
Exon II
35
35
35
35
35
35
35
35
35
35
ndhA (SSC)
Exon I
553
553
552
553
553
553
553
552
553
553
Intron I
1150
1157
1154
1148
1148
1149
1148
1158
1133
1158
Exon II
539
539
537
539
539
539
539
540
539
539
*rps12 gene is dividing gene. The 3′-rps12 locates on the IR-region, while the 5′-rps12 locates on the LSC region.
ABE:Atropa belladonna, CAN: Capsicum annuum, DST: Datura stramonium, NSY: Nicotiana sylvestris, NTA: Nicotiana tabacum, NTO: Nicotiana tomentosiformis, NUN: Nicotiana undulata, SBU: Solanum bulbocastanum, SLY: Solanum lycopersicum, and STU: Solanum tuberosum.


## 3.4. Pairwise Comparison of Plastid Genes of Solanaceae and InDel Analyses

Pairwise comparison of nucleotide sequences of individual gene sequences (45 combinations) for 116 genes was also performed to classify genes based on percent identity. Supplementary Table 1 (Supplementary Material available online athttp://dx.doi.org/10.1155/2014/424873) shows grouping of genes in different clusters based on percent identity in pairwise comparison. Genes which showed 100% identity in comparison were considered as highly conserved and the genes showing less than 95% identity at least once in the comparison were considered as highly divergent. These highly divergent genes were further explored at nucleotide as well as at protein level to probe the variations in detail. A total of 11 highly divergent genes were found whereas the number of highly conserved genes varied from 26 (for species pair:N. tomentosiformis andS. lycopersicum) to 107 (for species pair:N. sylvestris andN. tabacum). Most of the tRNA genes were found to be highly conserved. Genes accD, cemA, clpP, ndhA, rpl32, rpl36, rps16, sprA, trnA-UGC, trnL-UAA, and ycf1 were found to be highly diverged.Tables3 and 4 describe the summary of InDels observed in nucleotide and amino acid sequences, respectively. Partial multiple sequence alignment of 9 genes and 5 proteins is shown in Figures 1 and 2, respectively. The longest insertion of 141 bp was observed in accD gene sequence ofC. annuum. Since genes clpP, ndhA, rps16, and trnL-UAA contained introns, it was important to examine whether these InDels were present in exon or intron region. It was found that all the InDels reported in ndhA and trnL-UAA were present in introns whereas, in case of clpP, InDel 24 was located in exon of the gene. Similarly, the first and last InDels of gene rps16 were present in exons of the gene. Keeping in view the observations in number and length of InDels in nucleotide and protein sequences of genes under consideration, the variation for individual genes is discussed below.Table 3
InDels in nucleotide sequences of 9 genes of ten solanaceous plastid genomes.
S. number
Geneabc
Total number of InDels
InDel length (bp)
1
accDa
4
24, 9, 141, 6
2
clpPa
24
8(I), 14(I), 13(I), 7(I), 1(I), 2-3(I), 7(I), 1–7(I), 3(I), 2(I), 3(I), 1–7(I), 1–3(I), 1(I), 1(I), 1(I), 1–5(I), 4–7(I), 1(I), 9(I), 1-2(I), 3(I), 5(I), 24–30
3
ndhAb
14
9(I), 5-6(I), 3(I), 1(I), 9(I), 3(I), 4(I), 1–4(I), 1-2(I), 1–23(I), 1-2(I), 2(I), 1(I), 3(I)
4
rpl32b
2
2-3, 4
5
rps16a
11
1–38, 9(I), 1(I), 1(I), 5(I), 1-2(I), 5(I), 4(I), 6(I), 1(I), 9
6
sprAb
2
109, 7
7
trnA-UGCc
1
102–130
8
trnL-UAAa
4
1, 6, 71, 4
9
ycf1b
31
3, 18, 18, 21, 6, 6, 48, 9, 6, 6, 42, 3, 6, 30, 3, 15, 12–39, 18, 6, 9–36, 6, 6, 6, 9, 9, 12, 6, 6, 6, 57, 6
abcLocation in different regions; aLSC, bSSC, and cIR; I: InDels present in introns.Table 4
InDels in amino acid sequences of 5 proteins of ten solanaceous plastid genomes.
S. number
Protein
Total number of InDels
InDel length (bp)
1
accD
4
8, 3, 47, 2
2
clpP
2
2, 10
3
rpl32
1
1-2
4
rps16
1
3
5
ycf1
29
1, 6, 6, 7, 2, 2, 7, 3, 2, 2, 14, 1–10, 1, 5, 4–13, 6, 2, 3–12, 2, 2, 2, 3, 3, 4, 2, 2, 2, 19, 2Partial multiple sequence alignment of accD, clpP, ndhA, rpl32, rps16, sprA, tRNA-Ala (UGC), tRNA-Leu(UAA), and ycf1 gene sequences of ten solanaceous species showing location of InDels indicated by hyphens.Figure 2
Partial multiple sequence alignment of amino acid sequences of genes, namely, accD, clpP, ndhA, rpl32, rps16, sprA, tRNA-Ala(UGC), tRNA-Leu(UAA), and ycf1, of ten solanaceous species showing location of InDels indicated by hyphens.(1) accD. A total of four InDels were observed in accD gene as depicted in Figure 1. Insertion of 24 bp was present interestingly in allNicotiana species andD. stramonium followed by insertion of 9 bp in allSolanum species indicating stronger sequence conservation at genus level. These insertions were also reported by Chung et al. [25]. A 141 bp insertion was observed specifically inC. annuum which has also been reported by Jo et al. [29] and confirmed by RT-PCR. Similarly a species specific deletion of 6 bp was found inD. stramonium. All these InDels were also reflected in the corresponding protein sequences as shown in Figure 2. The accD gene has been reported to be one of the most variable plastid genes and is probably under diversifying selection [26].(2) clpP. In clpP gene InDels were found both in intron and in exon regions. Two major consequences were observed in the InDels in the exon regions. An insertion of 6 bp inS. bulbocastanum andS. tuberosum and 30 bp inS. lycopersicum at 3′ end (exon 3) of the clpP gene resulted in shifting of stop codon by 6, 6, and 30 bp downstream in respective species compared to other species of Solanaceae family, increasing the length of the coding sequence and the protein product (Figures 1 and 2). An interesting feature was observed as InDel 1 in protein sequence corresponding to insertion of a repeat of “I” amino acids inD. stramonium making exon 3 region longer by 6 bp. This region however corresponds to the end of intron 2 in clpP gene in all other species. SinceD. stramonium chloroplast genome has been sequenced recently, this observation needs to be experimentally validated.(3) ndhA. All the InDels found in ndhA were present in introns while the protein-coding regions (exons) were highly conserved. This indicates high diversifying selection on intronic region of this gene. Out of the total 14 InDels most of the InDels were observed with respect toC. annuum (InDels 1, 2, 5, 7, and 10). InDel 10 was observed to be shared byC. annuum andS. lycopersicum in full and byC. annuum andA. belladonna in part.(4) rpl32. In rpl32 insertion of 1 bp inD. stramonium and 3 bp inC. annuum was found in the 3′ region of gene while a deletion of 4 bp was observed inD. stramonium. The insertion of 3 bp inC. annuum only altered the length of the protein by making it longer by 1 amino acid. However, the small insertion of 1 bp inD. stramonium proved to be a frameshift mutation resulting in three changes in the amino acid sequence near the C-terminus. Moreover, deletion of 4 bp at the 3′ end resulted in premature termination of protein synthesis. The frameshift mutation and the 3′ end deletion finally reduced the gene product length by 1 amino acid. As the C-terminal of amino acid chain is well conserved in all the other species, the effect of above mentioned variations needs to be validated experimentally.(5) rps16. In rps16 also InDels were observed in introns as well as exons. Five of the major insertions in the intron regions were species specific. Insertion of 38 bp (InDel 1), 9 bp (InDel 2), 5 bp (InDel 7), 4 bp (InDel 8), and 6 bp (InDel 9) was observed inA. belladonna,S. lycopersicum,D. stramonium, andC. annuum. A deletion of 5 bp was observed in all the threeSolanum species andC. annuum. A deletion of 9 bp was observed in allNicotiana species resulting in an amino acid change (P to S) and shortening of protein by three amino acids in the C-terminal region. Similar deletion has also been observed by Kahlau et al. [27] and was suggested to be functionally neutral.(6) sprA. sprA gene has been reported as stable noncoding RNA of unknown function. This gene has been suggested to influence 16S rRNA maturation [38, 39]. In many species this gene seems to be present as remnant and shows large variations in its 5′ region. The largest deletion of 109 bp was observed inC. annuum. The rest of this gene appears to be more conserved with a deletion towards the 3′ end in allNicotiana species andA. belladonna. The manner in which this gene functions and the consequences of the above mentioned variations are yet to be investigated experimentally.(7) trnA-UGC. In this particular gene a long deletion of 102 bp was observed in allNicotiana species. Interestingly, this deletion was further extended to 130 bp in both directions inA. belladonna. These deletions were found in the intron region and so are unlikely to have any negative impact on gene product function.(8) trnL-UAA. The trend of variation in trnL-UAA was similar to that in ndhA as all InDels were observed in introns. The longest species specific deletion (InDel 3) was observed inC. annuum whereas short insertion of four nucleotides, a repeat of “T,” was observed specifically inD. stramonium. Another insertion of 6 bp was observed in twoNicotiana species, that is,N. sylvestris andN. tabacum.(9) ycf1. Many InDels (3′ region) were found in the fastest evolving gene, that is, ycf1 gene. Most of the InDels were found to be species specific. Maximum InDels (InDels 2, 3, 5, 7, 9, 16, 17, 19, 23, 24, 25, and 30) were observed inC. annuum followed byD. stramonium (InDels 4, 6, 20, 26, and 31), byN. tomentosiformis (InDels 8, 17, and 18), and byS. lycopersicum (InDels 16, 22, and 28). Two genus specific InDels (InDels 14 and 21) were observed in all the fourNicotiana species. However, InDel 19 was also present inD. stramonium. Another genus specific InDel (InDel 29) was observed inSolanum species. Most of the InDels altered the length of the gene product with maximum length of 1906 amino acids (aa) observed inC. annuum and the minimum of 1873 aa observed inD. stramonium. Among theSolanum species the length of protein (1887 aa) was conserved amongS. bulbocastanum andS. tuberosum. However,S. lycopersicum was having the amino acid sequence of 1891 aa, larger by 4 aa as compared to the other two species of the same genus. Among the fourNicotiana species the ycf1 gene product length was conserved amongN. sylvestris,N. tabacum, andN. undulata having protein lengths of 1901 aa, 1902 aa, and 1901 aa, respectively. However,N. tomentosiformis was observed to be the most variable member of the genusNicotiana having protein length of 1892 aa.


## 3.5. Phylogenetic Analysis of Solanaceous Plastomes

Evolutionary relationships between diverse plant species have been analyzed using several plastome markers including matK and rbcL (genes) or trnH-psbA and trnL-trnF (intergenic regions) due to sequence conservation among plant taxa blended with suitable variation [40, 41]. However, determination of phylogeny based on single gene sequences may be inaccurate [42]. Availability of complete chloroplast sequences for many species has made it possible to use many individual genes or concatenated gene sequences to deduce phylogenetic relationships among taxa [42–44].Efforts have been made to carry out phylogenetic analysis of solanaceous species using complete plastome sequences by Moore et al. [44] and Jansen et al. [45]. Evolutionary positions ofCapsicum andDatura in Solanaceae have been determined using a single or a few plastid genes [46, 47]. Recently, concatenated protein-coding gene sequences from completely sequenced plastomes were used to obtain reasonable phylogenetic relationships for solanaceous species [29]. In the present investigation we also used a similar approach to analyze the phylogenetic relationship for ten solanaceous species with completely sequenced plastomes. Individual multiple sequence alignments were concatenated for maximum likelihood phylogenetic tree generation. As depicted in Figure 3, taxa were divided into two clades with 100% bootstrap value of 500. The first clade consisted of fourNicotiana species while the species inSolanum,Capsicum,Atropa, andDatura were included in the second clade. These results are in line with previous phylogenetic analyses using concatenated protein-coding gene sequences as well as phylogenetic analyses using plastid ndhF and trnL-F sequences [29, 47]. However, in an analysis of 13 orfs of solanaceous plastomes, a different arrangement was shown in whichAtropa was shown to be separated fromSolanum and was grouped together withNicotiana [25].Figure 3
Maximum likelihood phylogenetic tree derived using concatenated nucleotide sequences of 75 protein-coding genes of ten solanaceous species and two outgroup species.


## 4. Conclusions

The analyses of complete plastid genomes of ten solanaceous species revealed overall similarity in terms of the gene content and organization. The sizes of LSC, SSC, and IR regions were found to be somewhat conserved among species but a significant variation was found between genera. Most of the coding regions were well conserved. However, many of the features in few genes were observed to be typical of a particular genus and even species, which can be used as molecular markers to investigate genetic diversity and evolution. These typical variations can be further utilized to develop more sophisticated DNA barcoding based techniques. Ten solanaceous species are divided into two clades on the basis of Phylogenetic analysis using concatenated alignment of gene sequences from coding regions of plastomes. The first clade consisted of fourNicotiana species and the second clade consisted of species ofSolanum,Capsicum,Atropa, andDatura.



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*Source: 424873-2014-11-17.xml*