Additional file 2 of Assembly and annotation of the Gossypium barbadense L. ‘Pima-S6’ genome raise questions about the chromosome structure and gene content of Gossypium barbadense genomes
Creators: name: Chávez Montes, Ricardo A.
name: Ulloa, Mauricio
name: Biniashvili, Tammy
name: Zackay, Arik
name: Kfir, Nir
name: Lopez-Arredondo, Damar
name: Herrera-Estrella, Luis
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Supplementary Figure 1. Annotation Edit Distance scores of the Pima-S6 genome annotation. This histogram shows the distribution of Annotation Edit Distance (AED) scores, a measure of the goodness of fit of an annotation to the evidence supporting it, for the 75,419 genes in the final Pima-S6 annotation. From the MAKER/MAKER-P protocol (Campbell, M. S., Holt, C., Moore, B. and Yandell, M. 2014. Genome Annotation and Curation Using MAKER and MAKER-P. Curr. Protoc. Bioinform. 48:4.11.1- 4.11.39.; doi: 10.1002/0471250953.bi0411s48): “AED is a number between 0 and 1, with an AED of zero denoting perfectconcordance with the available evidence and a value of one indicating a complete absence of support for the annotated gene model. In other words, the AED score provides a measure of each annotated transcript’s congruency with its supporting evidence.” Supplementary Figure 2. Overview of leaf and root gene expression in Pima-S6 and Pima-3-79 RagTag. RNA from one leaves and one roots sample was isolated and sequenced, and gene expression was quantified. Bars represent the number of expressed genes (TPM &gt; 1) in each species, organ and location on the A or D genome. Supplementary Figure 3.a LTR retrotransposon families distribution if four Gossypium assemblies, A genome. The 13 A genome chromosomes from Pima-S6, Pima-3-79 HGS, Hai7124 and TM-1 were analyzed using the Domain based ANnotation of Transposable Elements (DANTE) tool and the REXdb Viridiplantae v3.0 database. The output file was filtered on the Repeat Explorer Galaxy server at https://repeatexplorer-elixir.cerit-sc.cz/ using default parameters, and the number of sequencesper LTR retrotransposon family was plotted. Supplementary Figure 3. b LTR retrotransposon families distribution if four Gossypium assemblies, D genome. The 13 D genome chromosomes from Pima-S6, Pima-3-79 HGS, Hai7124 and TM-1 were analyzed using the Domain based ANnotation of Transposable Elements (DANTE) tool and the REXdb Viridiplantae v3.0 database. The output file was filtered on the RepeatExplorer Galaxy server at https://repeatexplorer-elixir.cerit-sc.cz/ using default parameters, and the number of sequences per LTR retrotransposon family was plotted. Supplementary Figure 4. Synteny plots between Pima-S6 and Pima-3-79 HGS, TM-1, Pima3-79 RagTag. and Pima3-79 RagTag-Gh In these synteny plots, the reference genome is represented by blue horizontal lines and the query genome by red horizontal lines. Vertical lines represent syntenic (grey), inverted (orange), translocated (green) and duplicated (blue) regions. Chromosome ids are indicated on the left side of the plots. The 26 chromosomes of our Pima-S6 assembly were aligned using minimap2 versus the 26 chromosomes of G. hirsutum TM-1 (a), Pima-3-79 HGS (b), Pima-3-79 HGS RagTag (our re-scaffolding of Pima-3-79 HGS using Pima-S6 as reference; c) or Pima-3-79 RagTag-Gh (our re-scaffolding of Pima-3-79 HGS using TM-1 as reference; d), and synteny analysis was carried out using syri. All major structural variations visible in the Pima-S6 vs TM-1 and Pima-S6 vs Pima-3-79 HGS plots are no longer present in the Pima-S6 vs Pima-3-79-RagTag plot, except for a ~4 Mbp inversion and ~0.5 Mbp duplication in chromosome A01, while the Pima-S6 vs Pima-3-79 RagTag-Gh plot recapitulates all the major chromosomal rearrangements from the Pima-S6 vs Pima-3-79 HGS plot. Supplementary Figure 5. Pima-S6 vs TM-1 chromosome A11 inversions. a Schematic representation of the chromosome A11 synteny. The TM-1 A11 chromosome is represented by a blue horizontal box and the scaffolds that form the Pima-S6 A11 chromosome are represented by red boxes. Scaffold ids are indicated below each box. The prefix “r” in a scaffold name indicates a scaffold placed in reverse orientation. Gaps between scaffolds represent the 100 bp N gaps introduced during chromosome reconstruction. The three major inversions (&gt; 1 Mbp) are represented by orange hourglasses. For each inversion a zoom on the sequence at the inversion start and end is shown, with the exact inversion boundaries highlighted by green boxes. Inversion1's boundaries traverse unambiguously assembled regions. Inversion2 starts at an unambiguously assembled region and ends at the start of a 1,000 bp N stretch. Inversion3 starts at the beginning of scaffold1213-2 and ends at an unambiguously assembled region. b Detailed view of the inversion2 to inversion3 region. Inversion2 is followed by a 1,000 bp N stretch (represented by the letter N inside rscaffold116) and 535 bp of unambiguous sequence. These 535 bp are themselves an inversion-duplication (invdp) nested within inversion2 on the TM-1 side. (c) IGV screenshot of the rscaffold116 1,000 N region. Re-alignment of the mate-pair reads showed uniquely mapped reads (bowtie2 XS flag null and not duplicate filter) aligned to rscaffold116's 535 bp end with their mate thousands of bp upstream, confirming the linkage evidence across the 1,000 bp N stretch. Supplementary Figure 5. TM-1 vs Pima-S6 synteny plots for chromosomes A03, A12 and D12. All inversion boundaires, except the end of inversion1 on chromosome A03, traverse unambiguously assembled regions. The 3' end of inversion1 on chromosome A03 is followed by a 10 bp N stretch and a 1,532 bp inversion-duplication of unambiguously assembled sequence that aligns to a chromosome A11 region on the TM-1 side. Supplementary Figure 6. Hi-C plots of Pima90 Hi-C reads aligned to the Pima90, Pima-S6 and Pima-3-79 HGS genomes. In these plots, the blue color indicates a chromatin contact. The coordinate 1 of each chromosome is located at the top left corner. Only chromosomes A09, A13 and D05 are shown. In the Pima-S6 plot, the inversions in these three chromosomes are clearly visible (orange arrows). In the Pima-3-79 HGS plot, the inversions in chromosomes A09 and D05 are also clearly visible, but an inversion in chromosome A13 is not apparent. The Pima90 plot is shown as reference. Supplementary Figure 7. Number of orthogroups shared between Pima-S6, Pima-3-79 HGS, Pima-3-79 HAU.2 and Hai7124. In these UpSet plots, set size indicates the number of orthogroups for each species, and intersection size indicates the number of orthogroups in each of the intersections shown below the corresponding bar. A total of 75,263 orthogroups were identified from the annotated proteins of G. hirsutum 'TM-1' (genome AD1), G. barbadense 'Pima-S6' (AD2; Pima-S6), G. barbadense 'Pima-3-79 HGS' (AD2; Pima-3-79 HGS), G. barbadense 'Pima-3-79' HAU.2 (AD2; HAU.2), G. barbadense Hai7124 (AD2; Hai7124), G. tomentosum (AD3), G. mustelinum (AD4), G. darwinii (AD5), G. herbaceum (A1), G. arboreum (A2) and G. raimondii (D5). (a) Number of orthogroups shared between Pima-S6 and Pima-3-79 HGS. The number of shared orthogroups is lower than the number of shared orthogroups between Pima-S6 and Pima-3-79 RagTag in Figure 5a. (b) Number of orthogroups shared between three Pima assemblies, Pima-S6, Pima-3-79 HGS and Pima-3-79 HAU.2. Pima-3-79 HGS and Pima-3-79 HAU.2 have an important number of proteins without an ortholog in any of the other two assemblies. (c) Number of orthogroups shared between Pima-S6, Pima-3-79 HGS and Hai7124. Pima-3-79 HGS has the highest number of orthogroups without orthologs in Pima-S6 or Hai7124. Supplementary Figure 8. Dot plots of Pima-S6 vs Pima-3-79 HGS and TM-1 genome assemblies alignments. The 26 chromosomes of the indicated genome assemblies were aligned using minimap2, and the PAF alignment file was plotted using D-Genies. Pima-S6 chromosome ids were renamed to the AD nomenclature using the best matching chromosome in Pima-3-79 HGS and TM-1: chromosome 1 was renamed A01, chromosome 2 D01, chromosome 3 A02, chromosome 4 D02, and so on. Supplementary Table 1. Statistics for Pima-S6 and Pima-3-79 RNA-seq leaf and root RNA-seq samples. Supplementary Table 2.