DOI: 10.5061/dryad.0vt4b8gwz
title: Evolution of Rosaceae chloroplast genomes highlights unique Cerasus diversification and independent origins of fruit cherry

description: Rosaceae plants comprise numerous fruit crops with huge economic values.
 The lack of genomic characteristics has largely blocked our understanding
 about the Rosaceae gene and plastome evolution. Here, we analyzed 121
 Rosaceae chloroplast (cp) genomes of 51 taxa from 19 genera, predominantly
 including the Cerasus plants and their relatives. To our knowledge, we
 generated the first comprehensive map of genomic variation across Rosaceae
 plastomes. Protein-coding genes of Rosaceae plastomes were characterized
 with high proportion (over 50%) of synonymous variants and InDels with
 multiple triplets. Four photosynthesis-related genes were under Darwin
 selection, which are unique in woody fruit trees of Rosaceae. We detected
 considerable variations in genome size among Rosaceae plastomes and
 observed trivial and obvious structural variation in the examined cp
 genomes of tribes Pyrodae and Amygdaleae. Phylogenomic analyses and
 molecular dating highlighted the independent evolution of true cherry,
 dwarf cherry and relatives. Our findings strongly support to taxonomically
 treat the monophyletic true cherry group as a separate genus excluding
 dwarf cherry. High levels of genomic differentiation and distinct
 phylogenetic relationships implied independent origins and domestication
 between fruit cherries, particularly between cultivated Cerasus
 psuedocerasus and Cerasus avium. We further proposed an evolutionary model
 to elucidate multiple genomic introgression events among true cherries
 occurring since ~15 Mya. Well-resolved maternal phylogeny suggested that
 the cultivated C. pseudocerasus might be originated from Longmenshan Fault
 zone, the eastern edge of Himalaya-Hengduan Mountains, where they have
 subjected to frequent genomic introgression between its presumed wild
 ancestors and other close relatives. In conclusion, comparative analyses
 of plastomes and chloroplast genes detected diverse evolutionary behaviors
 and divergent adaptive selection in Rosaceae. We provide robust evidences
 for the independent origins and domestication of fruit cherries.
description: 126 chloroplast genomes were preliminary selected, among which 91
 were newly assembled and 35 were downloaded from the NCBI database. Our
 samples covered 19 genera of subfamilies Spiraeoideae (Tribe Amygdaleae,
 Exochordeae, Spiraeeae and Pyrodae) and Rosoideae of family Rosaceae.
 Three species <i>Morus mongolica </i>(Moraceae)<i>,
 Ziziphus jujuba </i>(Rhamnaceae) and <i>Elaeagnus macrophylla
 </i> (Elaeagnaceae) were used as outgroups. Based on our previous
 studies, 91 <i>Cerasus </i> representative accessions were
 selected for whole-genome re-sequencing, consisting of 34 <i>C.
 pseudocerasus </i> accessions, 6 accessions referring to 4 European
 cherry species (<i>C. avium</i>, <i>C.
 fruticosa</i>, <i>C. vulgaris </i>and <i>C.
 mahaleb</i>), 5 dwarf cherry accessions (<i>C.
 glandulosa</i>, <i>C. tomentosa </i> and <i>C.
 tianshanica</i>) and 46 accessions covering 20 other
 <i>Cerasus </i> taxa. <i>Cerasus vulgaris </i> was
 supposed to be a natural hybrid between <i>C. fruticosa </i>
 and <i>C. avium </i> and confirmed by cytogenetic studies. 34
 <i>C. pseudocerasus </i> accessions included 11 landraces and
 23 wild individuals from diverse genotypes, phenotypes and geographical
 distributions. We also obtained the genomic pair-end reads of
 <i>Prunus cerasifera </i> (SRR4036106) from GenBank database
 to assemble its chloroplast genome. <i>Laurocerasus undulata
 </i>and <i>Cerasus glandulosa </i> were excluded due to
 the incomplete genome sequence and unreasonable branch length in
 phylogenetic tree (data not shown), hence a total of 124 chloroplast
 genomes were used for the subsequent analyses. I. We
 constructed the WCGD (whole chloroplast genome dataset, n=124) and PCGD
 (<i>Cerasus </i> and its relatives chloroplast genome dataset,
 n=107) datasets using complete chloroplast genome sequences in this study.
 For both datasets, we removed all missing data (N) and the long insertion
 (&gt; 50 bp) sequences that only detected in one individual.
 II. We kept large single-copy (LSC), short single-copy (SSC) and
 one conserved inverted repeat (IR) sequences to construct the WOID (whole
 one inverted-repeat dataset, n=124) and POID (<i>Cerasus </i>
 and its relatives one inverted-repeat dataset, n=107) datasets. All
 missing data were removed in both datasets. III. Based
 on the WCGD and PCGD datasets, the VSWD (Variant sites of whole
 chloroplast genome, n=124) and VSPD (Variant sites of<i> Cerasus
 </i> and its relatives chloroplast genome, n=107) datasets were
 constructed with custom bash script, both of which contained no
 InDels. IV. WGSD (whole gene sequence dataset, n=124)
 and PGSD (<i>Cerasus </i> and its relatives gene sequence
 dataset, n=107) datasets were constructed with 102 unique genes.
 V. PCWD (Protein-coding sequence of whole chloroplast genome,
 n=124) and PCPD (Protein-coding sequence of <i>Cerasus </i>
 and its relatives chloroplast genome, n=107) were constructed with the
 exons of 72 unique protein-coding genes. VI. Based on
 WCGD and PCGD datasets, we removed all ambiguous sites to construct the
 PWGD (Pruned whole chloroplast genome dataset, n=124) and PPGD (Pruned
 <i>Cerasus </i> and its relatives chloroplast genome dataset,
 n=107) using the GBLOCKS v.91b with the following parameters: minimum
 sequences per conserved position, 65; minimum sequences per flank
 position, 110 (PWGD) / 100 (PPGD); maximum number of contiguous
 non-conserved positions, 8; minimum block length, 10; allowed gap
 positions, none.