Phylogenomic and evolutionary dynamics of inverted repeats across Angelica plastomes.
- Ligusticum
- chloroplast genome
- chloroplasts
- cultivars
- fruits
- genetic variation
- leaf morphology
- phylogeny
BACKGROUND
Angelica L. (family Apiaceae) is an economically important genus comprising ca. One hundred ten species. Angelica species are found on all continents of the Northern Hemisphere, and East Asia hosts the highest number of species. Morphological characters such as fruit anatomy, leaf morphology and subterranean structures of Angelica species show extreme diversity. Consequently, the taxonomic classification of Angelica species is complex and remains controversial, as the classifications proposed by previous studies based on morphological data and molecular data are highly discordant. In addition, the phylogenetic relationships of major clades in the Angelica group, particularly in the Angelica s. s. clade, remain unclear. Chloroplast (cp) genome sequences have been widely used in phylogenetic studies and for evaluating genetic diversity.RESULTS
In this study, we sequenced and assembled 28 complete cp genomes from 22 species, two varieties and two cultivars of Angelica. Combined with 36 available cp genomes in GenBank from representative clades of the subfamily Apioideae, the characteristics and evolutionary patterns of Angelica cp genomes were studied, and the phylogenetic relationships of Angelica species were resolved. The Angelica cp genomes had the typical quadripartite structure including a pair of inverted repeats (IRs: 5836-34,706 bp) separated by a large single-copy region (LSC: 76,657-103,161 bp) and a small single-copy region (SSC: 17,433-21,794 bp). Extensive expansion and contraction of the IR region were observed among cp genomes of Angelica species, and the pattern of the diversification of cp genomes showed high consistency with the phylogenetic placement of Angelica species. Species of Angelica were grouped into two major clades, with most species grouped in the Angelica group and A. omeiensis and A. sinensis grouped in the Sinodielsia with Ligusticum tenuissimum.CONCLUSIONS
Our results further demonstrate the power of plastid phylogenomics in enhancing the phylogenetic reconstructions of complex genera and provide new insights into plastome evolution across Angelica L.
Wang M, Wang X, Sun J, Wang Y, Ge Y, Dong W, Yuan Q, Huang L. Phylogenomic and evolutionary dynamics of inverted repeats across Angelica plastomes.. BMC plant biology. 2021 Jan 07; 21(1):26.
BACKGROUND
Angelica L. (family Apiaceae) is an economically important genus comprising ca. One hundred ten species. Angelica species are found on all continents of the Northern Hemisphere, and East Asia hosts the highest number of species. Morphological characters such as fruit anatomy, leaf morphology and subterranean structures of Angelica species show extreme diversity. Consequently, the taxonomic classification of Angelica species is complex and remains controversial, as the classifications proposed by previous studies based on morphological data and molecular data are highly discordant. In addition, the phylogenetic relationships of major clades in the Angelica group, particularly in the Angelica s. s. clade, remain unclear. Chloroplast (cp) genome sequences have been widely used in phylogenetic studies and for evaluating genetic diversity.
RESULTS
In this study, we sequenced and assembled 28 complete cp genomes from 22 species, two varieties and two cultivars of Angelica. Combined with 36 available cp genomes in GenBank from representative clades of the subfamily Apioideae, the characteristics and evolutionary patterns of Angelica cp genomes were studied, and the phylogenetic relationships of Angelica species were resolved. The Angelica cp genomes had the typical quadripartite structure including a pair of inverted repeats (IRs: 5836-34,706 bp) separated by a large single-copy region (LSC: 76,657-103,161 bp) and a small single-copy region (SSC: 17,433-21,794 bp). Extensive expansion and contraction of the IR region were observed among cp genomes of Angelica species, and the pattern of the diversification of cp genomes showed high consistency with the phylogenetic placement of Angelica species. Species of Angelica were grouped into two major clades, with most species grouped in the Angelica group and A. omeiensis and A. sinensis grouped in the Sinodielsia with Ligusticum tenuissimum.
CONCLUSIONS
Our results further demonstrate the power of plastid phylogenomics in enhancing the phylogenetic reconstructions of complex genera and provide new insights into plastome evolution across Angelica L.
- NCBI accession MT921958; Angelica tianmuensis voucher HLQA10007 chloroplast, complete genome.
- NCBI accession MT921981; Angelica tsinlingensis voucher HLQA10041 chloroplast, complete genome.
- NCBI accession MT921982; Angelica morii voucher HLQA10005 chloroplast, complete genome.
- NCBI accession MT921983; Angelica sinensis voucher MXC01 chloroplast, complete genome.
- NCBI accession MT921984; Angelica sinensis voucher MXW01 chloroplast, complete genome.
- NCBI accession MT921985; Angelica gigas voucher HLQA10054 chloroplast, complete genome.
- NCBI accession MT921975; Angelica nitida voucher HLQA10048 chloroplast, complete genome.
- NCBI accession MT921973; Angelica porphyrocaulis voucher HLQA10044 chloroplast, complete genome.
- NCBI accession MT921980; Angelica dahurica voucher HLQA10051 chloroplast, complete genome.
- NCBI accession MT921979; Angelica dahurica voucher HLQA10060 chloroplast, complete genome.
- NCBI accession MT921972; Angelica dahurica voucher HLQA10043 chloroplast, complete genome.
- NCBI accession MT921978; Angelica dahurica voucher HLQA10059 chloroplast, complete genome.
- NCBI accession MT921974; Angelica dahurica voucher HLQA10047 chloroplast, complete genome.
- NCBI accession MT921971; Angelica dahurica var. formosana voucher HLQA10042 chloroplast, complete genome.
- NCBI accession MT921959; Angelica cartilaginomarginata var. foliosa voucher HLQA10008 chloroplast, complete genome.
- NCBI accession MT921976; Angelica cartilaginomarginata voucher HLQA10055 chloroplast, complete genome.
- NCBI accession MT921964; Angelica decursiva voucher HLQA10016 chloroplast, complete genome.
- NCBI accession MT921960; Angelica biserrata voucher HLQA10009 chloroplast, complete genome.
- NCBI accession MT921961; Angelica polymorpha voucher HLQA10010 chloroplast, complete genome.
- NCBI accession MT921962; Angelica megaphylla voucher HLQA10011 chloroplast, complete genome.
- NCBI accession MT921963; Angelica valida voucher HLQA10014 chloroplast, complete genome.
- NCBI accession MT921977; Angelica anomala voucher HLQA10057 chloroplast, complete genome.
- NCBI accession MT921965; Angelica kangdingensis voucher HLQA10017 chloroplast, complete genome.
- NCBI accession MT921966; Angelica apaensis voucher HLQA10019 chloroplast, complete genome.
- NCBI accession MT921967; Angelica maowenensis voucher HLQA10022 chloroplast, complete genome.
- NCBI accession MT921968; Angelica pseudoselinum voucher HLQA10027 chloroplast, complete genome.
- NCBI accession MT921969; Angelica laxifoliata voucher HLQA10031 chloroplast, complete genome.
- NCBI accession MT921970; Angelica omeiensis voucher HLQA10040 chloroplast, complete genome.