Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species.To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten gen...Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species.To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The Inverted Repeat(IR) regions in five plastomes had experienced small expansions(330 e983 bp) into the Large Single-Copy(LSC) region. The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs. The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR. A 270-bp inversion was detected in the Parasponia rugosa plastome, which might have been mediated by 18-bp inverted repeats. Repeat sequences, simple sequence repeats, and nucleotide substitution rates varied among these plastomes.Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified, which may be useful for further phylogenetic analysis and species identification. Our results show strong support for a sister relationship between Gironniera and Lozanell(BS ? 100). Celtis, CannabisHumulus, Chaetachme-Pteroceltis, and Trema-Parasponia formed a strongly supported clade, and their relationships were well resolved with strong support(BS ? 100). The availability of these ten plastomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.展开更多
The subfamily Dialioideae(Leguminosae)consists of 17 genera and about 85 species.Previous studies have detected significant plastid genome(plastome)structure variations in legumes,particularly in subfamilies Papiliono...The subfamily Dialioideae(Leguminosae)consists of 17 genera and about 85 species.Previous studies have detected significant plastid genome(plastome)structure variations in legumes,particularly in subfamilies Papilionoideae and Caesalpinioideae.Hence it is important to investigate plastomes from the newly recognized Dialioideae to better understand the plastome variation across the whole family.Here,we used nine plastomes representing nine genera of Dialioideae to explore plastome structural variation and intergeneric relationships in this subfamily.All plastomes of Dialioideae exhibited a typical quadripartite structure,and had relatively conserved structure compared with other legume subfamilies.However,the genome size ranged from 154,124 bp to 165,973 bp and gene numbers ranged from 129 to132,mainly due to the expansion and contraction of the inverted repeat(IR)regions.The IR of Distemonanthus benthamianus has experienced two separate expansions into the large single copy(LSC)region and the small single copy(SSC)region,and one contraction from SSC.Poeppigia procera has experienced two separate IR expansions into LSC,while Dicorynia paraensis has experienced an IR contraction from LSC.Highly divergent regions or genes(ndhC-trnV^(UAC),psbK-trnQ^(UUG),rps19-rps3,rpl33-rps18,accD-psaI,trnG^(UCC)-trnS^(GCU),psbI-trnS^(GCU),5'rps16-trnQ^(UUG)and ycf1)were identified as potential molecular markers for further species delimitation and population genetics analysis in legumes.Phylogenetic analysis based on 77 protein-coding sequences fully resolved the intergeneric relationships among nine genera except a moderately supported sister relationship between Petalostylis labicheoides and Labichea lanceolata.Our study reveals new insights into the structural variations of plastomes in subfamily Dialioideae and advances our understanding of the evolutionary trajectories of legume plastomes.展开更多
基金supported by grants from the National Natural Science Foundation of Chinakey international (regional) cooperative research project (31720103903)The Strategic Priority Research Program of the Chinese Academy of Sciences (XDPB0201)
文摘Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species.To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The Inverted Repeat(IR) regions in five plastomes had experienced small expansions(330 e983 bp) into the Large Single-Copy(LSC) region. The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs. The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR. A 270-bp inversion was detected in the Parasponia rugosa plastome, which might have been mediated by 18-bp inverted repeats. Repeat sequences, simple sequence repeats, and nucleotide substitution rates varied among these plastomes.Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified, which may be useful for further phylogenetic analysis and species identification. Our results show strong support for a sister relationship between Gironniera and Lozanell(BS ? 100). Celtis, CannabisHumulus, Chaetachme-Pteroceltis, and Trema-Parasponia formed a strongly supported clade, and their relationships were well resolved with strong support(BS ? 100). The availability of these ten plastomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.
基金supported by grants fromthe Large-scale Scientific Facilities of Chinese Academy of Sciences(No.2017-LSF-GBOWS-02)the Strategic Priority Research Program of Chinese Academy of Sciences(XDB31010000)the National Natural Science Foundation of China[key international(regional)cooperative research project No.31720103903]。
文摘The subfamily Dialioideae(Leguminosae)consists of 17 genera and about 85 species.Previous studies have detected significant plastid genome(plastome)structure variations in legumes,particularly in subfamilies Papilionoideae and Caesalpinioideae.Hence it is important to investigate plastomes from the newly recognized Dialioideae to better understand the plastome variation across the whole family.Here,we used nine plastomes representing nine genera of Dialioideae to explore plastome structural variation and intergeneric relationships in this subfamily.All plastomes of Dialioideae exhibited a typical quadripartite structure,and had relatively conserved structure compared with other legume subfamilies.However,the genome size ranged from 154,124 bp to 165,973 bp and gene numbers ranged from 129 to132,mainly due to the expansion and contraction of the inverted repeat(IR)regions.The IR of Distemonanthus benthamianus has experienced two separate expansions into the large single copy(LSC)region and the small single copy(SSC)region,and one contraction from SSC.Poeppigia procera has experienced two separate IR expansions into LSC,while Dicorynia paraensis has experienced an IR contraction from LSC.Highly divergent regions or genes(ndhC-trnV^(UAC),psbK-trnQ^(UUG),rps19-rps3,rpl33-rps18,accD-psaI,trnG^(UCC)-trnS^(GCU),psbI-trnS^(GCU),5'rps16-trnQ^(UUG)and ycf1)were identified as potential molecular markers for further species delimitation and population genetics analysis in legumes.Phylogenetic analysis based on 77 protein-coding sequences fully resolved the intergeneric relationships among nine genera except a moderately supported sister relationship between Petalostylis labicheoides and Labichea lanceolata.Our study reveals new insights into the structural variations of plastomes in subfamily Dialioideae and advances our understanding of the evolutionary trajectories of legume plastomes.
