Plastome evolution and phylogenetic relationships among Malvaceae subfamilies

Wang, Jianhua; Moore, Michael J.; Wang, Hongxin; Zhu, Zhi‐Xin; Wang, Huafeng

doi:10.1016/j.gene.2020.145103

Cited by 38 publications

(46 citation statements)

References 58 publications

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“…The mVISTA results revealed that coding regions were more conserved than the non-coding regions, and the SSC and LSC regions exhibited more variation than IR regions in all cp genomes. The results of this study are consistent with previous nings in other species [29,73,74,91]. In total, we identi ed ve genes present signi cant variations in these cp genomes, such as matK, accD, ycf1, ndhF, and rpl22.…”

Section: Features Of Complete Chloroplast Genome and Comparative Analysessupporting

confidence: 91%

“…On the contrary, the plastid genome has become extremely easy to obtain because of its highly conserved nature and much smaller size. Meanwhile, an increasing number of the chloroplast genomes have been widely applied to solve phylogenetic relationships at different taxonomical levels within angiosperms [22][23][24][25][26][27][28][29]. Besides, recent studies have demonstrated cp genome can serve as super barcodes for species and taxonomic groups [23,[30][31][32][33].…”

Section: Introductionmentioning

confidence: 99%

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Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

Yang

2021

Preprint

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Background Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. Results The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisted of Aesculus chinensis and A. wangii, strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. Conclusion This study revealed that the cp genome size of the Hippocastanoideae was generally smaller across Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.

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Section: Features Of Complete Chloroplast Genome and Comparative Analysessupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

Yang

2021

Preprint

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“…The GC content of the whole genome is 37.4%, which is similar to that of other species in this family (Alzahrani 2021 ; Wang et al. 2021 ).…”

supporting

confidence: 75%

“…The cp genome of this species encodes 130 genes, including 84 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The GC content of the whole genome is 37.4%, which is similar to that of other species in this family (Alzahrani 2021;Wang et al 2021).…”

supporting

confidence: 73%

Chloroplast genome and phylogenetic analysis ofGrewia biloba

Meng

Ren

et al. 2021

Mitochondrial DNA Part B

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Grewia biloba is a potential medicinal and ornamental resource, and this study is the first to assemble the chloroplast genome of this species using high-throughput sequencing data. The chloroplast genome of G. biloba has a typical composition for higher plant chloroplasts, containing one large single-copy region of 86,978 bp and one small single-copy region of 20,140 bp, which are separated by a pair of inverted-repeat regions of 25,473 bp. The chloroplast genome of this species encodes 130 genes, including 84 protein-coding genes, 38 tRNA genes and 8 rRNA genes. A maximum-likelihood phylogenetic tree was constructed based on sequence information of the chloroplast genomes. The chloroplast genome of G. biloba will provide valuable genetic information for evolutionary research and utilization of this species.

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“…In addition, we identified seven coding regions and 11 intergenic regions with the highest variation among the Oxalidaceae species. Several of these regions (e.g., matK , ycf1 , clpP , ndhF , rpl22 , trnH-GUG _ psbA , trnE-UUC_trnT-GGU , psaJ_rpl33 and ccsA_ndhD ) have been confirmed in other seed plant plastomes ( Ren et al., 2020 ; Wang et al., 2021 ; Tang et al, 2021 ). These hotspot regions may serve as potential molecular markers for species identification, assessment of genetic diversity, and research into the phylogeny of Oxalidaceae.…”

Section: Discussionmentioning

confidence: 80%

Comparative analysis of plastomes in Oxalidaceae: Phylogenetic relationships and potential molecular markers

Xiao-ping

Zhao

et al. 2021

Plant Diversity

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The wood sorrel family, Oxalidaceae, is mainly composed of annual or perennial herbs, a few shrubs, and trees distributed from temperate to tropical zones. Members of Oxalidaceae are of high medicinal, ornamental, and economic value. Despite the rich diversity and value of Oxalidaceae, few molecular markers or plastomes are available for phylogenetic analysis of the family. Here, we reported four new whole plastomes of Oxalidaceae and compared them with plastomes of three species in the family, as well as the plastome of Rourea microphylla in the closely related family Connaraceae. The eight plastomes ranged in length from 150,673 bp ( Biophytum sensitivum ) to 156,609 bp ( R. microphylla ). Genome annotations revealed a total of 129–131 genes, including 83–84 protein-coding genes, eight rRNA genes, 37 tRNA genes, and two to three pseudogenes. Comparative analyses showed that the plastomes of these species have minor variations at the gene level. The smaller plastomes of herbs B. sensitivum and three Oxalis species are associated with variations in IR region sizes, intergenic region variation, and gene or intron loss. We identified sequences with high variation that may serve as molecular markers in taxonomic studies of Oxalidaceae. The phylogenetic trees of selected superrosid representatives based on 76 protein-coding genes corroborated the Oxalidaceae position in Oxalidales and supported it as a sister to Connaraceae. Our research also supported the monophyly of the COM (Celastrales, Oxalidales, and Malpighiales) clade.

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Plastome evolution and phylogenetic relationships among Malvaceae subfamilies

Cited by 38 publications

References 58 publications

Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

Chloroplast genome and phylogenetic analysis ofGrewia biloba

Comparative analysis of plastomes in Oxalidaceae: Phylogenetic relationships and potential molecular markers

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