Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes
Zhang,Xu1,2,3; Sun,Yanxia1,2; Landis,Jacob B.4,5; Lv,Zhenyu6; Shen,Jun1,3; Zhang,Huajie1,2; Lin,Nan1,3; Li,Lijuan1,3; Sun,Jiao1,3; Deng,Tao6; Sun,Hang6; Wang,Hengchang1,2
Corresponding AuthorZhang,Xu(zhangxu173@mails.ucas.ac.cn) ; Sun,Hang(sunhang@mail.kib.ac.cn) ; Wang,Hengchang(hcwang@wbgcas.cn)
2020-07-17
Source PublicationBMC Plant Biology
Volume20Issue:1
AbstractAbstractBackgroundPlastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored. Moreover, structural and functional characteristics of plastomes indicate that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces, yet the genetic characteristics of plastid genes within a lineage remain poorly studied.ResultsWe sequenced and annotated 10 plastome sequences of Gentianeae. Phylogenomic analyses yielded robust relationships among genera within Gentianeae. We detected great variation of gene tree topologies and revealed that more than half of the genes, including one (atpB) of the three widely used plastid markers (rbcL, atpB and matK) in phylogenetic inference of Gentianeae, are likely contributing to phylogenetic ambiguity of Gentianeae. Estimation of nucleotide substitution rates showed extensive rate heterogeneity among different plastid genes and among different functional groups of genes. Comparative analysis suggested that the ribosomal protein (RPL and RPS) genes and the RNA polymerase (RPO) genes have higher substitution rates and genetic variations among plastid genes in Gentianeae. Our study revealed that just one (matK) of the three (matK, ndhB and rbcL) widely used markers show high phylogenetic informativeness (PI) value. Due to the high PI and lowest gene-tree discordance, rpoC2 is advocated as a promising plastid DNA barcode for taxonomic studies of Gentianeae. Furthermore, our analyses revealed a positive correlation of evolutionary rates with genetic variation of plastid genes, but a negative correlation with gene-tree discordance under purifying selection.ConclusionsOverall, our results demonstrate the heterogeneity of nucleotide substitution rates and genetic characteristics among plastid genes providing new insights into plastome evolution, while highlighting the necessity of considering gene-tree discordance into phylogenomic studies based on plastome-scale data.
KeywordPlastome Phylogenetic discordance Gentianeae Coalescence Gene trees Nucleotide substitution rates Gene characteristics Phylogenetic informativeness
DOI10.1186/s12870-020-02518-w
Language英语
WOS IDBMC:10.1186/s12870-020-02518-w
Citation statistics
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/72022
Collection中国科学院东亚植物多样性与生物地理学重点实验室
Corresponding AuthorZhang,Xu; Sun,Hang; Wang,Hengchang
Affiliation1.Wuhan Botanical Garden, Chinese Academy of Sciences; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture
2.Core Botanical Gardens, Chinese Academy of Sciences; Center of Conservation Biology
3.University of Chinese Academy of Sciences
4.University of California Riverside; Department of Botany and Plant Sciences
5.Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University; School of Integrative Plant Science
6.Kunming Institute of Botany, Chinese Academy of Sciences; Key Laboratory for Plant Diversity and Biogeography of East Asia
Recommended Citation
GB/T 7714
Zhang,Xu,Sun,Yanxia,Landis,Jacob B.,et al. Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes[J]. BMC Plant Biology,2020,20(1).
APA Zhang,Xu.,Sun,Yanxia.,Landis,Jacob B..,Lv,Zhenyu.,Shen,Jun.,...&Wang,Hengchang.(2020).Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes.BMC Plant Biology,20(1).
MLA Zhang,Xu,et al."Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes".BMC Plant Biology 20.1(2020).
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