Exploring the potential of nuclear and mitochondrial sequencing data generated through genome‐skimming for plant phylogenetics:A case study from a clade of neotropical lianas  

作　　者：Luiz Henrique M.Fonseca Lucia G.Lohmann 

机构地区：[1]Departamento de Botanica,Instituto de Biocencias,Universidade de Sao Paulo,Sao Paulo 05508‐090,Brazil

出　　处：《Journal of Systematics and Evolution》2020年第1期18-32,共15页植物分类学报（英文版）

基　　金：a postdoctoral fellowship to L.H.M.F.and a Pq-iB grant to L.G.L.(310871/2017-4)。

摘　　要：Few botanical studies have explored the potential of nuclear ribosomal DNA (nrDNA) and mitochondrial DNA (mtDNA) data obtained through genome skimming for phylogeny reconstruction. Here, we analyzed the phylogenetic information included in the nrDNA and mtDNA of 44 species of the “Adenocalymma‐Neojobertia” clade (Bignoniaceae). To deal with intraindividual polymorphisms within the nrDNA, different coding schemes were explored through the analyses of four datasets: (i) “nrDNA contig,” with base call following the majority rule;(ii) “nrDNA ambiguous,” with ambiguous base calls;(iii) “nrDNA informative,” with ambiguities converted to multistate characters;and, (iv) “mitochondrial,” with 39 mitochondrial genes. Combined analyses using the nrDNA and mtDNA data and previously published “plastid” datasets were also conducted. Trees were obtained using Maximum Likelihood and Bayesian criteria. The congruence among genomes was assessed. The nrDNA datasets were shown to be highly polymorphic within individuals, while the “mitochondrial” dataset was the least informative, with 0.36% of informative bases within the ingroup. The topologies inferred using the nrDNA and mtDNA datasets were broadly congruent with the tree derived from the analyses of the “plastid” dataset. The topological differences recovered were generally poorly supported. The topology that resulted from the analyses of the “combined” dataset largely resembles the “plastid” tree. These results highlight limitations of nuclear ribosomal DNA and mitochondrial genes for phylogeny reconstruction obtained through genome skimming and the need to include more data from both genomes. The different topologies observed among genomes also highlight the importance of exploring data from various genomes in plant phylogenetics.

关 键 词：35S cistron ETS ITS1 ITS2 MITOCHONDRIAL GENOME NRDNA 

分 类 号：Q943.2[生物学—植物学]