Phylotranscriptomic analyses in plants using Betulaceae as an example  

作　　者：Hui Ma Jing Lu Bing-Bing Liu Bing-Bing Duan Xiao-Dong He Jian-quan Liu 

机构地区：[1]State Key Laboratory of Grassland and Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, China [2]Ministry of Education Key Laboratory for Bio-resources and Eco-environment, College of Life Sciences, Sichuan University, Chengdu 610065, China

出　　处：《Journal of Systematics and Evolution》2015年第5期403-410,共8页植物分类学报（英文版）

摘　　要：With the advance of next-generation sequencing techniques, phylogenetic analyses based on genomic data are becoming frequent in plants. However, the efficacy of different methods used to retrieve orthologs for phylogenetic studies based on transcriptome sequences is rarely compared and examined for closely related species with low genetic differentiation. In this study, we used both low-copy gene-based approaches and mapping- based approaches to construct a phylogeny of Betulaceae. We found that both approaches showed no distinct differences in phylogeny construction and associated bootstrap support, although mapping-based methods seemed to be superior to the former in all analyses particularly when the summed length of orthologs was not long enough. Phylogenetic relationships within the family, largely consistent with those previously based on chloroplast DNA and nuclear internal transcribed spacer sequence variations, received high support for all clades and subclades. However, we found that support values for the sister relationship between two polyploid genera were lower than those between diploid groups if only a few orthologs were sampled. This may result from ortholog misidentiflcation due to genome duplications.With the advance of next-generation sequencing techniques, phylogenetic analyses based on genomic data are becoming frequent in plants. However, the efficacy of different methods used to retrieve orthologs for phylogenetic studies based on transcriptome sequences is rarely compared and examined for closely related species with low genetic differentiation. In this study, we used both low-copy gene-based approaches and mapping- based approaches to construct a phylogeny of Betulaceae. We found that both approaches showed no distinct differences in phylogeny construction and associated bootstrap support, although mapping-based methods seemed to be superior to the former in all analyses particularly when the summed length of orthologs was not long enough. Phylogenetic relationships within the family, largely consistent with those previously based on chloroplast DNA and nuclear internal transcribed spacer sequence variations, received high support for all clades and subclades. However, we found that support values for the sister relationship between two polyploid genera were lower than those between diploid groups if only a few orthologs were sampled. This may result from ortholog misidentiflcation due to genome duplications.

关 键 词：BETULACEAE ORTHOLOG PHYLOGENY transcriptome. 

分 类 号：Q943[生物学—植物学] Q949.736.2