Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae)

• Published in: Journal of systematics and evolution : JSE 2021-11, Vol.59 (6), p.1198-1208
• Main Authors: Chen, Chun‐Lin, Zhang, Lei, Li, Jia‐Liang, Mao, Xing‐Xing, Zhang, Lu‐Shui, Hu, Quan‐Jun, Liu, Jian‐Quan, Xi, Zhen‐Xiang
• Format: Article
• Language: English
• Subjects: Gene duplication; Genes; Genomes; Gentianaceae; Gentianinae; hybridization; Phylogeny; Polyploidy; Reproduction (copying); transcriptome; Transcriptomes
• ISSN: 1674-4918; 1759-6831
• DOI: 10.1111/jse.12651

Gene duplication plays an important role in plants for diversification and adaptation to new habitats. In this study, we aim to reconstruct the genome‐scale phylogeny and identify large‐scale gene duplication events for the subtribe Gentianinae (Gentianaceae), which is a great symbol of the alpine plants in the Qinghai–Tibet Plateau. We sequenced and assembled 70 transcriptomes from 67 species, representing all six recognized genera in the subtribe Gentianinae plus the closely related outgroups. Using phylogenomic approaches, the backbone relationships of Gentianinae were almost fully resolved with high bootstrap support. Although instances of conflicts were observed between nuclear and plastid phylogenies, six major clades of Gentianinae were consistently recovered in both phylogenies. In addition, we revealed a high occurrence of duplicated genes in our transcriptome assemblies. Using several gene tree reconciliation methods, we collectively identified 10 nodes in the species tree with large concentrations of duplicated genes. Further analysis indicated that many of these duplicated genes likely arose from hybrid polyploidy, which might also account for some of the topological incongruences between nuclear and plastid phylogenies in Gentianinae. We sequenced and assembled 70 transcriptomes from 67 species, representing all six recognized genera in the subtribe Gentianinae plus closely related outgroups. We resolved the backbone relationships of the subtribe with high bootstrap support. We conservatively identified 10 nodes in the species tree with large concentrations of duplicated genes. Our results highlight the diversification history of the Gentianinae.