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

Abstract

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.

Population Transcriptomics Reveals Gene Flow and Introgression Between Two Non-sister Alpine Gentians

“…Reference transcriptome was assembled by Trinity v2.8.4 (Grabherr et al, 2011) from the previously sequenced transcriptome of G. straminea (Chen et al, 2020) and only the longest isoforms were retained. The redundancy was evaluated using CD-HIT-EST v4.6.8 (W. Li and Godzik, 2006).…”

“…We then calculated the mutation rate via fossilcalibrated approach (i.e., µ = D * g/(2 * T), where D is the observed frequency of pairwise differences between two species, T is the estimated divergence time and g is the generation time for two species). To estimate D, the 1:1 orthologs between Swertia macrosperma C. B. Clarke (Chen et al, 2020) and G. straminea, G. siphonantha, respectively, were identified by Orthofinder version 2.2.3 (Emms and Kelly, 2015), which were followed by sequence alignment via Muscle version 3.8.1 (Edgar, 2004). The fourfold degenerate sites were extracted from the alignments, which was followed by pairwise difference calculation between two species.…”

“…The fourfold degenerate sites were extracted from the alignments, which was followed by pairwise difference calculation between two species. The divergence time was 30.4 Mya between Swertia and Gentiana (Chen et al, 2020). Based on the Ds and divergence times, estimated mutation rates were S. macrosperma-G. siphonantha, 8.38 × 10 −9 mutations per site per generation and S. macrosperma-G. straminea, 7.89 × 10 −9 mutations per site per generation, respectively.…”

“…Short reads from 33 individuals were newly generated in this research and the average number of reads per individual was 21,461,975 (ranging from 18,327,655 to 26,411,399). Meanwhile, we also included transcriptomic reads from two species (Gentiana lhsicca and G. waltonii) generated from a previous research as outgroups (Chen et al, 2020). In addition, transcriptomic reads of G. straminea generated from this study were used to assemble the reference transcriptome.…”

“…Thus, their natural distribution ranges overlap in the northeastern QTPsl, with a few geographic locations where they occur sympatrically (Hu et al, 2016). A recent phylotranscriptomic study has shown that these two gentians are not sister to each other (Chen et al, 2020), which can be well distinguished based on the shape of the inflorescence, the length of the calyx tube, and the color of the corolla (Figure 1). The flowers of G. siphonantha are crowded into terminal clusters, the calyx tube is 4-6 mm long, and the color of the corolla is dark blue-purple.…”