Comparative transcriptome resources of eleven Primulina species, a group of ‘stone plants’ from a biodiversity hot spot

Abstract

The genus Primulina is an emerging model system in studying the drivers and mechanisms of species diversification, for its high species richness and endemism, together with high degree of habitat specialization. In this study, we sequenced transcriptomes for eleven Primulina species across the phylogeny of the genus using the Illumina HiSeq 2000 platform. A total of 336 million clean reads were processed into 355 573 unigenes with a mean length of 1336 bp and an N50 value of 2191 bp after pooling and reassembling twelve individual pre-assembled unigene sets. Of these unigenes, 249 973 (70%) were successfully annotated and 256 601 (72%) were identified as coding sequences (CDSs). We identified a total of 38 279 simple sequence repeats (SSRs) and 367 123 single nucleotide polymorphisms (SNPs). Marker validation assay revealed that 354 (27.3%) of the 1296 SSR and 795 (39.6%) of the 2008 SNP loci showed successful genotyping performance and exhibited expected polymorphism profiles. We screened 834 putative single-copy nuclear genes and proved their high effectiveness in phylogeny construction and estimation of ancestral population parameters. We identified a total of 85 candidate orthologs under positive selection for 46 of the 66 species pairs. This study provided an efficient application of RNA-seq in development of genomic resources for a group of 'stone plants' from south China Karst regions, a biodiversity hot spot of the World. The assembled unigenes with annotations and the massive gene-associated molecular markers would help guide further molecular systematic, population genetic and ecological genomics studies in Primulina and its relatives.

Diversification of HawaiianCyrtandra(Gesneriaceae) under the influence of incomplete lineage sorting and hybridization

“…Libraries were barcoded using NEBNext multiplex oligos (New England Biolabs) and quantified using qPCR (NEBNext quant kit, New England Biolabs). Probes for target enrichment of our libraries were designed with the Hyb‐Seq protocol (Weitemier et al, ) using a Boea hygrometrica genome (Xiao et al, ) and Primulina pteropoda transcriptome (Ai et al, ) — two Old World species of Gesneriaceae. The Hyb‐Seq protocol was meant for use with a transcriptome and genome from the same species, but because there are no transcriptomes or complete genomes available for Cyrtandra , we opted to use two available and related Old World gesneriad taxa.…”

Paraboea wenshanensis, a new species of Gesneriaceae from Yunnan, China

“…Southern and south-western China has extensive areas of karst topography (Chenet al 2008) so that seed plants in this region show extreme diversity and are endemic on alkalescent limestone substrates (Xu 1993), a typical example being Gesneriaceae (Fang et al 1995, Wang et al 1998, Li and Wang 2004, Wei et al 2010, Ai et al 2015). …”

Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China

“…Finally, a total of 91,449 unigenes with a total length of 148,176,175 nt were detected, and the average length and N50 were 1,620 nt and 2,389 nt, respectively. The final assembled transcripts of B. clarkeana were longer than those of its sibling species, i.e., the Primulina species and B. hygrometrica , which were assembled using Illumina (Ai et al, 2015) and the 454 pyrosequencing platform (Zhu et al, 2015), respectively. As 454 pyrosequencing produces longer reads than Illumina, the sequencing results were ideal in this study (Zalapa et al, 2012).…”