title: 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.
authors.affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Ai
authors.forename: Yong
authors.initials: Y
authors.lastname: Gao
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Zhang
authors.forename: Junjie
authors.initials: J
authors.lastname: Tao
authors.forename: Ming
authors.initials: M
authors.lastname: Kang
authors.forename: Hongwen
authors.initials: H
authors.lastname: Huang
mesh_terms: D044822:Biodiversity; D002681:China; D005819:Genetic Markers; D014644:Genetic Variation; D060005:Genotyping Techniques; D000068378:Lamiales / Q000145:classification* / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
keywords: Primulina; positive selection; simple sequence repeats; single nucleotide polymorphisms; single-copy nuclear genes; transcriptome