Transcriptome sequencing of Pinus kesiya var. langbianensis and comparative analysis in the Pinus phylogeny

You-Jie Zhao,Juan Wang,Zhi Xiong,Yong Cao

doi:10.1186/s12864-018-5127-6

You-Jie Zhao, Juan Wang + Show 2 more

Open Access

https://doi.org/10.1186/s12864-018-5127-6

Copy DOI

Journal: BMC Genomics	Publication Date: Oct 3, 2018
Citations: 13	License type: open-access

Affiliation: Southwest Forestry University

Abstract

BackgroundPines are widely distributed in the Northern Hemisphere and have a long evolutionary history. The availability of transcriptome data has facilitated comparative transcriptomics for studying the evolutionary patterns associated with the different geographical distributions of species in the Pinus phylogeny.ResultsThe transcriptome of Pinus kesiya var. langbianensis was sequenced using the Illumina HiSeq 2000 platform, and a total of 68,881 unigenes were assembled by Trinity. Transcriptome sequences of another 12 conifer species were downloaded from public databases. All of the pairwise orthologues were identified by comparative transcriptome analysis in 13 conifer species, from which the rate of diversification was calculated and a phylogenetic tree inferred. All of the fast-evolving positive selection sequences were identified, and some salt-, drought-, and abscisic acid-resistance genes were discovered.ConclusionsmRNA sequences of P. kesiya var. langbianensis were obtained by transcriptome sequencing, and a large number of simple sequence repeat and short nucleotide polymorphism loci were detected. These data can be used in molecular marker-assisted selected in pine breeding. Divergence times were estimated in the 13 conifer species using comparative transcriptomic analysis. A number of positive selection genes were found to be related to environmental factors. Salt- and abscisic acid-related genes exhibited different selection patterns between coastal and inland Pinus. Our findings help elucidate speciation patterns in the Pinus lineage.

Highlights

Pines are widely distributed in the Northern Hemisphere and have a long evolutionary history
Transcriptome sequencing and de novo assembly The cDNA samples obtained from pine needles of P. kesiya var. langbianensis and other individuals were normalized to increase the sequencing efficiency of rare transcripts
A number of positive selection genes were found to be related to environmental factors (Table 6)

Summary

Introduction

Pines are widely distributed in the Northern Hemisphere and have a long evolutionary history. The availability of transcriptome data has facilitated comparative transcriptomics for studying the evolutionary patterns associated with the different geographical distributions of species in the Pinus phylogeny. Pines (Pinus) are widely distributed in the Northern Hemisphere and are the largest extant genus of conifers, constituting the most important source of wood in the forestry industry [1, 2]. Transcriptome sequencing technology can obtain all of the RNA information of an organism at a point in time, thereby providing a large amount of information for molecular biology studies [11,12,13]. Transcriptome sequencing can obtain a large number of single nucleotide polymorphism (SNP), simple sequence repeat (SSR), and other molecular markers [14, 15]. Molecular markers with good polymorphism can help researchers shorten the genetic breeding cycle [16]

Methods

Results

Discussion

Conclusion