文献类型：期刊文献

英文题名：A complete transcriptional landscape analysis of Pinus elliottii Engelm. Using third-generation sequencing and comparative analysis in the Pinus phylogeny

作者：Diao, Shu[1] Ding, Xianying[1] Luan, Qifu[1] Jiang, Jingmin[1]

第一作者：刁姝

通信作者：Luan, Qifu|[a0005e39f8d2a09d6b6a7]栾启福;

机构：[1] Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China

年份：2019

卷号：10

期号：11

外文期刊名：Forests

收录：EI(收录号：20194807746351);Scopus(收录号：2-s2.0-85075442504)

语种：英文

外文关键词：DNA sequences - Plants (botany)

摘要：The planting of Pinus elliottii Engelm. has now reached close to three million ha in China. Molecular breeding as part of the improvement program for P. elliottii in southern China has been carried out in recent years. Third-generation sequencing (Pacbio sequencing technology, TGS) was used to obtain the exome of P. elliottii for molecular breeding. A total of 35.8 Gb clean reads were generated using TGS. After removing the redundant reads, we obtained 80,339 high-accuracy transcripts. Significantly, a total of 76,411 transcripts (95.1%) were blasted to public annotation databases. We predicted 65,062 intact coding sequences (CDSs), 8916 alternative splicing events, 1937 long non-coding RNAs, and 22,109 simple sequence repeats (SSRs) based on these obtained transcripts. Using the public databases and the data obtained above, 23 orthologous single-copy genes were identified to analyze the phylogenetic relationships for Pinus firstly including P. elliottii. Many positive selection genes involved in important biological processes and metabolism pathways were identified between P. elliottii and other pines. These positive selection genes could be candidate genes to be researched on the genetic basis of superior performance. Our study is the first to reveal the full-length and well-annotated transcripts of P. elliottii, which could provide reference for short transcriptome sequences in the research of genetics, phylogenetics, and genetic improvement for the non-reference genome species. ? 2019 by the authors.