Liao Ting, Zhang Linyi, Wang Ye, Guo Liqin, Cao Jun, Liu Guobin
Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Front Genet. 2024 Jan 18;15:1345039. doi: 10.3389/fgene.2024.1345039. eCollection 2024.
As a unique and native conifer in China, is widely used in soil erosion control, garden landscapes, timber, and traditional Chinese medicine. However, due to the lack of reference genome and transcriptome, it is limited to the further molecular mechanism research and gene function mining. To develop a full-length reference transcriptome, tissues from five different parts of and four cone developmental stages were sequenced and analyzed by single-molecule real-time (SMRT) sequencing through the PacBio platform in this study. Overall, 37,111 isoforms were detected by PacBio with an N50 length of 2,317 nt, an average length of 1,999 bp, and the GC content of 41.81%. Meanwhile, 36,120 coding sequences, 5,645 simple sequence repeats (SSRs), 1,201 non-coding RNAs (lncRNAs), and 182 alternative splicing (AS) events with five types were identified using the results obtained from the PacBio transcript isoforms. Furthermore, 1,659 transcription factors (TFs) were detected and belonged to 51 TF families. A total of 35,689 transcripts (96.17%) were annotated through the NCBI nr, KOG, Swiss-Prot and KEGG databases, and 385 transcript isoforms related to 8 types of hormones were identified incorporated into plant hormone signal transduction pathways. The assembly and revelation of the full-length transcriptome of offer a pioneering insight for future investigations into gene function and genetic breeding within species.
作为中国特有的本土针叶树，[具体树种未给出]被广泛应用于水土流失治理、园林景观、木材及传统中药领域。然而，由于缺乏参考基因组和转录组，其进一步的分子机制研究和基因功能挖掘受到限制。在本研究中，通过PacBio平台利用单分子实时（SMRT）测序技术对[具体树种未给出]五个不同部位的组织以及四个球果发育阶段进行了测序和分析，以构建全长参考转录组。总体而言，通过PacBio检测到37,111个异构体，N50长度为2,317 nt，平均长度为1,999 bp，GC含量为41.81%。同时，利用PacBio转录异构体的结果鉴定出36,120个编码序列、5,645个简单序列重复（SSR）、1,201个非编码RNA（lncRNA）以及182个具有五种类型的可变剪接（AS）事件。此外，检测到1,659个转录因子（TF），属于51个TF家族。通过NCBI nr、KOG、Swiss-Prot和KEGG数据库对总共35,689个转录本（96.17%）进行了注释，并鉴定出385个与8种激素相关的转录异构体纳入植物激素信号转导途径。[具体树种未给出]全长转录组的组装和揭示为未来该树种的基因功能研究和遗传育种提供了开创性的见解。
