Characterization and analysis of the transcriptome response to drought in Larix kaempferi using PacBio full-length cDNA sequencing integrated with de novo RNA-seq reads
| Autor: | Chenghao Li, Fude Wang, Xin Zhang, Joobin Lee, Sen Yu, Wenlong Li, Wanqiu Lv, Jingli Yang |
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| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine China DNA Complementary Drought tolerance RNA-Seq Larix Plant Science Computational biology 01 natural sciences Transcriptome 03 medical and health sciences Gene Expression Regulation Plant Stress Physiological Genetics Consensus sequence MYB Gene biology fungi Alternative splicing food and beverages biology.organism_classification Droughts 030104 developmental biology Larix kaempferi 010606 plant biology & botany |
| Zdroj: | Planta. 253(2) |
| ISSN: | 1432-2048 |
| Popis: | A hypothetical model of drought tolerance mechanism of Larix kaempferi was established through SMRT-seq and Illumina HiSeq. Larix kaempferi is an important economic and ecological species and a major afforestation species in north-eastern China. To date, no information has been reliably derived regarding full-length cDNA sequencing information on L. kaempferi. By single-molecule long-read isoform sequencing (SMRT-seq), here we report a total of 26,153,342 subreads (21.24 Gb) and 330,371 circular consensus sequence (CCS) reads after the modification of site mismatch, and 35,414 unigenes were successfully collected. To gain deeper insights into the molecular mechanisms of L. kaempferi response to drought stress, we combined Illumina HiSeq with SMRT-seq to decode full-length transcripts. In this study, we report 27 differentially expressed genes (DEGs) involved in the perception and transmission of drought stress signals in L. kaempferi. A large number of DEGs responding to drought stress were detected in L. kaempferi, especially DEGs involved in the reactive oxygen species (ROS) scavenging, lignin biosynthesis, and sugar metabolism, and DEGs encoding drought stress proteins. We detected 73 transcription factors (TFs) under drought stress, including AP2/ERF, bZIP, TCP, and MYB. This study provides basic full sequence resources for L. kaempferi research and will help us to better understand the functions of drought-resistance genes in L. kaempferi. |
| Databáze: | OpenAIRE |
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