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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

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Abstract

Main conclusion

A hypothetical model of drought tolerance mechanism of Larix kaempferi was established through SMRT-seq and Illumina HiSeq.

Abstract

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.

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Data availability

The data from single-molecule long-read sequencing has been uploaded to the Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra) under Bioproject PRJNA648500. The data from RNA-seq has been submitted in the NCBI GEO database, and the GEO Accession Number is GSE154534 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154534).

Abbreviations

AS:

Alternative splicing

DEG:

Differentially expressed gene

GST:

Glutathione S-transferase

SMRT-seq:

Single-molecule long-read isoform sequencing

TF:

Transcription factor

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Acknowledgements

We acknowledge TopEdit LLC for the linguistic editing and proofreading during the preparation of this manuscript. This work was supported by the Genetically Modified Organisms Breeding Major Projects of China (Grant No. 2018ZX08020003), the 111 Project (B16010) and the Fundamental Research Funds for the Central Universities of China (2572018CL04).

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Authors and Affiliations

  1. State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China

    Wenlong Li, Joobin Lee, Sen Yu, Wanqiu Lv, Xin Zhang, Chenghao Li & Jingli Yang

  2. Institute of Forestry Science of Heilongjiang Province, 134 Haping Road, Harbin, 150040, China

    Fude Wang

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  1. Wenlong Li
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  2. Joobin Lee
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  3. Sen Yu
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Correspondence to Chenghao Li or Jingli Yang.

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425_2020_3555_MOESM6_ESM.tif

Supplementary Fig. S1: Phenotypic variation of Larix kaempferi under drought stress. CK, well-watered control; D14, 14 days of drought treatment (tif 200247 KB)

425_2020_3555_MOESM7_ESM.tif

Supplementary Fig. S2: Gene ontology (GO) classification. GO was summarized as three main categories: cellular component (green), molecular function (red), and biological process (blue). The number (Y-axis) of genes were also shown (tif 40330 KB)

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Li, W., Lee, J., Yu, S. et al. 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. Planta 253, 28 (2021). https://doi.org/10.1007/s00425-020-03555-3

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