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Full-length transcriptome characterization and comparative analysis of Gleditsia sinensis
Feng Xiao1, Yang Zhao2, Xiurong Wang1
1Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China.
BMC Genomics
|December 8, 2023
Summary
This study presents a comprehensive genetic analysis of Gleditsia sinensis using PacBio sequencing. The findings provide crucial genomic data to advance molecular breeding and understand the evolutionary mechanisms of this important tree species.
Area of Science:
- Plant genomics
- Transcriptomics
- Molecular evolution
Background:
- Gleditsia sinensis is an economically significant tree species with limited genetic information available.
- This lack of data impedes advancements in its molecular breeding and genetic improvement.
Purpose of the Study:
- To generate comprehensive transcriptomic data for Gleditsia sinensis using PacBio SMRT sequencing.
- To identify key genes, non-coding RNAs, and alternative splicing events.
- To provide a foundation for evolutionary studies and molecular breeding of Gleditsia.
Main Methods:
- PacBio single-molecule real-time (SMRT) sequencing was employed for transcriptomic analysis.
- Bioinformatic tools were used to identify non-redundant transcripts, open reading frames (ORFs), long non-coding RNAs (LncRNAs), and alternative splicing (AS) events.
- Orthologous gene identification and selection pressure analysis were performed.
Main Results:
- Generated 95,183 non-redundant transcript sequences, including 93,668 complete ORFs, 2,858 LncRNAs, and identified 18,855 AS events.
- Identified positively selected stress-related genes and optimal codons (AGA, AGG, CCA) within the Gleditsia genus.
- Discovered 315 Cytochrome P450 monooxygenases (CYP450s) and 147 uridine diphosphate (UDP)-glycosyltransferases (UGTs).
- Validated the transcriptome assembly reliability using GsIAA14 gene cloning.
Conclusions:
- The PacBio SMRT sequencing provides a valuable genomic resource for Gleditsia sinensis.
- This data will facilitate future research into the evolutionary history and molecular breeding strategies for this tree.
- Identified potential reference genes (EIF5A) and key gene families (CYP450s, UGTs) for further functional studies.
