Full-length transcriptome analysis of Adiantum flabellulatum gametophyte

PeerJ

article

Zeping Cai¹  Zhenyu Xie¹  Luyao Huang¹  Zixuan Wang¹  Min Pan¹  Xudong Yu¹  Shitao Xu²  Jiajia Luo³ 

[1]Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University

[2]College of Horticulture, Hainan University

[3]Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences

关键词: Ferns;    Three-generation sequencing;    Functional annotation;    Reference gene set;   

DOI  :  10.7717/peerj.13079

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Ferns are important components of plant communities on earth, but their genomes are generally very large, with many redundant genes, making whole genome sequencing of ferns prohibitively expensive and time-consuming. This means there is a significant lack of fern reference genomes, making molecular biology research difficult. The gametophytes of ferns can survive independently, are responsible for sexual reproduction and the feeding of young sporophytes, and play an important role in the alternation of generations. For this study, we selected Adiantum flabellulatum as it has both ornamental and medicinal value and is also an indicator plant of acidic soil. The full-length transcriptome sequencing of its gametophytes was carried out using PacBio three-generation sequencing technology. A total of 354,228 transcripts were obtained, and 231,705 coding sequences (CDSs) were predicted, including 5,749 transcription factors (TFs), 2,214 transcription regulators (TRs) and 4,950 protein kinases (PKs). The transcripts annotated by non-redundant protein sequence database (NR), Kyoto encyclopedia of genes and genomes (KEGG), eukaryotic ortholog groups (KOG), Swissprot, protein family (Pfma), nucleotide sequence database (NT) and gene ontology (GO) were 251,501, 197,474, 193,630, 194,639, 195,956, 113,069 and 197,883, respectively. In addition, 138,995 simple sequence repeats (SSRs) and 111,793 long non-coding RNAs (lncRNAs) were obtained. We selected nine chlorophyll synthase genes for qRT-PCR, and the results showed that the full-length transcript sequences and the annotation information were reliable. This study can provide a reference gene set for subsequent gene expression quantification.

【 授权许可】

CC BY