摘要: |
该研究以新鲜阴地蕨全株为材料,用Illumina HiSeq 2500平台进行全转录组测序,干净序列经组装后得单一基因(Unigene),将Unigene在非冗余蛋白/核酸数据库(nonredundant protein database, NR)、核酸序列数据库(nucleotide sequence database,NT)、基因本体论数据库(gene ontology,GO)、蛋白质真核同源数据库(clusters of eukaryotic orthologous groups,COG)、京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)、蛋白质序列数据库SwissProt和Interpro进行生物信息学分析。结果表明:共获得干净序列 6.67 Gb,组装后得到 58 646 个Unigene,平均长度为1 023 bp,Unigene在上述数据库的总体注释率为69.25%。其中,在GO数据库中,20 762个基因被注释到生物功能、细胞组分和分子功能3个本体的52个功能组,COG注释了20 633个基因并将其划分为25个功能簇; 在KEGG数据库中,比对注释了29 377个基因,可划分为5个大类、19个亚类代谢途径,据此筛选出八类植物激素信号转导相关的41个基因家族。通过比对共得到43 102个编码序列(coding sequence,CDS),平均长度为749 bp, N50为1 137; 筛选到60个转录因子(transcript factor,TF)家族共1 502个转录因子基因; 共发现17 195 个单核苷酸多态性(single-nucleotide polymorphism,SNP)位点,其中碱基转换11 122个,颠换6 073个; 发现了8 245个简单序列重复(simple sequence repeat,SSR),数量最多的为二核苷酸重复和三核苷酸重复。这些结果从功能和结构方面提供了阴地蕨全转录组信息和涉及植物激素信号转导的潜在基因,为进一步深入研究阴地蕨的生长发育、遗传、品种鉴别等提供了分子生物学的基础数据。 |
关键词: 阴地蕨, 转录组, 植物激素, 信号转导, 基因筛选 |
DOI:10.11931/guihaia.gxzw201907051 |
分类号:Q943 |
文章编号:1000-3142(2020)04-0536-10 |
Fund project:贵州省科技基金(QKH-JC- [2016]1137); 黔南科技基金(QNKHSZ [2016]-2); 黔南民族医学高等专科学校基金(QNYZ-201602,QNYZ-201801)[Supported by Guizhou Science and Technology Foundation(QKH-JC-[2016]1137); Qiannan Science and Technology Foundation(QNKHSZ [2016]-2); Foundation of Qiannan Medical College for Nationalities(QNYZ-201602, QNYZ-201801)]。 |
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Global transcriptome analysis of Botrychium ternatum and screening of its plant hormone signal transduction related genes |
ZHAND Linsu*, HAN Zhongyao, WANG Chuanming, DENG Xiankuo
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Department of Pharmacy, Qiannan Medical College for Nationalities,Duyun 558000, Guizhou, China
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Abstract: |
Botrychium ternatum is a commonly used folk medicinal plant, its growth and development have some typical representative characteristics of some fern plants. But researches on it mainly focus on chemical constituents, clinical and pharmacological effects, classification and distribution investigation, few about its molecular biology.Plant hormone is a sort of small signal molecular and has very important function to plant growth and development, and plant hormone signal transduction plays a key role in hormonal equilibrium. To obtain related information, Illumina HiSeq 2500 platform was used to perform transcriptome sequencing and bioinformatics analysis were carried out afterwards. Results showed 6.67 Gb clean reads was obtained and 58 646 Unigenes were assembled with an average length of 1 023 bp. Unigenes were annotated in nonredundant protein database(NR), nucleotide sequence database(NT), gene ontology(GO), clusters of eukaryotic orthologous groups(COG), Kyoto encyclopedia of genes and genomes(KEGG),Swissprot and Interpro databases with an overall annotation rate of 69.25%.Through GO annotation, 20 762 genes were annotated to three terms and 52 functional groups. A total of 20 633 genes were divided into 25 functional cluster by COG annotation. Through KEGG analysis, 29 377 genes were mapped to five groups and nineteen sub-groups pathways. In addition, 41 gene families related to eight plant hormone signal transduction pathways were screened. Through BLAST and ESTScan, 43 102 coding sequences(CDS)were found, with average length 749 bp, N50 1 137. 60 transcript factor gene families with total 1 520 genes were screened out, including C3H, MYB,MYB-related, bHLH,AP2-EREBP,WRKY and GRAS. 17 195 single-nucleotide polymorphisms(SNP)were found, including 11 122 transitions and 6 073 transversion. And 8 245 simple sequence repeats were found, among them di-nucleotide repeats and tri-nucleotide repeats rank the top two abundance. These data sets provide functional and structural information of global transcriptome and putative genes involving plant hormone signal transduction, and basic data for further research on the growth, development and variety identification of B. ternatum. |
Key words: Botrychium ternatum, transcriptome, plant hormone, signal transduction, gene screening |