Mangosteen Transcriptome and and Transdecoder Files

Mangosteen Illumina RNA sequences were obtained from the NCBI Sequence Read Archive (SRA) databases. Trimmomatic 0.39 was used to remove adaptor sequences and low-quality reads from Illumina data with default parameter (TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25). Next, the clean Illumina data was used for <i>de novo</i> transcriptome assembly using Trinity v.2.9.1 with default parameters (adding the following parameter: normalize_by_read_set; min_kmer_cov=2; no bowtie) to generate a single Trinity assembly. After assembly, non-redundant genes/ reference transcriptome were obtained using TGICL with default settings. Next, Transdecoder was used to generate a total of 93,923 predicted peptides.

本研究涉及的山竹Illumina RNA序列取自NCBI序列读取存档（Sequence Read Archive, SRA）数据库。使用Trimmomatic 0.39软件，以默认参数（TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25）对Illumina测序数据进行接头序列及低质量读段（reads）的去除操作。随后，将经质控过滤后的洁净Illumina数据用于从头（de novo）转录组组装：采用Trinity v.2.9.1软件，以默认参数为基础并额外添加如下参数：normalize_by_read_set、min_kmer_cov=2及不启用bowtie，最终生成单一Trinity组装结果。组装完成后，使用TGICL软件以默认设置获取非冗余基因与参考转录组。最后，借助Transdecoder软件共预测得到93923条肽段。