De novo assembly of the transcriptome of Aegiceras corniculatum, a mangrove species in the Indo-West Pacific region

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• 作者：Lu Fang^a ; Yuchen Yang^a ; Wuxia Guo^a ; Jianfang Li^a ; Cairong Zhong^b ; Yelin Huang^a ; Renchao Zhou^a ; ^{zhrench@mail.sysu.edu.cn" class="auth_mail" title="E-mail the corresponding author} ; Suhua Shi^a ; ^{lssssh@mail.sysu.edu.cn" class="auth_mail" title="E-mail the corresponding author}
• 关键词：Mangrove ; Transcriptome ; Sequencing ; De novo assembly ; Annotation
• 刊名：Marine Genomics
• 出版年：2016
• 出版时间：August 2016
• 年：2016
• 卷：28
• 期：Complete
• 页码：49-52
• 全文大小：528 K

文摘

Aegiceras corniculatum (L.) Blanco is one of the most salt tolerant mangrove species and can thrive in 3% salinity at the seaward edge of mangrove forests. Here we sequenced the transcriptome of A. corniculatum used Illumina GA platform to develop its genomic resources for ecological and evolutionary studies. We obtained about 50 million high-quality paired-end reads with 75 bp in length. Using the short read assembler Velvet, we yielded 49,437 contigs with the average length of 625 bp. A total of 32,744 (66.23%) contigs showed significant similarity to the GenBank non-redundant (NR) protein database. 30,911 and 18,004 of these sequences were assigned to Gene Ontology and eukaryotic orthologous groups of proteins (KOG). A total of 4942 transcripts from our assemblies had significant similarity with KEGG Orthologs and were involved in 144 KEGG pathways, while 9899 unigenes had enzyme commission (EC) numbers. In addition, 9792 transcriptome-derived SSRs were identified from 7342 sequences. With our strict criteria, 4165 candidate SNPs were also identified from 2058 contigs. Some of these SNPs were further validated by Sanger sequencing. Genomic resources generated in this study should be valuable in ecological, evolutionary, and functional genomics studies for this mangrove species.