De novo assembly of the transcriptome of Aegiceras corniculatum, a mangrove species in the Indo-West Pacific region.
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 75bp in length. Using the short read assembler Velvet, we yielded 49,437 contigs with the average length of 625bp. 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.
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
Lu
L
Fang
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
Yuchen
Y
Yang
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
Wuxia
W
Guo
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
Jianfang
J
Li
Hainan Dongzhai Harbor National Nature Reserve, Haikou 571129, China.
Cairong
C
Zhong
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
Yelin
Y
Huang
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China. Electronic address: zhrench@mail.sysu.edu.cn.
Renchao
R
Zhou
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China. Electronic address: lssssh@mail.sysu.edu.cn.
Suhua
S
Shi
D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D029623:Primulaceae / Q000235:genetics*; D017422:Sequence Analysis, DNA; D059467:Transcriptome
Annotation; De novo assembly; Mangrove; Sequencing; Transcriptome