title: De novo assembly of the transcriptomes of two yellow mangroves, Ceriops tagal and C. zippeliana, and one of their terrestrial relatives, Pellacalyx yunnanensis.
abstract: Mangroves are dominant woody plants in the intertidal zones and are of both ecological and economic importance. Species of Ceriops, also called yellow mangroves, have many adaptive traits (including vivipary) for coping with the harsh marine environments. However, little is known about the origination and evolutionary history of this genus. In this study, we aim to provide clues to these two questions by sequencing the transcriptomes of two Ceriops species, Ceriops tagal and Ceriops zippeliana, and one of their terrestrial relatives, Pellacalyx yunnanensis. 48.19, 10.50 and 35.37 million high-quality reads that were generated by Illumina sequencing were assembled into 50,807, 40,543 and 64,147 contigs for the three species, respectively. After removing redundancy and contigs with low coverage, 39,361, 34,362, and 51,668 contigs with the N50 values of 1553, 772 and 1833bp, respectively, were retained for further analysis. Of them, 17,348, 16,484 and 18,038 contigs were successfully annotated with the known gene ontology (GO) terms. GO classifications of the transcriptome profiles for the three species are similar. Most of the contigs were assigned to the cell and organelle related GO terms in the cellular component category, "binding" in the molecular function category, and "cellular process", "metabolic process" and "biological regulation" in the biological process category. We identified more than 6000 pairs of orthologs for each pair of the three species, with the peak of synonymous substitution rate (Ks) distribution of 0.03 between the two Ceriops species and 0.23 between each Ceriops species and P. yunnanensis. Our transcriptomic data provide a great amount of genomic resources for yellow mangroves and can be used for studying the origination and adaptive evolution of mangroves.
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Yuchen
authors.initials: Y
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Shuhuan
authors.initials: S
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Jianfang
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Xuan
authors.initials: X
authors.lastname: Li
authors.affiliation: Hainan Dongzhai Harbor National Nature Reserve, Haikou 571129, China.
authors.forename: Cairong
authors.initials: C
authors.lastname: Zhong
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Yelin
authors.initials: Y
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China. Electronic address: zhrench@mail.sysu.edu.cn.
authors.forename: Renchao
authors.initials: R
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China. Electronic address: lssssh@mail.sysu.edu.cn.
authors.forename: Suhua
authors.initials: S
authors.lastname: Shi
mesh_terms: D027901:Acanthaceae / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D005786:Gene Expression Regulation; D018749:RNA, Plant / Q000235:genetics; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D018749:RNA, Plant
keywords: Annotation; Ceriops; De novo assembly; Sequencing; Transcriptome