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Yang Y.,Sun Yat Sen University | Yang S.,Sun Yat Sen University | Li J.,Sun Yat Sen University | Li X.,Sun Yat Sen University | And 4 more authors.
Marine Genomics | Year: 2015

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 1833. bp, 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. © 2015 Elsevier B.V.

Chen Y.,Sun Yat Sen University | Chen Y.,University of Sichuan | Hou Y.,Sun Yat Sen University | Guo Z.,Sun Yat Sen University | And 4 more authors.
PLoS ONE | Year: 2015

The genus Rhizophora is one of the most important components of mangrove forests. It is an ideal system for studying biogeography, molecular evolution, population genetics, hybridization and conservation genetics of mangroves. However, there are no sufficient molecular markers to address these topics. Here, we developed 77 pairs of nuclear gene primers, which showed successful PCR amplifications across all five Rhizophora species and sequencing in R. apiculata. Here, we present three tentative applications using a subset of the developed nuclear genes to (I) reconstruct the phylogeny, (II) examine the genetic structure and (III) identify natural hybridization in Rhizophora. Phylogenetic analyses support the hypothesis that Rhizophora had disappeared in the Atlantic-East Pacific (AEP) region and was re-colonized from the IWP region approximately 12.7 Mya. Population genetics analyses in four natural populations of R. apiculata in Hainan, China, revealed extremely low genetic diversity, strong population differentiation and extensive admixture, suggesting that the Pleistocene glaciations, particularly the last glacial maximum, greatly influenced the population dynamics of R. apiculata in Hainan. We also verified the hybrid status of a morphologically intermediate individual between R. apiculata and R. stylosa in Hainan. Based on the sequences of five nuclear genes and one chloroplast intergenic spacer, this individual is likely to be an F1 hybrid, with R. stylosa as its maternal parent. The nuclear gene markers developed in this study should be of great value for characterizing the hybridization and introgression patterns in other cases of this genus and testing the role of natural selection using population genomics approaches. © 2015 Chen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Chen S.,Sun Yat Sen University | Zhou R.,Sun Yat Sen University | Huang Y.,Sun Yat Sen University | Zhang M.,Sun Yat Sen University | And 3 more authors.
Marine Genomics | Year: 2011

Mangroves are critical and threatened marine resources, yet few transcriptomic and genomic data are available in public databases. The transcriptome of a highly salt tolerant mangrove species, Sonneratia alba, was sequenced using the Illumina Genome Analyzer in this study. Over 15million 75-bp paired-end reads were assembled into 30,628 unique sequences with an average length of 581bp. Of them, 2358 SSRs were detected, with di-nucleotide repeats (59.2%) and tri-nucleotide repeats (37.7%) being the most common. Analysis of codon usage bias based on 20,945 coding sequences indicated that genes of S. alba were less biased than those of some microorganisms and Drosophila and that codon usage variation in S. alba was due primarily to compositional mutation bias, while translational selection has a relatively weak effect. Genome-wide gene ontology (GO) assignments showed that S. alba shared a similar GO slim classification with Arabidopsis thaliana. High percentages of sequences assigned to GO slim category 'mitochondrion' and four KEGG pathways, such as carbohydrates and secondary metabolites metabolism, may contribute to salt adaptation of S. alba. In addition, 1266 unique sequences matched to 273 known salt responsive genes (gene families) in other species were screened as candidates for salt tolerance of S. alba, and some of these genes showed fairly high coverage depth. At last, we identified four genes with signals of strong diversifying selection (Ka/Ks>1) by comparing the transcriptome sequences of S. alba with 249 known ESTs from its congener S. caseolaris. This study demonstrated a successful application of the Illumina platform to de novo assembly of the transcriptome of a non-model organism. Abundant SSR markers, salt responsive genes and four genes with signature of natural selection obtained from S. alba provide abundant sequence sources for future genetic diversity, salt adaptation and speciation studies. © 2011 Elsevier B.V.

Zhou R.,Sun Yat Sen University | Ling S.,CAS Beijing Institute of Genomics | Zhao W.,CAS Beijing Institute of Genomics | Osada N.,Japan National Institute of Biomedical Innovation | And 14 more authors.
Molecular Biology and Evolution | Year: 2011

Population genetics of species living in marginal habitats could be particularly informative about the genetics of adaptation, but such analyses have not been readily feasible until recently. Sonneratia alba, a mangrove species widely distributed in the Indo-West Pacific, provides a very suitable system for the study of local adaptation. In this study, we analyzed DNA variation by pooling 71 genes from 85-100 individuals for DNA sequencing. For each of the two nearby S. alba populations, we obtained ∼2,500 × coverage on the Illumina GA platform and for the Sanya population, an additional 5,400 × coverage on the AB SOLiD platform. For the Sanya sample, although each sequencing method called many putative single nucleotide polymorphisms, the two sets of calls did not overlap, suggesting platform-dependent errors. Conventional sequencing corroborated that each population is monomorphic. The two populations differ by 54 bp of 79,000 sites, but 90% of the variants are found in 10% of the genes. Strong local adaptation and high migration may help to explain the extensive monomorphism shared by the two populations in the presence of a small number of highly differentiated loci. © The Author 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All reserved.

Yang Y.,Sun Yat Sen University | Yang S.,Sun Yat Sen University | Li J.,Sun Yat Sen University | Deng Y.,CAS South China Botanical Garden | And 6 more authors.
BMC Genomics | Year: 2015

Background: Acanthus is a unique genus consisting of both true mangrove and terrestrial species; thus, it represents an ideal system for studying the origin and adaptive evolution of mangrove plants to intertidal environments. However, little is known regarding the two respects of mangrove species in Acanthus. In this study, we sequenced the transcriptomes of the pooled roots and leaves tissues for a mangrove species, Acanthus ilicifolius, and its terrestrial congener, A. leucostachyus, to illustrate the origin of the mangrove species in this genus and their adaptive evolution to harsh habitats. Results: We obtained 73,039 and 69,580 contigs with N50 values of 741 and 1557 bp for A. ilicifolius and A. leucostachyus, respectively. Phylogenetic analyses based on four nuclear segments and three chloroplast fragments revealed that mangroves and terrestrial species in Acanthus fell into different clades, indicating a single origin of the mangrove species in Acanthus. Based on 6634 orthologs, A. ilicifolius and A. leucostachyus were found to be highly divergent, with a peak of synonymous substitution rate (Ks) distribution of 0.145 and an estimated divergence time of approximately 16.8 million years ago (MYA). The transgression in the Early to Middle Miocene may be the major reason for the entry of the mangrove lineage of Acanthus into intertidal environments. Gene ontology (GO) classifications of the full transcriptomes did not show any apparent differences between A. ilicifolius and A. leucostachyus, suggesting the absence of gene components specific to the mangrove transcriptomes. A total of 99 genes in A. ilicifolius were identified with signals of positive selection. Twenty-three of the 99 positively selected genes (PSGs) were found to be involved in salt, heat and ultraviolet stress tolerance, seed germination and embryo development under periodic inundation. These stress-tolerance related PSGs may be crucial for the adaptation of the mangrove species in this genus to stressful marine environments and may contribute to speciation in Acanthus. Conclusions: We characterized the transcriptomes of one mangrove species of Acanthus, A. ilicifolius, and its terrestrial relative, A. leucostachyus, and provided insights into the origin of the mangrove Acanthus species and their adaptive evolution to abiotic stresses in intertidal environments. © 2015 Yang et al.

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