Renchao Zhou

MapView: visualization of short reads alignment on a desktop computer

UNLABELLED We introduce a new visual analytics tool named MapView to facilitate the representation of large-scale short reads alignment data and genetic variation analysis. MapView can handle hundreds of millions of short reads on a desktop computer with limited memory. It supports a compact alignment view for both single-end and paired end short reads, multiple navigation and zoom modes and multi-thread processing. Moreover, MapView offers automated genetic variation detection. MapView has been used in our lab and by over 10 research labs worldwide. AVAILABILITY http://evolution.sysu.edu.cn/mapview/. SUPPLEMENTARY INFORMATION Supplementary data are available at http://evolution.sysu.edu.cn/mapview/MVF.pdf.

Gene Expression Profiles in Response to Salt Stress in Hibiscus Tiliaceus

Hibiscus tiliaceus, a mangrove associate, is an ideal plant for studying salt tolerance and adaptation since it can inhabit both inland and littoral habitats. In this study, we explored the expression profiles of H. tiliaceus under salt stress using a full-length cDNA microarray. Four hundred eighty-six salt-responsive unigenes were identified in H. tiliaceus; 224 of which had high sequence similarity to Arabidopsis. Many genes identified are known to be salt-stress responsive. Furthermore we examined the physiological performance of H. tiliaceus under salt stress. Physiological analysis displayed decrease in ratio of K+/Na+ and negative influence on photosynthesis of H. tiliaceus. Our study indicated that to survive under high salinine intertidal environments, H. tiliaceus evolved its own mechanisms to re-gain both ionic and osmotic homeostasis through coordinated engagement of genes associated with gene transcription, signaling, and down-stream cell transport and detoxification pathways.

Genetic diversity of the endangered Chinese endemic herb Primulina tabacum (Gesneriaceae) revealed by amplified fragment length polymorphism (AFLP).

Primulina tabacum Hance, is a critically endangered perennial endemic to limestone area in South China. Genetic variability within and among four extant populations of this species was assessed using AFLP markers. We expected a low genetic diversity level of this narrowly distributed species, but our results revealed that a high level of genetic diversity remains, both at population level (55.5% of markers polymorphic, HE = 0.220, IS = 0.321), and at species level (P = 85.6% of markers polymorphic, HE = 0.339, IS = 0.495), probably resulting from its refugial history and/or breeding system. High levels of genetic differentiation among populations was apparent based on Nei’s genetic diversity analysis (Gst=0.350). The restricted gene flow between populations is a potential reason for the high genetic differentiation. The population genetic diversity of P. tabacum revealed here has clear implications for conservation and management. To maintain present levels of genetic diversity, in situ conservation of all populations is necessary.

MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads

BackgroundNext-generation sequencing technologies provide exciting avenues for studies of transcriptomics and population genomics. There is an increasing need to conduct spliced and unspliced alignments of short transcript reads onto a reference genome and estimate minor allele frequency from sequences of population samples.ResultsWe have designed and implemented MapNext, a software tool for both spliced and unspliced alignments of short sequence reads onto reference sequences, and automated SNP detection using neighbourhood quality standards. MapNext provides four main analyses: (i) unspliced alignment and clustering of reads, (ii) spliced alignment of transcript reads over intron boundaries, (iii) SNP detection and estimation of minor allele frequency from population sequences, and (iv) storage of result data in a database to make it available for more flexible queries and for further analyses. The software tool has been tested using both simulated and real data.ConclusionMapNext is a comprehensive and powerful tool for both spliced and unspliced alignments of short reads and automated SNP detection from population sequences. The simplicity, flexibility and efficiency of MapNext makes it a valuable tool for transcriptomic and population genomic research.

Molecular evidence for natural hybridization in the mangrove fern genus Acrostichum

BackgroundNatural hybridization is prevalent in ferns, and plays an important role in fern evolution and speciation. In the Indo West-Pacific region, the mangrove fern genus Acrostichum consists of two largely sympatric species, A. aureum and A. speciosum. Although there has been no report of interspecific hybridization before, we found some individuals morphologically intermediate between them in Guangdong and Hainan, China, for the first time, which were suspected to be hybrids. In this study, we aimed to test the hypothesis of natural hybridization between A. aureum and A. speciosum in Guangdong and Hainan using three low-copy nuclear genes. A chloroplast intergenic spacer was used to infer the hybridization direction once the hybrid status was confirmed. In addition, we examined spore shapes and germination for these taxa.ResultsBoth A. aureum and A. speciosum showed a low level of polymorphism at all three nuclear genes; however, they were well separated at these loci. At both locations, each individual of the putative hybrid showed additivity in chromatograms at all sites where the two species showed fixed differences. Haplotype analysis at all three nuclear genes indicated that each individual of the putative hybrid possessed two haplotypes, matching with those of A. aureum and A. speciosum, respectively. Sequencing of the chloroplast trnV-trnM regions showed that A. aureum differed from A. speciosum by eleven nucleotide substitutions and three indels (insertions/deletions), and all sampled individuals of the putative hybrid had the identical sequences with A. speciosum. Compared with A. aureum and A. speciosum, the putative hybrid had much reduced spore germination rate.ConclusionsSequence data of the three nuclear genes provide compelling evidence for natural hybridization between A. aureum and A. speciosum, and all the hybrid individuals are likely F1s. The hybridization is unidirectional and A. speciosum is the maternal parent of the hybrid based on the assumption of maternal inheritance of chloroplast DNA. Human disturbance on mangrove habitats may facilitate the establishment of hybrids of Acrostichum.

Testing a hypothesis of unidirectional hybridization in plants: Observations on Sonneratia, Bruguiera and Ligularia

BackgroundWhen natural hybridization occurs at sites where the hybridizing species differ in abundance, the pollen load delivered to the rare species should be predominantly from the common species. Previous authors have therefore proposed a hypothesis on the direction of hybridization: interspecific hybrids are more likely to have the female parent from the rare species and the male parent from the common species. We wish to test this hypothesis using data of plant hybridizations both from our own experimentation and from the literature.ResultsBy examining the maternally inherited chloroplast DNA of 6 cases of F1 hybridization from four genera of plants, we infer unidirectional hybridization in most cases. In all 5 cases where the relative abundance of the parental species deviates from parity, however, the direction is predominantly in the direction opposite of the prediction based strictly on numerical abundance.ConclusionOur results show that the observed direction of hybridization is almost always opposite of the predicted direction based on the relative abundance of the hybridizing species. Several alternative hypotheses, including unidirectional postmating isolation and reinforcement of premating isolation, were discussed.

Population Genetics in Nonmodel Organisms: II. Natural Selection in Marginal Habitats Revealed by Deep Sequencing on Dual Platforms

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.

Phylogenetic position of Ephedra rhytidosperma,a species endemic to China:evidence from chloroplast and ribosomal DNA sequences

The chloroplast genes matK. and rbcL, ribosomal gene 18S and ITS regions of nuclear ribosomal DNA fromEphedra rhytidosperma, a species endemic to China, were sequenced and its phylogenetic position was investigated. Independent and combined phylogenetic analyses for the DNA sequences from 16 taxa representing 15 species of the genusEphedra were performed using the maximum parsimony (MP), neighbor-joining (NJ), minimum evolution (ME) and maximum likelihood (ML) methods. The results indicate thatE. rhytidosperma is closely related toE. equisetina. The divergence time between them is estimated to be 10.85±2.44 Ma based on the results of the relative-rate tests and the evolutionary rate of rbcL gene.

Transcriptional Homeostasis of a Mangrove Species, Ceriops tagal, in Saline Environments, as Revealed by Microarray Analysis

Background Differential responses to the environmental stresses at the level of transcription play a critical role in adaptation. Mangrove species compose a dominant community in intertidal zones and form dense forests at the sea-land interface, and although the anatomical and physiological features associated with their salt-tolerant lifestyles have been well characterized, little is known about the impact of transcriptional phenotypes on their adaptation to these saline environments. Methodology and Principal findings We report the time-course transcript profiles in the roots of a true mangrove species, Ceriops tagal, as revealed by a series of microarray experiments. The expression of a total of 432 transcripts changed significantly in the roots of C. tagal under salt shock, of which 83 had a more than 2-fold change and were further assembled into 59 unigenes. Global transcription was stable at the early stage of salt stress and then was gradually dysregulated with the increased duration of the stress. Importantly, a pair-wise comparison of predicted homologous gene pairs revealed that the transcriptional regulations of most of the differentially expressed genes were highly divergent in C. tagal from that in salt-sensitive species, Arabidopsis thaliana. Conclusions/Significance This work suggests that transcriptional homeostasis and specific transcriptional regulation are major events in the roots of C. tagal when subjected to salt shock, which could contribute to the establishment of adaptation to saline environments and, thus, facilitate the salt-tolerant lifestyle of this mangrove species. Furthermore, the candidate genes underlying the adaptation were identified through comparative analyses. This study provides a foundation for dissecting the genetic basis of the adaptation of mangroves to intertidal environments.

Extensive Hybridization and Introgression between Melastoma candidum and M. sanguineum

Natural hybridization can lead to various evolutionary outcomes in plants, including hybrid speciation and interspecific gene transfer. It can also cause taxonomic problems, especially in plant genera containing multiple species. In this study, the hybrid status of Melastoma affine, the most widespread taxon in this genus, and introgression between its putative parental species, M. candidum and M. sanguineum, were assessed on two sites, Hainan and Guangdong, using 13 SSR markers and sequences of a chloroplast intergenic spacer. Bayesian-based STRUCTURE analysis detected two most likely distinct clusters for the three taxa, and 76.0% and 73.9% of the morphologically identified individuals of M. candidum and M. sanguineum were correctly assigned, respectively. 74.5% of the M. affine individuals had a membership coefficient to either parental species between 0.1 and 0.9, suggesting admixture between M. candidum and M. sanguineum. Furthermore, NewHybrids analysis suggested that most individuals of M. affine were F2 hybrids or backcross hybrids to M. candidum, and that there was extensive introgression between M. candidum and M. sanguineum. These SSR data thus provides convincing evidence for hybrid origin of M. affine and extensive introgression between M. candidum and M. sanguineum. Chloroplast DNA results were consistent with this conclusion. Much higher hybrid frequency on the more disturbed Guangdong site suggests that human disturbance might offer suitable habitats for the survival of hybrids, a hypothesis that is in need of further testing.