Dataset Information

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae).

ABSTRACT: Spartina species have a critical ecological role in salt marshes and represent an excellent system to investigate recurrent polyploid speciation. Using the 454 GS-FLX pyrosequencer, we assembled and annotated the first reference transcriptome (from roots and leaves) for two related hexaploid Spartina species that hybridize in Western Europe, the East American invasive Spartina alterniflora and the Euro-African S. maritima. The de novo read assembly generated 38?478 consensus sequences and 99% found an annotation using Poaceae databases, representing a total of 16?753 non-redundant genes. Spartina expressed sequence tags were mapped onto the Sorghum bicolor genome, where they were distributed among the subtelomeric arms of the 10 S. bicolor chromosomes, with high gene density correlation. Normalization of the complementary DNA library improved the number of annotated genes. Ecologically relevant genes were identified among GO biological function categories in salt and heavy metal stress response, C4 photosynthesis and in lignin and cellulose metabolism. Expression of some of these genes had been found to be altered by hybridization and genome duplication in a previous microarray-based study in Spartina. As these species are hexaploid, up to three duplicated homoeologs may be expected per locus. When analyzing sequence polymorphism at four different loci in S. maritima and S. alterniflora, we found up to four haplotypes per locus, suggesting the presence of two expressed homoeologous sequences with one or two allelic variants each. This reference transcriptome will allow analysis of specific Spartina genes of ecological or evolutionary interest, estimation of homoeologous gene expression variation using RNA-seq and further gene expression evolution analyses in natural populations.

SUBMITTER: Ferreira de Carvalho J

PROVIDER: S-EPMC3554450 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature

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Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae).

Ferreira de Carvalho J J Poulain J J Da Silva C C Wincker P P Michon-Coudouel S S Dheilly A A Naquin D D Boutte J J Salmon A A Ainouche M M

Heredity 20121114 2

Spartina species have a critical ecological role in salt marshes and represent an excellent system to investigate recurrent polyploid speciation. Using the 454 GS-FLX pyrosequencer, we assembled and annotated the first reference transcriptome (from roots and leaves) for two related hexaploid Spartina species that hybridize in Western Europe, the East American invasive Spartina alterniflora and the Euro-African S. maritima. The de novo read assembly generated 38 478 consensus sequences and 99% fo ...[more]

PMID: 23149455

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Project description:Background and aimsEcosystem-based flood defence including salt-marsh as a key component is increasingly applied worldwide due to its multifunctionality and cost-effectiveness. While numerous experiments have explored the wave-attenuation effects of salt-marsh plants critical to flood protection, little is known about the physiological and biochemical responses of these species to continuous wave exposure.MethodsTo address this knowledge gap, we developed a shallow-water wave simulator to expose individual Spartina alterniflora plants to waves in a greenhouse for 8 weeks. S. alterniflora individuals were partially submerged and experienced horizontal sinusoidal motion to mimic plant exposure to shallow water waves. A factorial experiment was used to test the effects of three wave heights (4.1 cm, 5.5 cm and a no-wave control) and two wave periods (2 s and 3 s) on the following key physiological and biochemical plant parameters: plant growth, antioxidant defence and photosynthetic capacity.Key resultsComparison of wave treatment and control groups supported our hypotheses that wave exposure leads to oxidative stress in plants and suppresses plant photosynthetic capacity and thereby growth. In response, the wave-exposed plants exhibited activated antioxidant enzymes. Comparison between the different wave treatment groups suggested the wave effects to be generally correlated positively with wave height and negatively with wave period, i.e. waves with greater height and frequency imposed more stress on plants. In addition, wave-exposed plants tended to allocate more biomass to their roots. Such allocation is favourable because it enhances root anchorage against the wave impact.ConclusionsSimulated wave exposure systems such as the one used here are an effective tool for studying the response of salt-marsh plants to long-term wave exposure, and so help inform ecosystem-based flood defence projects in terms of plant selection, suitable transplantation locations and timing, etc. Given the projected variability of the global wave environment due to climate change, understanding plant response to long-term wave exposure has important implications for salt-marsh conservation and its central role in natural flood defence.

Project description:Among invasive species, aquatic plants pose serious threats to local biodiversity and ecosystem functions. Spartina alterniflora Loisel. (Poaceae), native to the eastern United States, was introduced unintentionally into Japan (Aichi and Kumamoto Prefectures) at around 2010. This invasive species could easily and rapidly spread to estuarine areas of Japan via vigorous trade and transport, making the prediction of its future invasion necessary. Here, the distribution and structure of the genetic variation of S. alterniflora in Japan were examined using chloroplast DNA (cpDNA) and microsatellite genotyping analyses for clarifying its invasion route and process. According to the cpDNA analysis, S. alterniflora populations in Japan had a single haplotype (haplotype C4) that is the most dominant genotype around the Florida Peninsula, the region of its origin, and is also widely found in the introduced populations in the East Asia. Microsatellite analysis also showed a loss of genetic diversity in Japanese S. alterniflora populations (allelic richness (A R) = 1.20-1.39) compared with that in its native region (A R = 4.58-4.59), suggesting a founder effect on S. alterniflora that might have occurred after invasion of the species into Japan. The principal coordinate analysis and The STRUCTURE analysis indicated that no gene mixing among Japanese local populations (Aichi, northern and southern Kumamoto) was observed, indicating that Spartina invasion occurred independently into these regions. Among the three regions, trading between the ports of northern Kumamoto and the U.S. was obviously lower than trading with China. We concluded that invasive S. alterniflora might have independently invaded Japan at different times through an East Asia route, particularly via China (i.e., secondary introduction). Therefore, it is important to strengthen the quarantine control on the importation of commodities, especially of transport vehicles at potential donor spots (i.e., border control/border biosecurity system), and to share information networks on invasive species between each region/port for minimizing further risks of biological species such as Spartina.

Dataset Information

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae).

Publications

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae).

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