Dataset Information

Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae).

ABSTRACT: In this study, we report the assembly and annotation of five reference transcriptomes for the European hexaploid Spartina species (S. maritima, S. alterniflora and their homoploid hybrids S. x townsendii and S. x neyrautii) and the allododecaploid invasive species S. anglica These transcriptomes were constructed from various leaf and root cDNA libraries that were sequenced using both Roche-454 and Illumina technologies. Considering the high ploidy levels of the Spartina genomes under study, and considering the absence of diploid reference genome and the need of an appropriate analytical strategy, we developed generic bioinformatics tools to (1) detect different haplotypes of each gene within each species and (2) assign a parental origin to haplotypes detected in the hexaploid hybrids and the neo-allopolyploid. The approach described here allows the detection of putative homeologs from sets of short reads. Synonymous substitution rate (KS) comparisons between haplotypes from the hexaploid species revealed the presence of one KS peak (likely resulting from the tetraploid duplication event). The procedure developed in this study can be applied for future differential gene expression or genomics experiments to study the fate of duplicated genes in the invasive allododecaploid S. anglica.

SUBMITTER: Boutte J

PROVIDER: S-EPMC5633685 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae).

Boutte Julien J Ferreira de Carvalho Julie J Rousseau-Gueutin Mathieu M Poulain Julie J Da Silva Corinne C Wincker Patrick P Ainouche Malika M Salmon Armel A

Genome biology and evolution 20161005 9

In this study, we report the assembly and annotation of five reference transcriptomes for the European hexaploid Spartina species (S. maritima, S. alterniflora and their homoploid hybrids S. x townsendii and S. x neyrautii) and the allododecaploid invasive species S. anglica These transcriptomes were constructed from various leaf and root cDNA libraries that were sequenced using both Roche-454 and Illumina technologies. Considering the high ploidy levels of the Spartina genomes under study, and ...[more]

PMID: 27614235

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Project description:Gene expression dynamics is a key component of polyploid evolution, varying in nature, intensity, and temporal scales, most particularly in allopolyploids, where two or more sub-genomes from differentiated parental species and different repeat contents are merged. Here, we investigated transcriptome evolution at different evolutionary time scales among tetraploid, hexaploid, and neododecaploid Spartina species (Poaceae, Chloridoideae) that successively diverged in the last 6-10 my, at the origin of differential phenotypic and ecological traits. Of particular interest are the recent (19th century) hybridizations between the two hexaploids Spartina alterniflora (2n = 6x = 62) and S. maritima (2n = 6x = 60) that resulted in two sterile F1 hybrids: Spartina × townsendii (2n = 6x = 62) in England and Spartina × neyrautii (2n = 6x = 62) in France. Whole genome duplication of S. × townsendii gave rise to the invasive neo-allododecaploid species Spartina anglica (2n = 12x = 124). New transcriptome assemblies and annotations for tetraploids and the enrichment of previously published reference transcriptomes for hexaploids and the allododecaploid allowed identifying 42,423 clusters of orthologs and distinguishing 21 transcribed transposable element (TE) lineages across the seven investigated Spartina species. In 4x and 6x mesopolyploids, gene and TE expression changes were consistent with phylogenetic relationships and divergence, revealing weak expression differences in the tetraploid sister species Spartina bakeri and Spartina versicolor (<2 my divergence time) compared to marked transcriptome divergence between the hexaploids S. alterniflora and S. maritima that diverged 2-4 mya. Differentially expressed genes were involved in glycolysis, post-transcriptional protein modifications, epidermis development, biosynthesis of carotenoids. Most detected TE lineages (except SINE elements) were found more expressed in hexaploids than in tetraploids, in line with their abundance in the corresponding genomes. Comparatively, an astonishing (52%) expression repatterning and deviation from parental additivity were observed following recent reticulate evolution (involving the F1 hybrids and the neo-allododecaploid S. anglica), with various patterns of biased homoeologous gene expression, including genes involved in epigenetic regulation. Downregulation of TEs was observed in both hybrids and accentuated in the neo-allopolyploid. Our results reinforce the view that allopolyploidy represents springboards to new regulatory patterns, offering to worldwide invasive species, such as S. anglica, the opportunity to colonize stressful and fluctuating environments on saltmarshes.

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

Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae).

Publications

Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae).

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