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A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea ArchiMer
Berthelier, Jeremy; Casse, Nathalie; Daccord, Nicolas; Jamilloux, Veronique; Saint-jean, Bruno; Carrier, Gregory.
Background Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution. Results To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: https://doi.org/10.17882/51795), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its...
Tipo: Text Palavras-chave: Transposable elements; Genome assembly; Pipeline; Tool; Annotation; Algae; Haptophyte; Tisochrysis lutea.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00441/55250/56732.pdf
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Analysis of genome-wide differentiation between native and introduced populations of the cupped oysters Crassostrea gigas and Crassostrea angulata ArchiMer
Gagnaire, Pierre-alexandre; Lamy, Jean-baptiste; Cornette, Florence; Heurtebise, Serge; Degremont, Lionel; Flahauw, Emilie; Boudry, Pierre; Bierne, Nicolas; Lapegue, Sylvie.
The Pacific cupped oyster is genetically subdivided into two sister taxa, Crassostrea gigas and C. angulata, which are in contact in the north-western Pacific. The nature and origin of their genetic and taxonomic differentiation remains controversial due the lack of known reproductive barriers and the high degree of morphologic similarity. In particular, whether the presence of ecological and/or intrinsic isolating mechanisms contributes to species divergence is unknown. The recent co-introduction of both taxa into Europe offers a unique opportunity to test how genetic differentiation is maintained under new environmental and demographic conditions. We generated a pseudo-chromosome assembly of the Pacific oyster genome using a combination of BAC-end...
Tipo: Text Palavras-chave: Cupped oysters; Genome assembly; Species divergence; Reproductive barriers; Recombination rate.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00455/56622/58337.pdf
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