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. 2024 Nov 1:57:111094.
doi: 10.1016/j.dib.2024.111094. eCollection 2024 Dec.

A dataset of 40 assembled and annotated transcriptomes from 34 species in Silene and related genera

Patrik Cangren  1 , Yann J K Bertrand  2 , John M Braverman  3 , Gregor Duncan Gilfillan  4 , Matthew B Hamilton  5 , Bengt Oxelman  1
Affiliations

A dataset of 40 assembled and annotated transcriptomes from 34 species in Silene and related genera

Patrik Cangren et al. Data Brief. .

Abstract

A dataset of 40 assembled and annotated transcriptomes from 34 different species sampled from phylogenetically diverse parts of the flowering plant genus Silene (Caryophyllaceae) and the related genera Agrostemma, Atocion, Eudianthe, Heliosperma, Petrocoptis and Viscaria. RNA extracted from roots, stems, leaves, buds and flowers were sequenced using paired end reads on the Illumina Hiseq platform. A total of 716 million raw reads were produced and assembled into 2.67 million isogroups ("genes"). Contigs from all samples were annotated using UniProt/SwissProt and assigned with GO-terms. A total of 974274 annotations were made (per sample average 24357, stdev 7034), giving an annotation proportion of 37% (per sample average 39%, stdev 9.75%). 741087 of the annotations had taxonomic identities within Magnoliopsida (per sample average 18527, stdev 3931), resulting in assignment of 4519488 GO-terms (per sample average 112987, stdev 22536). The data set can be further utilized for biological research and phylogenetic studies, evolutionary questions, functional analyses of genes, polyploidy as well as for marker development.

Keywords: Assembly; Functional-annotation; Genomics; Nucleotide; Phylogenetics; RNA-transcripts; Sileneae.

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References

    1. Jafari F., Zarre S., Gholipour A., Eggens F., Rabeler R.K., Oxelman B. A new taxonomic backbone for the infrageneric classification of the species-rich genus Silene (Caryophyllaceae) Taxon. 2020;69(2):337–368. doi: 10.1002/tax.12230. - DOI
    1. Wang G., Wang G., Zhang X., Wang F., Song R. Isolation of high quality RNA from cereal seeds containing high levels of starch. Phytochem. Anal. 2012;23:159–163. doi: 10.1002/pca.1337. - DOI - PubMed
    1. Bolger A.M., Lohse1 M., Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. -0815. - DOI - PMC - PubMed
    1. Haas B.J., Papanicolaou A., Yassour M., Grabherr M., Blood P.D., Bowden J., Couger M.B., Eccles D., Li B., Lieber M., MacManes M.D., Ott M., Orvis J., Pochet N., Strozzi F., Weeks N., Westerman R., William T., Dewey C.N., Henschel R., LeDuc R.D., Friedman N., Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols. 2013;8:1494–1512. doi: 10.1038/nprot.2013.084. 8. - DOI - PMC - PubMed
    1. Boutet E., Lieberherr D., Tognolli M., Schneider M., Bansal P., Bridge A.J., Poux S., Bougueleret L., Xenarios I. UniProtKB/Swiss-Prot, the manually annotated section of the uniprot knowledgebase: how to use the entry view. Methods Mol. Biol. 2016;1374:23–54. doi: 10.1007/978-1-4939-3167-5_2. - DOI - PubMed

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