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

Patrik Cangren; Yann J K Bertrand; John M Braverman; Gregor Duncan Gilfillan; Matthew B Hamilton; Bengt Oxelman

doi:10.1016/j.dib.2024.111094

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

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

Authors

Patrik Cangren¹, Yann J K Bertrand², John M Braverman³, Gregor Duncan Gilfillan⁴, Matthew B Hamilton⁵, Bengt Oxelman¹

Affiliations

¹ Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 7B, Goteborg 413 90, Sweden.
² Laboratory of Molecular Biology and Bioinformatics. Institute of Botany, Academy of Sciences of the Czech Republic, CZ-252 43 Průhonice, Czech Republic.
³ Department of Biology, The Science Center, Saint Josephs University, 5600 City Ave. Philadelphia, PA 19131, USA.
⁴ Department of Medical Genetics, Oslo University Hospital and University of Oslo, Kirkeveien 166, 0450 Oslo, Norway.
⁵ Department of Biology, Georgetown University, 37th and O Streets NW Washington, DC 20057, USA.

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.