40 Transcriptomes from Sileneae

Published: 25 June 2024| Version 2 | DOI: 10.17632/vykf3g4z5g.2
Patrik Cangren


A set of 40 transcriptomes from 34 different species of the flowering plant genus Silene (Caryophyllaceae) and the related genera Agrostemma, Atocion, Eudianthe, Heliosperma, Petrocoptis and Viscaria. The files included in this data set contains contigs assembled using Trinity together with information on annotation against the UniProt/SwissProt database.


Steps to reproduce

Samples were grown from seeds in the botanical gardens in Gothenburg or Copenhagen, or collected in the wild and preserved with RNAlater (ThermoFisher). Sequencing libraries were constructed from RNA extracted from all major parts of the plants and sequenced using Illumina HiSeq platform. Adapter removal and quality filtering of raw reads were performed using Trimmomatic. Filtered reads were assembled with Trinity v.2.9.1 using default settings. Assembled contigs were searched against the UniProt/Swiss-Prot using BLASTx v. 2.2.31+. Annotated contigs were filtered to exclude hits for accessions with taxa outside of Angiosperms. Information on assigned GO-terms for each filtered hit were downloaded from UniProt/Swiss-Prot.


Goteborgs universitet Institutionen for Biologi och Miljovetenskap


Genomics, Nucleotide, RNA, Transcriptome, Phylogenetics