Sets of 142 probes for Sileneae. (Original and improved)

Description

Two sets of probes for Sileneae with 142 markers. -Original set of 142 probes based on Sanger, Genbank and transcriptomes. Transcriptome based probes with only exons. -Improved set of 142 probes updated with sequence data from Silene acaulis sequencing using Illumina Miseq to add intron and improve sequence matching.

Steps to reproduce

An initial set of 142 markers were created by collecting 106 allegedly single-copy genes from the transcriptomes published in "Cangren, Patrik (2024), “40 Transcriptomes from Sileneae”, Mendeley Data, V2, doi: 10.17632/vykf3g4z5g.2". To this set 36 sequences with both exon and introns were added, of which eight had previously been utilized for Sileneae phylogenetics, whereas the remaining 28 sequences were found on Genbank and determined as putatively single-copy from blasting the set of 40 Sileneae transcriptomes. This probe set were used to sequence 96 samples from five Silene species using Illumina Miseq. To improve the probe set we assembled new sequences from the sequenced data. For exon-only markers, new reference sequences containing both exons and introns were inferred from contigs assembled using CLC-assembler. Assembled contigs were BLAST searched against the probe set to retrieve homologues and matching contigs were aligned using MAFFT. All alignments were inspected manually before merging contigs into final consensus sequences. If all exons could not be connected by introns the longest continuous sequence were selected and unconnected exons were removed. Through this process the exon only markers were complemented with introns to create full length sequences. To further improve and extend the probes an iterative mapping approach was utilized using the software CLC Mapper. The consensus sequences generated by mapping reads against the probe references were used as references for the next round of mapping until the number of mapped reads stabilized. The sequences produced were used to create an improved set of 142 markers based on complete nuclear sequences. This set was used to sequence additional species in Silene to test the performance of the markers.

Institutions

• University of Gothenburg

  Västra Götaland, Gothenburg

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