An updated and extended version of the Melastomataceae probe set for target capture

Abstract

PremiseA probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae.MethodsIn order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version.ResultsThe final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery.DiscussionThis updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant‐targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.

Systematics of the fleshy-fruited Sonerileae (Melastomataceae)

“…Raw reads of target capture and RNA-seq data were processed to remove adaptors, trim low-quality bases, trim polyG and polyX tails, and filter out very short reads with fastp (-g -x -r -l 30 -5 --cut_front_window_size 1 -3 _tail_window_size 1 --detect_adapter_for_pe) (Chen & al., 2018). HybPiper (Johnson & al., 2016) was used to recover targeted nuclear loci using the updated Melastomataceae probe set (Dagallier & Michelangeli, 2024) as reference file. Diamond (Buchfink & al., 2015), instead of BWA , was employed for read mapping to have better recovery.…”