GeneMiner: a tool for extracting phylogenetic markers from next-generation sequencing data

Abstract

The advancement of Next-generation Sequencing (NGS) technologies has led to a revolution in the field of evolutionary biology. With the increasing number of available genomes and transcriptomes, researchers can mine various types of molecular markers that are vital for phylogenetic, evolutionary, and ecological studies. Numerous tools have been developed to extract these molecular markers from NGS data. However, due to a limited number of well-annotated reference genomes for non-model organisms, it is still challenging to obtain these markers accurately and efficiently. Here, we present GeneMiner, an improved and expanded version of our previous tool, Easy353. GeneMiner involves the reference-guided de Bruijn Graph assembly with seed self-discovery and greedy extension. Additionally, it includes a verification step using a parameter-bootstrap method to reduce the negative impact on assembly caused by the relatively distant reference. Our results using both experimental and simulation data showed GeneMiner can accurately acquire phylogenetic molecular markers for plants using transcriptomic, genomic, and other NGS data. GeneMiner is designed to be user-friendly, fast, and memory-efficient, and is compatible with Linux, Windows, and macOS. All source codes are publicly available on GitHub for easy accessibility and transparency (https://github.com/happywithxpl/GeneMiner).

Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets

“…Assessing the performance of tools designed for capturing Angiosperms353 genes is crucial to ensure the effectiveness and practical application of Angiosperms353 data. Notable tools for Angiosperms353 capture include MarkerMiner (Chamala et al 2015), HybPiper (Johnson et al 2016), Phyluce (Faircloth 2016), HybPhaser (Nauheimer et al 2021), Easy353 (Zhang et al 2022), PhyloHerb (Cai et al 2022), and GeneMiner (Xie et al 2023). Phyluce is a software package originally developed for analyzing data from ultraconserved elements in organismal genomes.…”

“…A companion pipeline, putative paralog detection (PPD; Zhou et al 2022), is an extension to the HybPiper pipeline, and identifies putative paralogs based on sequence similarity and the presence of heterozygous sites at each locus (Zhou et al 2022). Furthermore, Easy353 efficiently retrieves Angiosperms353 genes, and an enhanced version called GeneMiner has recently been developed (Xie et al 2023). GeneMiner is flexible with input formats and accommodating options such as the GenBank file format and Fasta format.…”