VEHoP: A Versatile, Easy-to-use, and Homology-based Phylogenomic pipeline accommodating diverse sequences

Abstract

Phylogenomics has become a prominent method in systematics, conservation biology, and biomedicine, as it can leverage hundreds to thousands of genes derived from genomic or transcriptomic data to infer evolutionary relationships. However, obtaining high-quality genomes and transcriptomes requires samples preserved with high-quality DNA and RNA and demands considerable sequencing costs and lofty bioinformatic efforts (e.g., genome/transcriptome assembly and annotation). Notably, only fragmented DNA reads are accessible in some rare species due to the difficulty in sample collection and preservation, such as those inhabiting the deep sea. To address this issue, we here introduce the VEHoP (Versatile, Easy-to-use Homology-based Phylogenomic) pipeline, designed to infer protein-coding regions from DNA assemblies and generate alignments of orthologous sequences, concatenated matrices, and phylogenetic trees. This pipeline aims to 1) expand taxonomic sampling by accommodating a wide range of input files, including draft genomes, transcriptomes, and well-annotated genomes, and 2) simplify the process of conducting phylogenomic analyses and thus make it more accessible to researchers from diverse backgrounds. We first evaluated the performance of VEHoP using datasets of Ostreida, yielding robust phylogenetic trees with strong bootstrap support. We then applied VEHoP to reconstruct the phylogenetic relationship in the enigmatic deep-sea gastropod order Neomphalida, obtaining a robust phylogenetic backbone for this group. The VEHoP is freely available on GitHub (https://github.com/ylify/VEHoP), whose dependencies can be easily installed using Bioconda.