VEHoP: A Versatile, Easy-to-use, and Homology-based Phylogenomic pipeline accommodating diverse sequences DOI Creative Commons
Yunlong Li,

Liu Xu,

Chong Chen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 24, 2024

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

Language: Английский

Integrative taxonomy of two new peltospirid gastropods from Mid-Atlantic Ridge hot vents, including a potentially symbiotic species DOI Creative Commons
Chong Chen, Florence Pradillon, Coral Diaz‐Recio Lorenzo

et al.

Zoological Journal of the Linnean Society, Journal Year: 2025, Volume and Issue: 204(2)

Published: June 1, 2025

ABSTRACT Deep-sea hydrothermal vents host lush communities of animals relying on bacterial chemosynthetic primary production, where intimate symbioses often form. Peltospiridae are a family gastropods endemic to hot vents, whose members exhibit variety feeding strategies ranging from grazing total reliance endosymbiosis. Here, we report and describe two new peltospirid snails, Peltospira gargantua sp. nov. Lirapex pantagruel nov., recently discovered vent fields the Mid-Atlantic Ridge. is clearly distinct other congeners by its much larger size, differences in number arrangement epipodial tentacles, notably, hypertrophied oesophageal gland. also largest known species genus, differing shell shape sculpture. Phylogenetic reconstructions using mitochondrial cytochrome c oxidase subunit I (COI) gene agree with their respective generic placements. An expanded gland peltospirids was only endosymbiotic genera Chrysomallon Gigantopelta, it used symbionts, indicating that P. probably endosymbiotic. This would represent another case likely convergently acquired endosymbiosis family, first record gastropod Ridge vents.

Language: Английский

Citations

0
VEHoP: A Versatile, Easy-to-use, and Homology-based Phylogenomic pipeline accommodating diverse sequences DOI Creative Commons
Yunlong Li,

Liu Xu,

Chong Chen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 24, 2024

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

Language: Английский

Citations

2