Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra

Josué Barrera-Redondo; Jaruwatana Sodai Lotharukpong; Hajk-Georg Drost; Susana M. Coelho

doi:10.1186/s13059-023-02895-z

Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra

Josué Barrera-Redondo (Lead / Corresponding author), Jaruwatana Sodai Lotharukpong, Hajk-Georg Drost (Lead / Corresponding author), Susana M. Coelho (Lead / Corresponding author)

Computational Biology

Research output: Contribution to journal › Article › peer-review

11 Citations (Scopus)

15 Downloads (Pure)

Abstract

We present GenEra (https://github.com/josuebarrera/GenEra), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.

Original language	English
Article number	54
Number of pages	21
Journal	Genome Biology
Volume	24
DOIs	https://doi.org/10.1186/s13059-023-02895-z
Publication status	Published - 24 Mar 2023

Keywords

Evolutionary novelty
Gene age
Gene emergence
Genomic phylostratigraphy
Homology detection failure
Multicellularity
Taxonomically restricted genes
Terrestrialization
Tree of life

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

Access to Document

10.1186/s13059-023-02895-zLicence: CC BY

Final published versionFinal published version, 2.85 MBLicence: CC BY

Cite this

@article{47c13433de1348d5842f2d95bfa332cf,

title = "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra",

abstract = "We present GenEra (https://github.com/josuebarrera/GenEra), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.",

keywords = "Evolutionary novelty, Gene age, Gene emergence, Genomic phylostratigraphy, Homology detection failure, Multicellularity, Taxonomically restricted genes, Terrestrialization, Tree of life",

author = "Josu{\'e} Barrera-Redondo and Lotharukpong, {Jaruwatana Sodai} and Hajk-Georg Drost and Coelho, {Susana M.}",

note = "Publisher Copyright: {\textcopyright} 2023, The Author(s).",

year = "2023",

month = mar,

day = "24",

doi = "10.1186/s13059-023-02895-z",

language = "English",

volume = "24",

journal = "Genome Biology",

issn = "1474-7596",

publisher = "BioMed Central Ltd.",

}

Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. / Barrera-Redondo, Josué (Lead / Corresponding author); Lotharukpong, Jaruwatana Sodai; Drost, Hajk-Georg (Lead / Corresponding author) et al.
In: Genome Biology, Vol. 24, 54, 24.03.2023.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra

AU - Barrera-Redondo, Josué

AU - Lotharukpong, Jaruwatana Sodai

AU - Drost, Hajk-Georg

AU - Coelho, Susana M.

PY - 2023/3/24

Y1 - 2023/3/24

N2 - We present GenEra (https://github.com/josuebarrera/GenEra), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.

AB - We present GenEra (https://github.com/josuebarrera/GenEra), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.

KW - Evolutionary novelty

KW - Gene age

KW - Gene emergence

KW - Genomic phylostratigraphy

KW - Homology detection failure

KW - Multicellularity

KW - Taxonomically restricted genes

KW - Terrestrialization

KW - Tree of life

UR - http://www.scopus.com/inward/record.url?scp=85150995128&partnerID=8YFLogxK

U2 - 10.1186/s13059-023-02895-z

DO - 10.1186/s13059-023-02895-z

M3 - Article

C2 - 36964572

AN - SCOPUS:85150995128

SN - 1474-7596

VL - 24

JO - Genome Biology

JF - Genome Biology

M1 - 54

ER -

Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this