MATEdb, a data repository of high-quality metazoan transcriptome assemblies to accelerate phylogenomic studies

Fernández, Rosa; Tonzo, Vanina; Guerrero, Carolina Simon; Lozano‐Fernandez, Jesus; Martinez-Redondo, Gemma I; Balart‐García, Pau; Aristide, Leandro; Eleftheriadi, Klara; Vargas-Chávez, Carlos

doi:10.24072/pcjournal.177

Cited by 13 publications

(18 citation statements)

References 27 publications

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“…To obtain the phylogenetic relatedness information required for the phylogenetic comparative methods, we combined the time‐scaled ultrametric species trees for each phylum. Vertebrate and onychophoran time trees were obtained from the literature (Baker et al, 2021; Irisarri et al, 2017) and pruned to keep only a selection of 13 vertebrate species whose aquaporins have previously been studied (Finn et al, 2014) and the four onychophorans (or closely‐related species) that were included in MATEdb (Fernández et al, 2022), respectively. For the rest of the phyla, arthropods, molluscs and annelids, time‐scaled ultrametric trees were inferred independently by using a node‐dating approach on species trees that followed the most recent topologies (Anderson & Lindgren, 2021; Ballesteros et al, 2022; Colgan et al, 2007; Cunha & Giribet, 2019; Doğan et al, 2020; Erséus et al, 2020; Fernández et al, 2018; González et al, 2015; Johnson et al, 2018; Kallal et al, 2021; Kawahara et al, 2019; Kocot et al, 2011, 2013, 2020, 2017, 2019; Lee et al, 2019; Lindgren, 2010; Lozano‐Fernandez et al, 2019; McKenna et al, 2019; Misof et al, 2014; Moles & Giribet, 2021; Ontano et al, 2021; Pabst & Kocot, 2018; Peters et al, 2017; Razkin et al, 2015; Richter, 2001; Salvi & Mariottini, 2016; Schwentner et al, 2018; Smith, 2021; Smith et al, 2011; Sun et al, 2020; Uribe et al, 2016; Uribe & Zardoya, 2017; Wang et al, 2017; Wiegmann et al, 2011; Yang et al, 2018).…”

Section: Methodsmentioning

confidence: 99%

Parallel duplication and loss of aquaporin‐coding genes during the “out of the sea” transition as potential key drivers of animal terrestrialization

et al. 2023

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One of the most important physiological challenges animals had to overcome during terrestrialization (i.e., the transition from sea to land) was water loss, which alters their osmotic and hydric homeostasis. Aquaporins are a superfamily of membrane water transporters heavily involved in osmoregulatory processes. Their diversity and evolutionary dynamics in most animal lineages remain unknown, hampering our understanding of their role in marine–terrestrial transitions. Here, we interrogated aquaporin gene repertoire evolution across the main terrestrial animal lineages. We annotated aquaporin‐coding genes in genomic data from 458 species from seven animal phyla where terrestrialization episodes occurred. We then explored aquaporin gene evolutionary dynamics to assess differences between terrestrial and aquatic species through phylogenomics and phylogenetic comparative methods. Our results revealed parallel aquaporin‐coding gene duplications during the ecological transition from marine to nonmarine environments (e.g., brackish, freshwater and terrestrial), rather than from aquatic to terrestrial ones, with some notable duplications in ancient lineages. In contrast, we also recovered a significantly lower number of superaquaporin genes in terrestrial arthropods, suggesting that more efficient oxygen homeostasis in land arthropods might be linked to a reduction in this type of aquaporin. Our results thus indicate that aquaporin‐coding gene duplication and loss might have been one of the key steps towards the evolution of osmoregulation across animals, facilitating the “out of the sea” transition and ultimately the colonization of land.

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Section: Methodsmentioning

confidence: 99%

Parallel duplication and loss of aquaporin‐coding genes during the “out of the sea” transition as potential key drivers of animal terrestrialization

et al. 2023

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“…Data from the remaining 415 invertebrate species were obtained from MATEdb (Fernández et al, 2022), which provides standard comparable proteomes for phylogenomic studies. We downloaded the gene annotation of those species (longest isoform for each gene), and their taxonomic and habitat information.…”

Section: Methodsmentioning

confidence: 99%

“…Vertebrate and onychophoran time trees were obtained from the literature (Baker, Buckman-Young, Costa, & Giribet, 2021; Irisarri et al, 2017) and pruned to keep only a selection of 13 vertebrate species whose aquaporins have previously been studied (Finn et al, 2014) and the 4 onychophorans (or closely-related species) that were included in MATEdb (Fernández et al, 2022), respectively.…”

Section: Methodsmentioning

confidence: 99%

Parallel duplication and loss of aquaporin-coding genes during the ‘out of the sea’ transition as potential key drivers of animal terrestrialization

Martinez-Redondo

Guerrero

Aristide

et al. 2022

Preprint

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One of the most important physiological challenges animals had to overcome during terrestrialization (i.e., the transition from sea to land) is water loss, which alters their osmotic and hydric homeostasis. Aquaporins are a superfamily of membrane water transporters heavily involved in osmoregulatory processes. Their diversity and evolutionary dynamics in most animal lineages remain unknown, hampering our understanding of their role in marine-terrestrial transitions. Here, we interrogated aquaporin gene repertoire evolution across the main terrestrial animal lineages. We annotated aquaporin-coding genes in genomic data from 458 species from 7 animal phyla where terrestrialization episodes occurred. We then explored aquaporin gene evolutionary dynamics to assess differences between terrestrial and aquatic species through phylogenomics and phylogenetic comparative methods. Our results revealed parallel aquaporin-coding gene duplications in aquaporins transporting water, glycerol and ammonia in the transition from marine to non-marine environments (e.g., brackish, freshwater and terrestrial), rather than from aquatic to terrestrial ones, with some notable duplications in ancient lineages. Contrarily, we also recovered a significantly lower number of oxygen peroxide-transporting aquaporin-coding genes in terrestrial arthropods, suggesting that more efficient oxygen homeostasis in land arthropods might be linked to a reduction in this type of aquaporins. Our results thus indicate that aquaporin-coding gene duplication and loss might have been one of the key steps towards the evolution of osmoregulation across animals, facilitating the "out of the sea" transition and ultimately the colonisation of land.

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“…We followed the raw data processing pipeline explained in (Fernández et al 2022) with a few modifications. For RNA-seq data, adapters and low-quality reads were trimmed using fastp v.0.20.041, and de novo assembly was performed using Trinity v2.1142 with default parameters.…”

Section: Methodsmentioning

confidence: 99%

Highly dynamic evolution of the chemosensory system driven by gene gain and loss across subterranean beetles

Balart‐García

Bradford

Beasley‐Hall

et al. 2022

Preprint

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Chemical cues in subterranean habitats differ highly from those on the surface due to the contrasting environmental conditions, such as absolute darkness, high humidity or food scarcity. Subterranean animals underwent changes to their sensory systems to facilitate the perception of essential stimuli for underground lifestyles. Despite representing unique systems to understand biological adaptation, the genomic basis of chemosensation across cave-dwelling species remains unexplored from a macroevolutionary perspective. Here, we explore the evolution of chemoreception in three beetle tribes that underwent at least six independent transitions to the underground through a phylogenomics spyglass. Our findings suggest that the chemosensory gene repertoire varies dramatically between species. Overall, no parallel changes in the net rate of evolution of chemosensory gene families were detected prior, during, or after the habitat shift among subterranean lineages. Contrarily, we found evidence of lineage-specific changes within surface and subterranean lineages. Our results reveal key duplications and losses shared between some of the lineages transitioning to the underground, including the loss of sugar receptors and gene duplications of the highly conserved ionotropic receptors IR25a and IR8a, involved in thermal and humidity sensing among other olfactory roles in insects. These duplications were detected both in independent subterranean lineages and their surface relatives, suggesting parallel evolution of these genes across lineages giving rise to cave-dwelling species. Overall, our results shed light on the genomic basis of chemoreception in subterranean beetles and contribute to deepen our understanding of the genomic underpinnings of adaptation to the subterranean lifestyle at a macroevolutionary scale.

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MATEdb, a data repository of high-quality metazoan transcriptome assemblies to accelerate phylogenomic studies

Abstract: Vargas-Chávez (2022) MATEdb, a data repository of high-quality metazoan transcriptome assemblies to accelerate phylogenomic studies,

Cited by 13 publications

References 27 publications

Parallel duplication and loss of aquaporin‐coding genes during the “out of the sea” transition as potential key drivers of animal terrestrialization

Parallel duplication and loss of aquaporin‐coding genes during the “out of the sea” transition as potential key drivers of animal terrestrialization

Parallel duplication and loss of aquaporin-coding genes during the ‘out of the sea’ transition as potential key drivers of animal terrestrialization

Highly dynamic evolution of the chemosensory system driven by gene gain and loss across subterranean beetles

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