What is the difference between marine and limnetic‐terrestrial associations of nematodes with invertebrates?

Tchesunov, Alexei V.; Ivanenko, Viatcheslav N.

doi:10.1111/1749-4877.12595

Cited by 9 publications

(4 citation statements)

References 61 publications

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“…Raw reads of nematodes from the family Monhysteridae were included as an outgroup and to assist in identifying possible contaminant sources. Species from the Monhysteridae family frequently occur as endoparasites or in association with numerous crustacean species ( Baylis 1915 ; Chitwood 1935 ; Tchesunov and Ivanenko 2022 ; Westerman et al 2022 ) and were thus deemed useful as a mechanism to filter out potential nonarthropod contaminant sequences during downstream analyses. Full details on the species and their tissues included, accession identifiers, and corresponding raw read and transcriptome metadata can be found in Supplementary File 1 .…”

Section: Methodsmentioning

confidence: 99%

CrusTome: a transcriptome database resource for large-scale analyses across Crustacea

Pérez‐Moreno

Kozma

DeLeo

et al. 2023

G3: Genes, Genomes, Genetics

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Transcriptomes from nontraditional model organisms often harbor a wealth of unexplored data. Examining these data sets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption, access to genomic and transcriptomic resources for nontraditional model organisms remains limited. Crustaceans, for example, being among the most numerous, diverse, and widely distributed taxa on the planet, often serve as excellent systems to address ecological, evolutionary, and organismal questions. While they are ubiquitously present across environments, and of economic and food security importance, they remain severely underrepresented in publicly available sequence databases. Here, we present CrusTome, a multispecies, multitissue, transcriptome database of 201 assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoans for phylogenetic context) as an evolving and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ genomic/transcriptomic techniques and data sets. CrusTome is presented in BLAST and DIAMOND formats, providing robust data sets for sequence similarity searches, orthology assignments, phylogenetic inference, etc. and thus allowing for straightforward incorporation into existing custom pipelines for high-throughput analyses. In addition, to illustrate the use and potential of CrusTome, we conducted phylogenetic analyses elucidating the identity and evolution of the cryptochrome/photolyase family of proteins across crustaceans.

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Section: Methodsmentioning

confidence: 99%

CrusTome: a transcriptome database resource for large-scale analyses across Crustacea

Pérez‐Moreno

Kozma

DeLeo

et al. 2023

G3: Genes, Genomes, Genetics

View full text Add to dashboard Cite

show abstract

“…Sequencing reads of nematodes from the family Monhysteridae were also included as species from this family are frequently found as parasites or in association with numerous crustacean species (Baylis 1915; Chitwood 1935; Westerman et al . 2022; Tchesunov and Ivanenko), and were thus deemed useful as a mechanism to filter out potential non-crustacean contaminant sequences during downstream analyses. Full details on the transcriptomes included, Accession Identifiers, and corresponding raw read and transcriptome metadata can be found in Supplementary File 2.…”

Section: Methodsmentioning

confidence: 99%

CrusTome: A transcriptome database resource for large-scale analyses across Crustacea

Pérez‐Moreno

Kozma

DeLeo

et al. 2022

Preprint

View full text Add to dashboard Cite

Transcriptomes from non-traditional model organisms often harbor a wealth of unexplored data. Examining these datasets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption, access to genomic and transcriptomic resources for non-traditional model organisms remains limited. Crustaceans, for example, being amongst the most numerous, diverse, and widely distributed taxa on the planet, often serve as excellent systems to address ecological, evolutionary, and organismal questions. While they are ubiquitously present across environments, and of economic and food security importance, they remain severely underrepresented in publicly available sequence databases. Here, we present CrusTome, a multi-species, multi-tissue, transcriptome database of 201 assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoan outgroups) as an evolving, and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ genomic/transcriptomic techniques and datasets. CrusTome is presented in BLAST and DIAMOND formats, providing robust datasets for sequence similarity searches, orthology assignments, phylogenetic inference, etc., and thus allowing for straight-forward incorporation into existing custom pipelines for high-throughput analyses. In addition, to illustrate the use and potential of CrusTome, we conducted phylogenetic analyses elucidating the identity and evolution of the Cryptochrome Photolyase Family of proteins across crustaceans.

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“…Among these, the most well-known examples are in vertebrates (reptiles, birds and mammals) and of course arthropods, invertebrates with jointed legs and exoskeletons such as spiders and insects. Additionally, soft-bodied groups with generally poor fossil records [ 14 , 15 ], such as molluscs (including the land snails and slugs [ 16 ]), onychophorans (velvet worms [ 17 ]), annelids (including earthworms [ 18 ]), nematoids (roundworms and horsehair worms, including many parasitic groups that have followed their hosts on land [ 18 , 19 , 20 , 21 ]), tardigrades (water bears [ 22 ]), and platyhelminthes (flatworms [ 23 ]) contain land-living lineages, but these are mostly dependent on moisture-rich terrestrial environments for survival. Life on land requires a series of adaptations that may be paralleled across different groups—we can refer to this as terrestrialization: the process by which aquatic organisms adapt to terrestrial life.…”

Section: Introductionmentioning

confidence: 99%

Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization

Tihelka

Howard

Cai

et al. 2022

Biology

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Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian–Devonian, the fossil record attests to arthropods becoming the first animals to colonize land, However, a growing body of molecular dating and palaeontological evidence suggests that the three major terrestrial arthropod groups (myriapods, hexapods, and arachnids), as well as vascular plants, may have invaded land as early as the Cambrian–Ordovician. These dates precede the oldest fossil evidence of those groups and suggest an unrecorded continental “Cambrian explosion” a hundred million years prior to the formation of early complex terrestrial ecosystems in the Silurian–Devonian. We review the palaeontological, phylogenomic, and molecular clock evidence pertaining to the proposed Cambrian terrestrialization of the arthropods. We argue that despite the challenges posed by incomplete preservation and the scarcity of early Palaeozoic terrestrial deposits, the discrepancy between molecular clock estimates and the fossil record is narrower than is often claimed. We discuss strategies for closing the gap between molecular clock estimates and fossil data in the evolution of early ecosystems on land

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What is the difference between marine and limnetic‐terrestrial associations of nematodes with invertebrates?

Cited by 9 publications

References 61 publications

CrusTome: a transcriptome database resource for large-scale analyses across Crustacea

CrusTome: a transcriptome database resource for large-scale analyses across Crustacea

CrusTome: A transcriptome database resource for large-scale analyses across Crustacea

Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization

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