The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution

Tue Sparholt Jørgensen, Bent Petersen, Haidi Cecilie Petersen, Patrick Denis Browne, Stefan Prost, Jonathon Stillman, Lars Hestbjerg Hansen, Benni Winding Hansen

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

Members of the crustacean subclass Copepoda are likely the most abundant metazoans worldwide. Pelagic marine species are critical in converting planktonic microalgae to animal biomass, supporting oceanic food webs. Despite their abundance and ecological importance, only five copepod genomes are publicly available, owing to a number of factors including large genome size, repetitiveness, GC-content,and small animal size. Here, we report the sixth representative copepod genome and the first genome and transcriptome from the calanoid copepod species Acartia tonsa Dana, which is among the most numerous mesozooplankton in boreal coastal and estuarine waters. The ecology, physiology and behavior of A. tonsa has been studied extensively. The genetic resources contributed in this work will allow researchers to link experimental results to molecular mechanisms. From PCRfree WGS and mRNA Illumina data, we assemble the largest copepod genome to date. We estimate A. tonsa has a total genome size of 2.5 Gb including repetitive elements we could not resolve. The non-repetitive fraction of the genome assembly is estimated to be 566Mb. Our DNA sequencing-based analyses suggest there is a 14-fold difference in genome size between the six members of Copepoda with available genomic information through NCBI. This finding complements nucleus staining genome size estimations, where 100-fold difference has been reported within 70 species. We briefly analyze the repeat structure in the existing copepod WGS datasets. The information presented here confirms the evolution of genome size in Copepoda and expands the scope for evolutionary inferences in Copepoda by providing several levels of genetic information from a key planktonic crustacean species.
OriginalsprogEngelsk
TidsskriftGenome Biology and Evolution
Vol/bind11
Udgave nummer5
Sider (fra-til)1440-1450
Antal sider11
DOI
StatusUdgivet - 2019

Citer dette

Jørgensen, Tue Sparholt ; Petersen, Bent ; Petersen, Haidi Cecilie ; Browne, Patrick Denis ; Prost, Stefan ; Stillman, Jonathon ; Hansen, Lars Hestbjerg ; Hansen, Benni Winding. / The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution. I: Genome Biology and Evolution. 2019 ; Bind 11, Nr. 5. s. 1440-1450.
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title = "The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution",
abstract = "Members of the crustacean subclass Copepoda are likely the most abundant metazoans worldwide. Pelagic marine species are critical in converting planktonic microalgae to animal biomass, supporting oceanic food webs. Despite their abundance and ecological importance, only five copepod genomes are publicly available, owing to a number of factors including large genome size, repetitiveness, GC-content,and small animal size. Here, we report the sixth representative copepod genome and the first genome and transcriptome from the calanoid copepod species Acartia tonsa Dana, which is among the most numerous mesozooplankton in boreal coastal and estuarine waters. The ecology, physiology and behavior of A. tonsa has been studied extensively. The genetic resources contributed in this work will allow researchers to link experimental results to molecular mechanisms. From PCRfree WGS and mRNA Illumina data, we assemble the largest copepod genome to date. We estimate A. tonsa has a total genome size of 2.5 Gb including repetitive elements we could not resolve. The non-repetitive fraction of the genome assembly is estimated to be 566Mb. Our DNA sequencing-based analyses suggest there is a 14-fold difference in genome size between the six members of Copepoda with available genomic information through NCBI. This finding complements nucleus staining genome size estimations, where 100-fold difference has been reported within 70 species. We briefly analyze the repeat structure in the existing copepod WGS datasets. The information presented here confirms the evolution of genome size in Copepoda and expands the scope for evolutionary inferences in Copepoda by providing several levels of genetic information from a key planktonic crustacean species.",
author = "J{\o}rgensen, {Tue Sparholt} and Bent Petersen and Petersen, {Haidi Cecilie} and Browne, {Patrick Denis} and Stefan Prost and Jonathon Stillman and Hansen, {Lars Hestbjerg} and Hansen, {Benni Winding}",
year = "2019",
doi = "10.1093/gbe/evz067",
language = "English",
volume = "11",
pages = "1440--1450",
journal = "Genome Biology and Evolution",
issn = "1759-6653",
publisher = "Oxford University Press",
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The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution. / Jørgensen, Tue Sparholt; Petersen, Bent; Petersen, Haidi Cecilie; Browne, Patrick Denis; Prost, Stefan; Stillman, Jonathon; Hansen, Lars Hestbjerg; Hansen, Benni Winding.

I: Genome Biology and Evolution, Bind 11, Nr. 5, 2019, s. 1440-1450.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution

AU - Jørgensen, Tue Sparholt

AU - Petersen, Bent

AU - Petersen, Haidi Cecilie

AU - Browne, Patrick Denis

AU - Prost, Stefan

AU - Stillman, Jonathon

AU - Hansen, Lars Hestbjerg

AU - Hansen, Benni Winding

PY - 2019

Y1 - 2019

N2 - Members of the crustacean subclass Copepoda are likely the most abundant metazoans worldwide. Pelagic marine species are critical in converting planktonic microalgae to animal biomass, supporting oceanic food webs. Despite their abundance and ecological importance, only five copepod genomes are publicly available, owing to a number of factors including large genome size, repetitiveness, GC-content,and small animal size. Here, we report the sixth representative copepod genome and the first genome and transcriptome from the calanoid copepod species Acartia tonsa Dana, which is among the most numerous mesozooplankton in boreal coastal and estuarine waters. The ecology, physiology and behavior of A. tonsa has been studied extensively. The genetic resources contributed in this work will allow researchers to link experimental results to molecular mechanisms. From PCRfree WGS and mRNA Illumina data, we assemble the largest copepod genome to date. We estimate A. tonsa has a total genome size of 2.5 Gb including repetitive elements we could not resolve. The non-repetitive fraction of the genome assembly is estimated to be 566Mb. Our DNA sequencing-based analyses suggest there is a 14-fold difference in genome size between the six members of Copepoda with available genomic information through NCBI. This finding complements nucleus staining genome size estimations, where 100-fold difference has been reported within 70 species. We briefly analyze the repeat structure in the existing copepod WGS datasets. The information presented here confirms the evolution of genome size in Copepoda and expands the scope for evolutionary inferences in Copepoda by providing several levels of genetic information from a key planktonic crustacean species.

AB - Members of the crustacean subclass Copepoda are likely the most abundant metazoans worldwide. Pelagic marine species are critical in converting planktonic microalgae to animal biomass, supporting oceanic food webs. Despite their abundance and ecological importance, only five copepod genomes are publicly available, owing to a number of factors including large genome size, repetitiveness, GC-content,and small animal size. Here, we report the sixth representative copepod genome and the first genome and transcriptome from the calanoid copepod species Acartia tonsa Dana, which is among the most numerous mesozooplankton in boreal coastal and estuarine waters. The ecology, physiology and behavior of A. tonsa has been studied extensively. The genetic resources contributed in this work will allow researchers to link experimental results to molecular mechanisms. From PCRfree WGS and mRNA Illumina data, we assemble the largest copepod genome to date. We estimate A. tonsa has a total genome size of 2.5 Gb including repetitive elements we could not resolve. The non-repetitive fraction of the genome assembly is estimated to be 566Mb. Our DNA sequencing-based analyses suggest there is a 14-fold difference in genome size between the six members of Copepoda with available genomic information through NCBI. This finding complements nucleus staining genome size estimations, where 100-fold difference has been reported within 70 species. We briefly analyze the repeat structure in the existing copepod WGS datasets. The information presented here confirms the evolution of genome size in Copepoda and expands the scope for evolutionary inferences in Copepoda by providing several levels of genetic information from a key planktonic crustacean species.

UR - https://www.biorxiv.org/content/biorxiv/early/2019/02/25/560102.full.pdf

U2 - 10.1093/gbe/evz067

DO - 10.1093/gbe/evz067

M3 - Journal article

VL - 11

SP - 1440

EP - 1450

JO - Genome Biology and Evolution

JF - Genome Biology and Evolution

SN - 1759-6653

IS - 5

ER -