Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication
International audience Background: The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod crustaceans with strong implications in crustacean p...
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Online Access: | https://hal.science/hal-02295475 https://hal.science/hal-02295475/document https://hal.science/hal-02295475/file/Absence%20of%20evidence%20is%20not%20evidence%20of%20absence.pdf https://doi.org/10.1186/s12864-019-5704-3 |
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ftunivpoitiers:oai:HAL:hal-02295475v1 2024-02-27T08:40:17+00:00 Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication Gan, Han Ming Grandjean, Frédéric Jenkins, Tom Austin, Christopher Mervyn Monash University Malaysia Deakin University Burwood Écologie et biologie des interactions (EBI) Université de Poitiers = University of Poitiers (UP)-Centre National de la Recherche Scientifique (CNRS) University of Exeter 2019 https://hal.science/hal-02295475 https://hal.science/hal-02295475/document https://hal.science/hal-02295475/file/Absence%20of%20evidence%20is%20not%20evidence%20of%20absence.pdf https://doi.org/10.1186/s12864-019-5704-3 en eng HAL CCSD BioMed Central info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-019-5704-3 hal-02295475 https://hal.science/hal-02295475 https://hal.science/hal-02295475/document https://hal.science/hal-02295475/file/Absence%20of%20evidence%20is%20not%20evidence%20of%20absence.pdf doi:10.1186/s12864-019-5704-3 PUBMEDCENTRAL: PMC6500004 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess EISSN: 1471-2164 BMC Genomics https://hal.science/hal-02295475 BMC Genomics, 2019, 20 (1), pp.335. ⟨10.1186/s12864-019-5704-3⟩ Homarus gammarus Mitogenome Nanopore sequencing Lobster Tandem duplication PCR bias [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics [SDV.BID]Life Sciences [q-bio]/Biodiversity info:eu-repo/semantics/article Journal articles 2019 ftunivpoitiers https://doi.org/10.1186/s12864-019-5704-3 2024-01-31T17:40:31Z International audience Background: The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod crustaceans with strong implications in crustacean phylogenetics. Such atypical mitochondrial features will benefit greatly from validation with emerging long read sequencing technologies such as Oxford Nanopore that can more accurately identify structural variation.Results: We re-sequenced the H. gammarus mitogenome on an Oxford Nanopore Minion flowcell and performed a long-read only assembly, generating a complete mitogenome assembly for H. gammarus. In contrast to previous reporting, we found an intact mitochondrial nad2 gene in the H. gammarus mitogenome and showed that its gene organization is broadly similar to that of the American lobster (H. americanus) except for the presence of a large tandemly duplicated region with evidence of pseudogenization in one of each duplicated protein-coding genes.Conclusions: Using the European lobster as an example, we demonstrate the value of Oxford Nanopore long read technology in resolving problematic mitogenome assemblies. The increasing accessibility of Oxford Nanopore technology will make it an attractive and useful tool for evolutionary biologists to verify new and existing unusual mitochondrial gene rearrangements recovered using first and second generation sequencing technologies, particularly those used to make phylogenetic inferences of evolutionary scenarios. Article in Journal/Newspaper European lobster Homarus gammarus Université de Poitiers: Publications de nos chercheurs.ses (HAL) BMC Genomics 20 1 |
institution |
Open Polar |
collection |
Université de Poitiers: Publications de nos chercheurs.ses (HAL) |
op_collection_id |
ftunivpoitiers |
language |
English |
topic |
Homarus gammarus Mitogenome Nanopore sequencing Lobster Tandem duplication PCR bias [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics [SDV.BID]Life Sciences [q-bio]/Biodiversity |
spellingShingle |
Homarus gammarus Mitogenome Nanopore sequencing Lobster Tandem duplication PCR bias [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics [SDV.BID]Life Sciences [q-bio]/Biodiversity Gan, Han Ming Grandjean, Frédéric Jenkins, Tom Austin, Christopher Mervyn Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication |
topic_facet |
Homarus gammarus Mitogenome Nanopore sequencing Lobster Tandem duplication PCR bias [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics [SDV.BID]Life Sciences [q-bio]/Biodiversity |
description |
International audience Background: The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod crustaceans with strong implications in crustacean phylogenetics. Such atypical mitochondrial features will benefit greatly from validation with emerging long read sequencing technologies such as Oxford Nanopore that can more accurately identify structural variation.Results: We re-sequenced the H. gammarus mitogenome on an Oxford Nanopore Minion flowcell and performed a long-read only assembly, generating a complete mitogenome assembly for H. gammarus. In contrast to previous reporting, we found an intact mitochondrial nad2 gene in the H. gammarus mitogenome and showed that its gene organization is broadly similar to that of the American lobster (H. americanus) except for the presence of a large tandemly duplicated region with evidence of pseudogenization in one of each duplicated protein-coding genes.Conclusions: Using the European lobster as an example, we demonstrate the value of Oxford Nanopore long read technology in resolving problematic mitogenome assemblies. The increasing accessibility of Oxford Nanopore technology will make it an attractive and useful tool for evolutionary biologists to verify new and existing unusual mitochondrial gene rearrangements recovered using first and second generation sequencing technologies, particularly those used to make phylogenetic inferences of evolutionary scenarios. |
author2 |
Monash University Malaysia Deakin University Burwood Écologie et biologie des interactions (EBI) Université de Poitiers = University of Poitiers (UP)-Centre National de la Recherche Scientifique (CNRS) University of Exeter |
format |
Article in Journal/Newspaper |
author |
Gan, Han Ming Grandjean, Frédéric Jenkins, Tom Austin, Christopher Mervyn |
author_facet |
Gan, Han Ming Grandjean, Frédéric Jenkins, Tom Austin, Christopher Mervyn |
author_sort |
Gan, Han Ming |
title |
Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication |
title_short |
Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication |
title_full |
Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication |
title_fullStr |
Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication |
title_full_unstemmed |
Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication |
title_sort |
absence of evidence is not evidence of absence: nanopore sequencing and complete assembly of the european lobster (homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication |
publisher |
HAL CCSD |
publishDate |
2019 |
url |
https://hal.science/hal-02295475 https://hal.science/hal-02295475/document https://hal.science/hal-02295475/file/Absence%20of%20evidence%20is%20not%20evidence%20of%20absence.pdf https://doi.org/10.1186/s12864-019-5704-3 |
genre |
European lobster Homarus gammarus |
genre_facet |
European lobster Homarus gammarus |
op_source |
EISSN: 1471-2164 BMC Genomics https://hal.science/hal-02295475 BMC Genomics, 2019, 20 (1), pp.335. ⟨10.1186/s12864-019-5704-3⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-019-5704-3 hal-02295475 https://hal.science/hal-02295475 https://hal.science/hal-02295475/document https://hal.science/hal-02295475/file/Absence%20of%20evidence%20is%20not%20evidence%20of%20absence.pdf doi:10.1186/s12864-019-5704-3 PUBMEDCENTRAL: PMC6500004 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1186/s12864-019-5704-3 |
container_title |
BMC Genomics |
container_volume |
20 |
container_issue |
1 |
_version_ |
1792047399611400192 |