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.
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 atyp...
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ftdeakinunifig:oai:figshare.com:article/20758858 2024-06-23T07:52:35+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. Han Ming Gan Frederic Grandjean Tom L Jenkins Chris Austin 2019-05-03T00:00:00Z http://hdl.handle.net/10536/DRO/DU:30121494 https://figshare.com/articles/journal_contribution/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_/20758858 unknown http://hdl.handle.net/10536/DRO/DU:30121494 https://figshare.com/articles/journal_contribution/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_/20758858 All Rights Reserved Homarus gammarus Lobster Mitogenome Nanopore sequencing PCR bias Tandem duplication 3104 Evolutionary biology Text Journal contribution 2019 ftdeakinunifig 2024-06-06T01:28:34Z 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 DRO - Deakin Research Online |
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Open Polar |
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DRO - Deakin Research Online |
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ftdeakinunifig |
language |
unknown |
topic |
Homarus gammarus Lobster Mitogenome Nanopore sequencing PCR bias Tandem duplication 3104 Evolutionary biology |
spellingShingle |
Homarus gammarus Lobster Mitogenome Nanopore sequencing PCR bias Tandem duplication 3104 Evolutionary biology Han Ming Gan Frederic Grandjean Tom L Jenkins Chris Austin 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 Lobster Mitogenome Nanopore sequencing PCR bias Tandem duplication 3104 Evolutionary biology |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Han Ming Gan Frederic Grandjean Tom L Jenkins Chris Austin |
author_facet |
Han Ming Gan Frederic Grandjean Tom L Jenkins Chris Austin |
author_sort |
Han Ming Gan |
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. |
publishDate |
2019 |
url |
http://hdl.handle.net/10536/DRO/DU:30121494 https://figshare.com/articles/journal_contribution/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_/20758858 |
genre |
European lobster Homarus gammarus |
genre_facet |
European lobster Homarus gammarus |
op_relation |
http://hdl.handle.net/10536/DRO/DU:30121494 https://figshare.com/articles/journal_contribution/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_/20758858 |
op_rights |
All Rights Reserved |
_version_ |
1802643926453059584 |