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
Abstract 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. S...
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| Format: | Article |
| Language: | English |
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BMC
2019-05-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5704-3 |
| _version_ | 1818512410246381568 |
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| author | Han Ming Gan Frederic Grandjean Tom L. Jenkins Christopher Mervyn Austin |
| author_facet | Han Ming Gan Frederic Grandjean Tom L. Jenkins Christopher Mervyn Austin |
| author_sort | Han Ming Gan |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-10T23:46:26Z |
| format | Article |
| id | doaj.art-b647b5c0bfab4566af0bf597e429fad8 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T23:46:26Z |
| publishDate | 2019-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-b647b5c0bfab4566af0bf597e429fad82022-12-22T01:28:55ZengBMCBMC Genomics1471-21642019-05-0120111110.1186/s12864-019-5704-3Absence 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 duplicationHan Ming Gan0Frederic Grandjean1Tom L. Jenkins2Christopher Mervyn Austin3Deakin Genomics Centre, Deakin UniversityLaboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267 Equipe Ecologie Evolution Symbiose 5 rue Albert TurpinDepartment of Biosciences, College of Life and Environmental Sciences, University of ExeterDeakin Genomics Centre, Deakin UniversityAbstract 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.http://link.springer.com/article/10.1186/s12864-019-5704-3Homarus gammarusMitogenomeNanopore sequencingLobsterTandem duplicationPCR bias |
| spellingShingle | Han Ming Gan Frederic Grandjean Tom L. Jenkins Christopher Mervyn 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 BMC Genomics Homarus gammarus Mitogenome Nanopore sequencing Lobster Tandem duplication PCR bias |
| 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_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_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_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 |
| topic | Homarus gammarus Mitogenome Nanopore sequencing Lobster Tandem duplication PCR bias |
| url | http://link.springer.com/article/10.1186/s12864-019-5704-3 |
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