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, Frederic, Jenkins, Tom L. and Austin, Christopher 2019, 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, vol. 20, no. 1, doi: 10.1186/s12864-019-5704-3.

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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
Author(s) Gan, Han MingORCID iD for Gan, Han Ming orcid.org/0000-0001-7987-738X
Grandjean, Frederic
Jenkins, Tom L.
Austin, ChristopherORCID iD for Austin, Christopher orcid.org/0000-0003-1848-6267
Journal name BMC genomics
Volume number 20
Issue number 1
Article ID 335
Total pages 11
Publisher BioMed Central
Place of publication London, Eng.
Publication date 2019-05-03
ISSN 1471-2164
Keyword(s) Homarus gammarus
Lobster
Mitogenome
Nanopore sequencing
PCR bias
Tandem duplication
Science & Technology
Life Sciences & Biomedicine
Biotechnology & Applied Microbiology
Genetics & Heredity
COMPLETE MITOCHONDRIAL GENOME
FRESH-WATER CRAYFISH
CRUSTACEA DECAPODA
AMERICAN LOBSTER
ORDER
ASTACIDEA
PHYLOGENY
ALIGNMENT
REARRANGEMENTS
VISUALIZATION
Summary 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.
Language eng
DOI 10.1186/s12864-019-5704-3
Field of Research 06 Biological Sciences
11 Medical and Health Sciences
08 Information and Computing Sciences
HERDC Research category C1 Refereed article in a scholarly journal
Copyright notice ©2019, The Authors
Persistent URL http://hdl.handle.net/10536/DRO/DU:30121494

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