Characterization of Penaeus vannamei mitogenome focusing on genetic diversity

The diversity of the Penaeus vannamei mitochondrial genome has still been poorly characterized, there are no validated mitochondrial markers available for populational studies, and the heteroplasmy has not yet been investigated in this species. In this study, metagenomic reads extracted from the muscle of a single individual were used to assemble the mitochondrial genome (mtDNA). These data associated with mitochondrial genomes previously described allowed to evaluate the inter-individual variability and heteroplasmy. Comparison among 45 mtDNA control regions led to the detection of conserved and variable segments and the characterization of two hypervariable regions. The analysis of diversity revealed mostly low frequency polymorphisms, and heteroplasmy was found in practically all mitochondrial genes, with a high occurrence of indels. These results indicate that the design of mitochondrial markers for P. vannamei must be done with caution. The mapping of conserved and variable regions and the characterization of heteroplasmy presented here will contribute to increasing the efficiency of mitochondrial markers for population or individual studies.

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Characterization of nematode mitochondrial genomes.

Techniques for work with plant and soil nematodes ◽

10.1079/9781786391759.0250 ◽

2021 ◽

pp. 250-264

Author(s):

Danny A. Humphreys-Pereira ◽

Taeho Kim ◽

Joong-Ki Park

Keyword(s):

Polymerase Chain Reaction ◽

Mitochondrial Genome ◽

Genome Annotation ◽

Pcr Amplification ◽

Gene Identification ◽

Mitochondrial Genomes ◽

Pcr Cloning ◽

Chain Reaction ◽

Polymerase Chain

Abstract This chapter presents procedures on polymerase chain reaction (PCR) amplification, protocols for PCR, cloning and sequencing, and mitochondrial genome annotation and gene identification for the characterization of nematodes.

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Widespread co-occurrence of two distantly related mitochondrial genomes in individuals of the leaf beetle Gonioctena intermedia

Biology Letters ◽

10.1098/rsbl.2017.0570 ◽

2017 ◽

Vol 13 (11) ◽

pp. 20170570 ◽

Cited By ~ 6

Author(s):

Chedly Kastally ◽

Patrick Mardulyn

Keyword(s):

Mitochondrial Genome ◽

Sanger Sequencing ◽

Leaf Beetle ◽

Universal Primers ◽

Mitochondrial Genomes ◽

Single Individual ◽

Sequencing Technologies ◽

Pcr Products ◽

Nucleotide Divergence ◽

Genomic Variant

Mitochondrial genome heteroplasmy—the presence of more than one genomic variant in individuals—is considered only occasional in animals, and most often involves molecules differing only by a few recent mutations. Thanks to new sequencing technologies, a large number of DNA fragments from a single individual can now be sequenced and visualized separately, allowing new insights into intra-individual mitochondrial genome variation. Here, we report evidence from both (i) massive parallel sequencing (MPS) of genomic extracts and (ii) Sanger sequencing of PCR products, for the widespread co-occurrence of two distantly related (greater than 1% nucleotide divergence, excluding the control region) mitochondrial genomes in individuals of a natural population of the leaf beetle Gonioctena intermedia . Sanger sequencing of PCR products using universal primers previously failed to identify heteroplasmy in this population. Its occurrence was detected with MPS data and may have important implications for evolutionary studies. It suggests the need to re-evaluate, using MPS techniques, the proportion of animal species displaying heteroplasmy.

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Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae)

PeerJ ◽

10.7717/peerj.6866 ◽

2019 ◽

Vol 7 ◽

pp. e6866 ◽

Cited By ~ 3

Author(s):

Gengyun Niu ◽

Yaoyao Zhang ◽

Zhenyi Li ◽

Meicai Wei

Keyword(s):

Mitochondrial Genome ◽

New Genus ◽

Complete Mitochondrial Genome ◽

Sister Group ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Protein Coding Genes ◽

A New Species ◽

High Support

A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.

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Characterization of nematode mitochondrial genomes.

Techniques for work with plant and soil nematodes ◽

10.1079/9781786391759.0014 ◽

2021 ◽

pp. 250-264

Author(s):

Danny A. Humphreys-Pereira ◽

Taeho Kim ◽

Joong-Ki Park

Keyword(s):

Polymerase Chain Reaction ◽

Mitochondrial Genome ◽

Genome Annotation ◽

Pcr Amplification ◽

Gene Identification ◽

Mitochondrial Genomes ◽

Pcr Cloning ◽

Chain Reaction ◽

Polymerase Chain

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Recent appearance and molecular characterization of mitochondrial DNA deletions within a defined nematode pedigree.

Genetics ◽

10.1093/genetics/124.4.845 ◽

1990 ◽

Vol 124 (4) ◽

pp. 845-853

Author(s):

B C Hyman ◽

T M Slater

Keyword(s):

Mitochondrial Dna ◽

Mitochondrial Genome ◽

Parasitic Nematode ◽

Mitochondrial Genomes ◽

Direct Repeats ◽

Recent Event ◽

Dna Deletions ◽

Selection Of ◽

Deletion Junction

Abstract The mitochondrial genome of Romanomermis culicivorax, a parasitic nematode of mosquitoes, contains an amplified 3.0-kilobase (kb) locus organized as direct repeats and as noncontiguous, inverted copies. These amplified sequences are actively undergoing rearrangement. One recent event has resulted in a 1133-base pair (bp) deletion located entirely within a single amplified segment. The deletion junction occurs between two imperfect 58-bp repeats, implicating strand pairing in this alteration. A second event has generated mitochondrial DNA (mtDNA) forms differing by a single, intact 3.0-kb repeating unit. By analyzing molecules derived from independently reared subcultures, it appears these new mtDNA forms arose within the last 170 nematode generations. Our results indicate that the occurrence and selection of novel animal mitochondrial genomes can now be studied in this experimentally manipulable nematode system.

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