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

Genetics ◽  
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.

Characterization of nematode mitochondrial genomes.

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.

Sequence amplification and gene rearrangement in parasitic nematode mitochondrial DNA.

Genetics ◽  
1988 ◽  
Vol 120 (3) ◽  
pp. 707-712
Author(s):  
B C Hyman ◽  
J L Beck ◽  
K C Weiss
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Gene Rearrangement ◽  
Tandem Repeats ◽  
Parasitic Nematode ◽  
Mitochondrial Gene ◽  
Sequence Organization ◽  
Large Size ◽  
Mitochondrial Gene Order

Abstract The nematode Romanomermis culicivorax, an obligate mosquito parasite, possesses a 26 kilobase (kb) mitochondrial genome. The unusually large size is due to transcriptionally active DNA sequences present as 3.0 kb direct tandem repeats and as inverted portions of the repeating unit located elsewhere in the mitochondrial DNA (mtDNA). The genome rearrangements involved in establishing this unusual sequence organization may have dramatically altered conventional mitochondrial gene order. Genes for subunits of the cytochrome c oxidase complex (COI and COII) are normally closely linked in animal mtDNAs, but are separated by approximately 8 kb in this mitochondrial genome.

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

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6866 ◽  
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.

The plant mitochondrial genome: homologous recombination as a mechanism for generating heterogeneity

1988 ◽  
Vol 319 (1193) ◽  
pp. 149-163 ◽  
Keyword(s):  
Mitochondrial Dna ◽  
Homologous Recombination ◽  
Mitochondrial Genome ◽  
Higher Plants ◽  
Genome Structure ◽  
Rapid Evolution ◽  
Mitochondrial Genomes ◽  
Base Sequence ◽  
Plant Mitochondrial Genome ◽  
Organelle Genomes

The mitochondrial genomes of higher plants are among the largest and most complex organelle genomes described. They are generally multicircular or partly linear; in some species, extrachromosomal plasmids are present. It is proposed that inter- and intramolecular homologous recombination can account for the diversity of the observed genome organizations. The ability of mitochondria to fuse establishes a panmictic mitochondrial DNA population which is in recombinational equilibrium. It is suggested that this suppresses the base mutation rate, and unequal partitioning of the cytoplasm during cell division can lead to the rapid evolution of mitochondrial genome structure. This contrasts with the observed rates of base-sequence and genome evolution in chloroplasts. This difference can be accounted for solely by the inability of chloroplasts to fuse, thereby preventing chloroplast genome panmixis.

A one-megabase physical map provides insights on gene organization in the enormous mitochondrial genome of cucumber

Genome ◽  
2009 ◽  
Vol 52 (4) ◽  
pp. 299-307 ◽  
Author(s):  
Grzegorz Bartoszewski ◽  
Piotr Gawronski ◽  
Marek Szklarczyk ◽  
Henk Verbakel ◽  
Michael J. Havey
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Physical Map ◽  
Mitochondrial Gene ◽  
Mitochondrial Genes ◽  
Gene Organization ◽  
Mitochondrial Genomes ◽  
Bac Contig ◽  
Repetitive Dnas ◽  
Dna Motifs

Cucumber ( Cucumis sativus ) has one of the largest mitochondrial genomes known among all eukaryotes, due in part to the accumulation of short 20 to 60 bp repetitive DNA motifs. Recombination among these repetitive DNAs produces rearrangements affecting organization and expression of mitochondrial genes. To more efficiently identify rearrangements in the cucumber mitochondrial DNA, we built two nonoverlapping 800 and 220 kb BAC contigs and assigned major mitochondrial genes to these BACs. Polymorphism carried on the largest BAC contig was used to confirm paternal transmission. Mitochondrial genes were distributed across BACs and physically distant, although occasional clustering was observed. Introns in the nad1, nad4, and nad7 genes were larger than those reported in other plants, due in part to accumulation of short repetitive DNAs and indicating that increased intron sizes contributed to mitochondrial genome expansion in cucumber. Mitochondrial genes atp6 and atp9 are physically close to each other and cotranscribed. These physical contigs will be useful for eventual sequencing of the cucumber mitochondrial DNA, which can be exploited to more efficiently screen for unique rearrangements affecting mitochondrial gene expression.

scholarly journals Characterization of Penaeus vannamei mitogenome focusing on genetic diversity

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255291
Author(s):  
Paulo Eduardo T. Soares ◽  
Márcia Danielle A. Dantas ◽  
Rita de Cássia B. Silva-Portela ◽  
Lucymara F. Agnez-Lima ◽  
Daniel Carlos F. Lanza
Keyword(s):  
Mitochondrial Genome ◽  
Low Frequency ◽  
Individual Variability ◽  
Mitochondrial Genomes ◽  
Penaeus Vannamei ◽  
Single Individual ◽  
Variable Regions ◽  
Mitochondrial Markers ◽  
Hypervariable Regions

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.

scholarly journals Mitochondrial Fostering: The Mitochondrial Genome May Play a Role in Plant Orphan Gene Evolution

2020 ◽  
Vol 11 ◽  
Author(s):  
Seth O’Conner ◽  
Ling Li
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Gene Evolution ◽  
Nuclear Genome ◽  
Bioinformatic Analysis ◽  
Land Plants ◽  
Mitochondrial Genomes ◽  
Recombination Rates ◽  
Orphan Genes ◽  
Orphan Gene

Plant mitochondrial genomes exhibit unique evolutionary patterns. They have a high rearrangement but low mutation rate, and a large size. Based on massive mitochondrial DNA transfers to the nucleus as well as the mitochondrial unique evolutionary traits, we propose a “Mitochondrial Fostering” theory where the organelle genome plays an integral role in the arrival and development of orphan genes (genes with no homologs in other lineages). Two approaches were used to test this theory: (1) bioinformatic analysis of nuclear mitochondrial DNA (Numts: mitochondrial originating DNA that migrated to the nucleus) at the genome level, and (2) bioinformatic analysis of particular orphan sequences present in both the mitochondrial genome and the nuclear genome of Arabidopsis thaliana. One study example is given about one orphan sequence that codes for two unique orphan genes: one in the mitochondrial genome and another one in the nuclear genome. DNA alignments show regions of this A. thaliana orphan sequence exist scattered throughout other land plant mitochondrial genomes. This is consistent with the high recombination rates of mitochondrial genomes in land plants. This may also enable the creation of novel coding sequences within the orphan loci, which can then be transferred to the nuclear genome and become exposed to new evolutionary pressures. Our study also reveals a high correlation between the amount of mitochondrial DNA transferred to the nuclear genome and the number of orphan genes in land plants. All the data suggests the mitochondrial genome may play a role in nuclear orphan gene evolution in land plants.

scholarly journals DNA-polymerase guided elimination of paternal mitochondrial genomes: An escape-proof obstacle to their transmission

2016 ◽  
Author(s):  
Zhongsheng Yu ◽  
Patrick H. O'Farrell ◽  
Nikita Yakubovich ◽  
Steven Z. DeLuca
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Dna Polymerase ◽  
Future Generations ◽  
Mitochondrial Genomes ◽  
Genetic Conflict ◽  
Direct Contribution ◽  
Dna Elimination ◽  
Mitochondrial Dna Polymerase

Mitochondrial DNA is predominantly inherited from only one parent. In animals this is usually the mother. This program is not in the interest of the paternal mitochondrial genome whose potential to contribute to future generations is restricted. However, in a dramatic example of genetic conflict, nuclear programs ensure the outcome. Two large mitochondria extend the length of Drosophila sperm tails. The hundreds of nucleoids in these mitochondria vanish during spermatogenesis eliminating their potential for transmission. Our previous work showed that mutational inactivation of EndoG, a nuclear encoded mitochondrial endonuclease, slows elimination of mitochondrial genomes. Here, we show that knockdown of the nuclearly encoded mitochondrial DNA polymerase, Tamas, produces a much more complete block of mtDNA loss. Recruitment of Tamas to the nucleoid at the time of its disappearance suggests a direct contribution to the elimination, but the 3'-exonuclease function of the polymerase is not needed. While DNA elimination is a surprising function for DNA polymerase, its use to restrict paternal genomes provides a strategy that cannot easily be evaded by the mitochondrial genome without compromising its replication.

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