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 Reduced Variation in Drosophila simulans Mitochondrial DNA

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1519-1528
Author(s):  
J William O Ballad ◽  
Joy Hatzidakis ◽  
Timothy L Karr ◽  
Martin Kreitman
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Evolutionary Dynamics ◽  
Selective Sweep ◽  
Mitochondrial Gene ◽  
Drosophila Simulans ◽  
Dramatic Reduction ◽  
Nucleotide Variability ◽  
Pooled Samples ◽  
Mitochondrial Gene Mutation

We investigated the evolutionary dynamics of infection of a Drosophila simulans population by a maternally inherited insect bacterial parasite, Wolbachia, by analyzing nucleotide variability in three regions of the mitochondrial genome in four infected and 35 uninfected lines. Mitochondrial variability is significantly reduced compared to a noncoding region of a nuclear-encoded gene in both uninfected and pooled samples of flies, indicating a sweep of genetic variation. The selective sweep of mitochondrial DNA may have been generated by the fixation of an advantageous mitochondrial gene mutation in the mitochondrial genome. Alternatively, the dramatic reduction in mitochondrial diversity may be related to Wolbachia.

scholarly journals Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9309
Author(s):  
Viktoria Yu Shtratnikova ◽  
Mikhail I. Schelkunov ◽  
Aleksey A. Penin ◽  
Maria D. Logacheva
Keyword(s):  
Mitochondrial Genome ◽  
Rna Editing ◽  
Transcriptome Sequencing ◽  
Unique Feature ◽  
Genetic Material ◽  
Mitochondrial Genes ◽  
Vaccinium Macrocarpon ◽  
Mitochondrial Genomes ◽  
Plastid Genomes ◽  
Trans Splicing

Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.

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.

Physical map and gene organization of the mitochondrial genome of Chondrus crispus (Rhodophyta, Gigartinales)

1994 ◽  
Vol 26 (2) ◽  
pp. 691-697 ◽  
Author(s):  
Catherine Boyen ◽  
Catherine Leblanc ◽  
Bernard Kloareg ◽  
Susan Loiseaux-de Go�r
Keyword(s):  
Mitochondrial Genome ◽  
Physical Map ◽  
Gene Organization ◽  
Chondrus Crispus

scholarly journals Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region

2018 ◽  
Author(s):  
Ji Haishuo ◽  
Xu Xiaofeng ◽  
Jin Xiufeng ◽  
Cheng Zhi ◽  
jin Hong ◽  
...  
Keyword(s):  
Steady State ◽  
High Resolution ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Transcription Initiation ◽  
Tandem Repeats ◽  
Mitochondrial Gene ◽  
Mitochondrial Genomes ◽  
Small Rna Sequencing ◽  
Antisense Gene

In this study, we used a small RNA sequencing (sRNA-seq) based method to annotate the mitochondrial genome of the insect Erthesina fullo Thunberg at 1 bp resolution. Most of the new annotations were consistent with the previous annotations which were obtained using PacBio full-length transcripts. Two important findings are that animals transcribe both entire strands of mitochondrial genomes and the tandem repeat in the control region of the E. fullo mitochondrial genome contains the repeated Transcription Initiation Sites (TISs) of the H-strand. In addition, we found that the copy numbers of tandem repeats showed a great diversity within an individual, enriching the fundamental knowledge of mitochondrial biology. This sRNA-seq based method uses 5′ and 3′ end small RNAs to annotate nuclear non-coding and mitochondrial genes at 1 bp resolution and can also be used to identify new steady-state RNAs, particularly long non-coding RNAs (lncRNAs). Animal mitochondrial genomes containing one control region only encode two steady-state lncRNAs, which are the Mitochondrial D-loop 1 (MDL1) and its antisense gene (MDL1AS), while all other reported mitochondrial lncRNAs could be degraded fragments of transient RNAs or random breaks during experimental processing. The high-resolution annotations of mitochondrial genomes can be used to study the phylogenetics and molecular evolution of animals or to investigate mitochondrial gene transcription, RNA processing, RNA maturation and several other related topics.

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.

scholarly journals Complete mitochondrial genome of Nanorana pleskei (Amphibia: Anura: Dicroglossidae) and evolutionary characteristics

2011 ◽  
Vol 57 (6) ◽  
pp. 785-805 ◽  
Author(s):  
Guiying Chen ◽  
Bin Wang ◽  
Jiongyu Liu ◽  
Feng Xie ◽  
Jianping Jiang
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Tandem Duplication ◽  
Complete Mitochondrial Genome ◽  
Gene Organization ◽  
Tibet Plateau ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Protein Coding

Abstract The complete mitochondrial genome of Nanorana pleskei from the Qinghai-Tibet Plateau was sequenced. It includes 17,660 base pairs, containing 13 protein-coding genes, two rRNAs and 23 tRNAs. A tandem duplication of tRNAMet gene was found in this mitochondrial genome, and the similarity between the two tRNAMet genes is 85.8%, being the highest in amphibian mitochondrial genomes sequenced thus far. Based on gene organization, 24 types were found from 145 amphibian mitochondrial genomes. Type 1 was present in 108 species, type 11 in 11 species, types 5, 16, 17, and 20 each in two species, and the others each present in one species. Fifteen types were found in Anura, being the most diversity in three orders of the Lissamphibia. Our phylogenetic results using 11 protein-coding gene sequences of 145 amphibian mitochondrial genomes strongly support the monophyly of the Lissamphibia, as well as its three orders, the Gymnophiona, Caudata, and Anura, among which the relationships were ((Gymnophiona (Caudata, Anura)). Based on the phylogenetic trees, type 1 was recognized as the ancestral type for amphibians, and type 11 was the synapomorphic type for the Neobatrachia. Gene rearrangements among lineages provide meaningful phylogenetic information. The rearrangement of the LTPF tRNA gene cluster and the translocation of the ND5 gene only found in the Neobatrachia support the monophyly of this group; similarly, the tandem duplication of the tRNAMet genes only found in the Dicroglossidae support the monophyly of this family.

scholarly journals The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum

2018 ◽  
Vol 4 ◽  
Author(s):  
Helen E. Robertson ◽  
Philipp H. Schiffer ◽  
Maximilian J. Telford
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Limited Support ◽  
Cell Layers

Abstract The Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14 247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a unique gene order. The data we have analysed from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical of the Metazoa. The cox1 gene from dicyemid species has a series of conserved, in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.

scholarly journals The First Evidence of a Host-to-Parasite Mitochondrial Gene Transfer in Orobanchaceae

2017 ◽  
Vol 59 (1) ◽  
pp. 13-22 ◽  
Author(s):  
Dagmara Kwolek ◽  
Magdalena Denysenko-Bennett ◽  
Grzegorz Góralski ◽  
Magdalena Cygan ◽  
Patryk Mizia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Mitochondrial Genome ◽  
Genome Evolution ◽  
Horizontal Transfer ◽  
Mitochondrial Gene ◽  
Genetic Material ◽  
Parasitic Plants ◽  
Mitochondrial Genes ◽  
Mitochondrial Genome Evolution

AbstractSeveral parasitic plants are known to have acquired mitochondrial genes via a horizontal transfer from their hosts. However, mitochondrial gene transfer in this direction has not yet been found in the parasite-rich family Orobanchaceae. Based on a phylogenetic analysis of the mitochondrialatp6gene in selected species ofOrobanches.l., we provide evidence of a host-to-parasite transfer of this gene inO. coerulescens, which is a Eurasiatic species that parasitisesArtemisia(Asteraceae). We did not find the originalOrobanche atp6gene in this species, which suggests that it has been replaced by a gene that was acquired from Asteraceae. In addition, our data suggest the occurrence of a second HGT event in theatp6sequence – from Asteraceae toPhelipanche. Our results support the view that the transfer of genetic material from hosts to parasites influences the mitochondrial genome evolution in the latter.

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