The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences

Abstract The mitochondrial genome of 23 wild-type strains belonging to three different species of The mitochondrial genome the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

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Cost of Having the Largest Mitochondrial Genome: Evolutionary Mechanism of Plant Mitochondrial Genome

Journal of Botany ◽

10.1155/2010/620137 ◽

2010 ◽

Vol 2010 ◽

pp. 1-12 ◽

Cited By ~ 29

Author(s):

Kazuyoshi Kitazaki ◽

Tomohiko Kubo

Keyword(s):

Mitochondrial Genome ◽

Current Knowledge ◽

Open Reading Frames ◽

Plant Mitochondrial Genome ◽

Unknown Mechanism ◽

Evolutionary Mechanism ◽

Copy Numbers ◽

Intergenic Regions ◽

Genome Alteration ◽

Reading Frames

The angiosperm mitochondrial genome is the largest and least gene-dense among the eukaryotes, because its intergenic regions are expanded. There seems to be no functional constraint on the size of the intergenic regions; angiosperms maintain the large mitochondrial genome size by a currently unknown mechanism. After a brief description of the angiosperm mitochondrial genome, this review focuses on our current knowledge of the mechanisms that control the maintenance and alteration of the genome. In both processes, the control of homologous recombination is crucial in terms of site and frequency. The copy numbers of various types of mitochondrial DNA molecules may also be controlled, especially during transmission of the mitochondrial genome from one generation to the next. An important characteristic of angiosperm mitochondria is that they contain polypeptides that are translated from open reading frames created as byproducts of genome alteration and that are generally nonfunctional. Such polypeptides have potential to evolve into functional ones responsible for mitochondrially encoded traits such as cytoplasmic male sterility or may be remnants of the former functional polypeptides.

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The complete mitochondrial genome of the lipid-producing yeast Rhodotorula toruloides

FEMS Yeast Research ◽

10.1093/femsyr/foaa048 ◽

2020 ◽

Vol 20 (6) ◽

Author(s):

Renhui Zhou ◽

Zhiwei Zhu ◽

Sufang Zhang ◽

Zongbao Kent Zhao

Keyword(s):

Mitochondrial Genome ◽

Ribosomal Rna ◽

Complete Mitochondrial Genome ◽

Nuclear Genome ◽

Open Reading Frames ◽

Circular Dna ◽

Transfer Rnas ◽

Fundamental Information ◽

Significant Genetic Divergence ◽

Reading Frames

ABSTRACT Mitochondria are semi-autonomous organelles with their own genome and crucial to cellular material and energy metabolism. Here, we report the complete mitochondrial genome of a lipid-producing basidiomycetous yeast Rhodotorula toruloides NP11. The mitochondrial genome of R. toruloides NP11 was assembled into a circular DNA molecule of 125937bp, encoding 15 proteins, 28 transfer RNAs, 2 ribosomal RNA subunits and 10 open reading frames with unknown function. The G + C content (41%) of the mitochondrial genome is substantially lower than that of the nuclear genome (62%) of R. toruloides NP11. Further reanalysis of the transcriptome data confirmed the transcription of four mitochondrial genes. The comparison of the mitochondrial genomes of R. toruloides NP11 and NBRC0880 revealed a significant genetic divergence. These data can complement our understanding of the genetic background of R. toruloides and provide fundamental information for further genetic engineering of this strain.

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Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii

PeerJ ◽

10.7717/peerj.8356 ◽

2020 ◽

Vol 8 ◽

pp. e8356

Author(s):

Darrin T. Schultz ◽

Jordan M. Eizenga ◽

Russell B. Corbett-Detig ◽

Warren R. Francis ◽

Lynne M. Christianson ◽

...

Keyword(s):

Mitochondrial Genome ◽

Hypothesis Test ◽

Open Reading Frames ◽

Mitochondrial Genomes ◽

Intergenic Sequence ◽

Computational Tools ◽

Protein Coding ◽

Bayesian Hypothesis Test ◽

And Function ◽

Reading Frames

To date, five ctenophore species’ mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.

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Structural analysis of TRAS1, a novel family of telomeric repeat-associated retrotransposons in the silkworm, Bombyx mori.

Molecular and Cellular Biology ◽

10.1128/mcb.15.8.4545 ◽

1995 ◽

Vol 15 (8) ◽

pp. 4545-4552 ◽

Cited By ~ 62

Author(s):

S Okazaki ◽

H Ishikawa ◽

H Fujiwara

Keyword(s):

Bombyx Mori ◽

Repetitive Sequence ◽

Repetitive Sequences ◽

Complete Sequence ◽

Open Reading Frames ◽

Ltr Retrotransposons ◽

Reading Frames ◽

28S Ribosomal Dna ◽

Silkworm Bombyx Mori

We characterized TRAS1, a retrotransposable element which was inserted into the telomeric repetitive sequence (CCTAA)n of the silkworm, Bombyx mori. The complete sequence of TRAS1, a stretch of 7.8 kb with a poly(A) tract at the 3' end, was determined. No long terminal repeat (LTR) was found at the termini of the element. TRAS1 contains gag- and pol-like open reading frames (ORFs) which are similar to those of non-LTR retrotransposons. The two ORFs overlap but are one nucleotide out of frame (+1 frameshift). Most of the approximately 250 copies of TRAS1 elements in the genome were highly conserved in the structure. Chromosomal in situ hybridization showed that TRAS1 elements are clustered at the telomeres of Bombyx chromosomes. A phylogenetic analysis using the amino acid sequence of the reverse transcriptase domain within the pol-like ORF revealed that TRAS1 falls into one lineage with R1, which is a family of non-LTR retrotransposons inserted into the same site within the 28S ribosomal DNA unit in most insects. TRAS1 may have been derived from R1 and changed the target specificity so that TRAS1 inserts into the telomeric repetitive sequence (CCTAA)n. Southern hybridization and Bal 31 exonuclease analyses showed that TRAS1 elements are clustered proximal to the terminal long tract of (CCTAA)n. TRAS1 is a novel family of non-LTR retrotransposons which are inserted into the telomeric repetitive sequences as target sites.

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Heteroplasmy and repeat expansion in the plant-like mitochondrial genome of a bivalve mollusc

10.1101/2020.09.23.310516 ◽

2020 ◽

Author(s):

Andrew D Calcino ◽

Christian Baranyi ◽

Andreas Wanninger

Keyword(s):

Mitochondrial Genome ◽

Error Correction ◽

Plant Mitochondria ◽

Bivalve Mollusc ◽

Open Reading Frames ◽

Quagga Mussel ◽

Gene Repertoire ◽

Repeat Content ◽

Repeat Expansions ◽

Reading Frames

Background: Animal mitochondrial genomes are typically circular, 14-20 kb in length, maternally inherited, contain 13 coding genes, two ribosomal genes and are homoplasmic. In contrast, plant mitogenomes display frequent gene rearrangements, often contain greatly expanded repetitive regions, encode various open reading frames of unknown function and may be heteroplasmic due to differential repeat expansions between molecules. Error correction by recombination is common in plant mitochondria and has been proposed as the driver behind the rearrangements and repeat expansions that are often observed. In contrast, most animal mitochondria never or only very seldomly recombine and their utilisation of other repair mechanisms for mitochondrial genome error correction is a potential driver of their non-coding DNA reduction. Results: Using PacBio long reads for genome assembly and structural variant detection, we identify evidence of heteroplasmy in the form of variable repeat lengths within two blocks of repetitive DNA within the expanded 46 kb mitochondrial genome of the bivalve mollusc, quagga mussel, Dreissena rostriformis. The quagga mussel also has a greatly expanded repertoire of coding genes in comparison to most animals which includes an additional nine open reading frames (ORFs) encoding predicted transmembrane peptides of unknown orthology. Conclusions: The genome size, repeat content and coding gene repertoire of the quagga mussel mitogenome closely resemble those of plants and the identification of repeat-associated heteroplasmy is consistent with the utilisation of plant-like recombination-based error correction mechanisms. Given the frequency of mitochondrial repeat expansions within the Bivalvia, recombination may be an underappreciated mechanism for mitogenomic error correction within this and other animal lineages.

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Composite transposable elements in the Xenopus laevis genome.

Molecular and Cellular Biology ◽

10.1128/mcb.9.7.3018 ◽

1989 ◽

Vol 9 (7) ◽

pp. 3018-3027 ◽

Cited By ~ 25

Author(s):

J E Garrett ◽

D S Knutzon ◽

D Carroll

Keyword(s):

Xenopus Laevis ◽

Transposable Elements ◽

Repetitive Sequences ◽

Open Reading Frames ◽

The Other ◽

Inverted Repeats ◽

Terminal Inverted Repeats ◽

Gag Proteins ◽

High Degree ◽

Reading Frames

Members of two related families of transposable elements, Tx1 and Tx2, were isolated from the genome of Xenopus laevis and characterized. In both families, two versions of the elements were found. The smaller version in each family (Tx1d and Tx2d) consisted largely of two types of 400-base-pair tandem internal repeats. These elements had discrete ends and short inverted terminal repeats characteristic of mobile DNAs that are presumed to move via DNA intermediates, e.g., Drosophila P and maize Ac elements. The longer versions (Tx1c and Tx2c) differed from Tx1d and Tx2d by the presence of a 6.9-kilobase-pair internal segment that included two long open reading frames (ORFs). ORF1 had one cysteine-plus-histidine-rich sequence of the type found in retroviral gag proteins. ORF2 showed more substantial homology to retroviral pol genes and particularly to the analogs of pol found in a subclass of mobile DNAs that are supposed retrotransposons, such as mammalian long interspersed repetitive sequences, Drosophila I factors, silkworm R1 elements, and trypanosome Ingi elements. Thus, the Tx1 elements present a paradox by exhibiting features of two classes of mobile DNAs that are thought to have very different modes of transposition. Two possible resolutions are considered: (i) the composite versions are actually made up of two independent elements, one of the retrotransposon class, which has a high degree of specificity for insertion into a target within the other, P-like element; and (ii) the composite elements are intact, autonomous mobile DNAs, in which the pol-like gene product collaborates with the terminal inverted repeats to cause transposition of the entire unit.

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