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1.
Artigo em Chinês | MEDLINE | ID: mdl-32185925

RESUMO

OBJECTIVE: To compare the complete mitochondrial genome sequences of two phenotypes of Paragonimus westermani isolated from Fujian Province with different sizes of metacercariae, and perform a phylogenetic analysis of various geographical isolates of P. westermani from Asia, so as to identify the possible genetic characteristics associated with the P. westermani phenotypes. METHODS: P. westermani metacercariae with different sizes (large metacercariae, 380-420 µm in diameter; small metacercariae, 320-340 µm) isolated from freshwater crabs were used to infect dogs, and the eggs and adult worms of P. westermani were collected from the dog stool samples and lung tissues. Then, the egg size and morphology were compared. In addition, genomic DNA was extracted from the adult worms of the two phenotypes of P. westermani and used for the PCR amplification to yield the complete mitochondrial genome sequence. Sequence structure and phylogenetic analyses were performed based on the complete mitochondrial genome of P. westermani. RESULTS: Following infection with large and small P. westermani metacercariae, the adult worms recovered from the dog lung had a thick body, and had oral and ventral suckers. The ventral sucker was located slightly in front of the midline of the body, and testes, ovary and vitelline gland were seen in the adult worms. Following fixation, the adults appeared oval, with an approximately 1.7∶1 of the length-width ratio. The length and width of the eggs isolated from the fecal samples of dogs infected with large and small P. westermani metacercariae varied significantly, and the large metacercariae produced bigger eggs than the smaller metacercariae. Based on the morphological features of adults and eggs and the ITS2 sequences, both phenotypes were identified as P. westermani. The complete mitochondrial genome sequence analysis of adults showed almost consistent sequences in the protein-coding region of the mitochondrial genome of adult worms derived from large and small metacercariae, with a major variation seen in the former non-coding region. Sliding window analysis revealed the most polymorphic region within the ND4 gene across the mitochondrial genome from various geographical isolates of P. westermani, and phylogenetic analysis showed that both phenotypes were clustered into the Chinese branch of P. westermani, which was close to the Japanese branch and distinct from the South/Southeast Asian branch. CONCLUSIONS: The genetic distance between the phenotypes of P. westermani isolated from Fujian Province is near at a mitochondrial genome level, with no remarkable genetic differentiation seen; however, the mutation and structural changes in the non-coding region may result in the phenotypic variations. In addition, there is a distinct variation of the evolutionary rate in the mitochondrial coding genes, suggesting the selection of appropriate molecular markers during the phylogenic researches.


Assuntos
Genoma Mitocondrial , Paragonimus westermani , Filogenia , Animais , Ásia , China , DNA de Helmintos/genética , Cães , Feminino , Genoma Mitocondrial/genética , Paragonimus westermani/classificação , Paragonimus westermani/genética
2.
J Parasitol ; 106(1): 71-81, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31995717

RESUMO

An unusual coccidian parasite was described previously from the prostate of a male Antechinus flavipes (family: Dasyuridae; common name: yellow-footed antechinus). Morphometrics and a partial nuclear 18S small subunit rDNA (18S rDNA) sequence were used to assign this parasite to the genus Eimeria; it was named Eimeria taggarti. We generated full nuclear 18S rDNA and mitochondrial genome sequences from this parasite and used the newly completed 18S rDNA and mitochondrial cytochrome c oxidase subunit I (COI) sequences to perform a more in-depth phylogenetic analysis. The parasite clustered closely with Choleoeimeria spp. and Acroeimeria spp. infecting herptiles in a well-supported clade that was the sister lineage to the Eimeriidae sensu stricto. The mitochondrial genome of this parasite contained 2 inverted segments compared to mitochondrial genomes from parasites in the Eimeriidae sensu stricto (i.e., Stieda body-possessing coccidia with 4 dizoic sporocysts); this mitochondrial genome arrangement was shared with the only Choleoeimeria species for which sequence data were available publicly. Examination of histological preparations and TEM images uncovered bivalvate sporocysts and otherwise confirmed previously described morphological features of the parasite. Based on our phylogenetic analyses and histological observations, we propose the generic reclassification of E. taggarti to Choleoeimeria taggarti n. comb.


Assuntos
Coccidiose/veterinária , Eimeriidae/genética , Genoma Mitocondrial/genética , Marsupiais/parasitologia , Próstata/parasitologia , Animais , Coccidiose/parasitologia , DNA de Protozoário/química , DNA Ribossômico/química , Eimeriidae/classificação , Eimeriidae/isolamento & purificação , Eimeriidae/ultraestrutura , Complexo IV da Cadeia de Transporte de Elétrons/genética , Masculino , Anotação de Sequência Molecular , Oocistos/ultraestrutura , Filogenia , Reação em Cadeia da Polimerase , RNA de Protozoário/genética , RNA Ribossômico 18S/genética , Alinhamento de Sequência
3.
Parasitol Res ; 119(2): 713-724, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31912276

RESUMO

Intra-leukocytic gamonts consistent with the description of Hepatozoon griseisciuri Clark, 1958 are reported for the first time in Canadian eastern gray squirrels (Sciurus carolinensis Gmelin, 1788). Polymerase chain reaction (PCR) amplification and direct Sanger sequencing identified a pair of distinct genotypes at both a nuclear and mitochondrial locus; two 18S ribosomal RNA gene sequences (rDNA; genotype A and genotype B: 1816 base pairs (bp); 98.8% pairwise identity) and 2 distinct complete mitochondrial genome sequences (genotype A: 6311 bp; genotype B: 6114 bp; 89.1% pairwise identity) were obtained from 3 H. griseisciuri-infected squirrels sampled in Guelph, Ontario. The genetic content of both circular-mapping mitochondrial genomes was conventional for apicomplexan protists; each encoded for 3 protein-coding genes (cytochrome c oxidase subunit I (COI); cytochrome c oxidase subunit III (COIII); and cytochrome B (CytB)), 14 fragmented large subunit rDNA, 10 fragmented small subunit rDNA, and 8 unassigned rDNA. These genotypes, based on sequences obtained from a pair of loci from two parasite genomes, confirm the presence of at least two Hepatozoon species infecting Ontario eastern gray squirrels, one of which is likely to be conspecific with H. griseisciuri.


Assuntos
Eucoccidiida/classificação , Eucoccidiida/genética , Sciuridae/parasitologia , Animais , Citocromos b/genética , DNA Ribossômico/genética , Complexo IV da Cadeia de Transporte de Elétrons/genética , Eucoccidiida/isolamento & purificação , Genoma Mitocondrial/genética , Genótipo , Tipagem de Sequências Multilocus , Ontário , Filogenia , RNA Ribossômico 18S/genética
4.
Hum Genet ; 139(3): 381-399, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31997134

RESUMO

Our cells operate based on two distinct genomes that are enclosed in the nucleus and mitochondria. The mitochondrial genome presumably originates from endosymbiotic bacteria. With time, a large portion of the original genes in the bacterial genome is considered to have been lost or transferred to the nuclear genome, leaving a reduced 16.5 Kb circular mitochondrial DNA (mtDNA). Traditionally only 37 genes, including 13 proteins, were thought to be encoded within mtDNA, its genetic repertoire is expanding with the identification of mitochondrial-derived peptides (MDPs). The biology of aging has been largely unveiled to be regulated by genes that are encoded in the nuclear genome, whereas the mitochondrial genome remained more cryptic. However, recent studies position mitochondria and mtDNA as an important counterpart to the nuclear genome, whereby the two organelles constantly regulate each other. Thus, the genomic network that regulates lifespan and/or healthspan is likely constituted by two unique, yet co-evolved, genomes. Here, we will discuss aspects of mitochondrial biology, especially mitochondrial communication that may add substantial momentum to aging research by accounting for both mitonuclear genomes to more comprehensively and inclusively map the genetic and molecular networks that govern aging and age-related diseases.


Assuntos
Envelhecimento/genética , DNA Mitocondrial/genética , Animais , Núcleo Celular/genética , Genoma Mitocondrial/genética , Genômica/métodos , Humanos , Longevidade/genética , Mitocôndrias/genética
5.
Gene ; 731: 144362, 2020 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-31935512

RESUMO

Acrididae family is characterized by diverse phylogenetic uncertainties, with different paraphyletic subfamilies. This study characterized the mitogenome of the grasshopper Rhammatocerus brasiliensis and determined its phylogenetic position in the family Acrididae. Sequencing was performed on an Illumina platform. The Short Oligonucleotide Analysis Package (SOAP) was used for genome assembly and the MITOS Web Server for annotation. Phylogenetic analysis was performed using mtDNA nucleic acid and protein sequences of R. brasiliensis and more 63 species belonging to 12 subfamilies of Acrididae. Phylogenetic trees were reconstructed using Bayesian inference with a relaxed molecular clock to estimate the speciation divergence time between taxa. The mitochondrial genome of R. brasiliensis has 15,571 bp of length, is rich in AT (72%), and contains 37 genes, including 13 protein-encoding genes, 22 genes encoding transfer RNA and two genes encoding ribosomal RNA. In addition, we also have annotated intergenic spacers and gene overlaps. The phylogenetic trees based on nucleic acid and amino acid sequences showed similar topologies. Phylogenetic analysis revealed that R. brasiliensis is grouped as an early offset of the Acrididae family. Phylogenetic analyses also corroborated the presence of several paraphyletic subfamilies in the family Acrididae including Gomphocerinae. The positioning of R. brasiliensis in the mtDNA phylogenetic tree further supports paraphyly of this subfamily. Moreover, the basal position of R. brasiliensis suggests that Gomphocerinae probably originated in South America.


Assuntos
Genoma Mitocondrial/genética , Gafanhotos/classificação , Gafanhotos/genética , Animais , Teorema de Bayes , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Filogenia , Análise de Sequência de DNA
6.
Gene ; 725: 144161, 2020 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-31639432

RESUMO

Bivalve species with doubly uniparental inheritance of mitochondria have been shown to contain additional mtDNA-encoded proteins suspected to be involved in sex-specific transmission of the female (F) and male (M) mitochondrial genomes. This is true for freshwater mussels and marine clams but was still unclear for marine mussel Mytilus spp. Here we present evidence that a F mtDNA-specific open reading frame (ORF) identified in the control region of M. edulis codes for a protein. The protein was detected, using western blots, in both female and male mantle tissues, which contain the gonads. The protein was also localized, using immunochemistry, in sperm mitochondria.


Assuntos
DNA Mitocondrial/genética , Mytilus/genética , Animais , Bivalves/genética , Feminino , Genoma Mitocondrial/genética , Masculino , Mitocôndrias/genética , Fases de Leitura Aberta/genética , Fatores Sexuais , Espermatozoides/metabolismo
7.
Parasitol Res ; 118(12): 3253-3265, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31729573

RESUMO

Metacercariae of Clinostomum Leidy, 1856 are frequently encountered in freshwater fish. In 2015, a provisional species of Clinostomum in People's Republic of China (PRC) was distinguished from C. complanatum (Rudolphi, 1819) in Europe based on divergent cytochrome c oxidase I (CO1). However, in subsequent studies in East Asia, the same divergent CO1 genotype was identified as C. complanatum. These matching sequences suggest that either the provisional East Asian species was incorrectly distinguished from C. complanatum in 2015 or that C. complanatum in East Asia was misidentified in later studies. We tested these alternatives by sequencing the mitochondrial genome of C. complanatum in Italy, which was 5.7% divergent from a previously published sequence from Clinostomum in PRC, including differences in 80 of 3390 (2.4%) translated amino acids. Partial CO1 sequences of specimens from PRC and those from Italy, Romania, and Turkey also each formed reciprocally monophyletic clades. Partial CO1 from the East Asian clade varied by mean 3.6% (range 2.4-4.8%) from C. complanatum from Italy, Romania, and Turkey; mean intra-clade CO1 variation was 0.3% (range 0-1.9%). Metacercariae from Europe and East Asia display significant morphometric variation, and data from the literature suggest morphological differences in the genital complex of adults. Although sequences of nuclear rDNA did not differ between isolates from the west and East Asia, taken together, these results lead us to describe a new species of Clinostomum.


Assuntos
Filogenia , Trematódeos/classificação , Animais , Ásia , DNA Ribossômico/genética , Peixes/parasitologia , Água Doce/parasitologia , Genoma Mitocondrial/genética , Metacercárias/anatomia & histologia , Metacercárias/classificação , Metacercárias/genética , Especificidade da Espécie , Trematódeos/anatomia & histologia , Trematódeos/genética
8.
BMC Genomics ; 20(1): 765, 2019 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-31640544

RESUMO

BACKGROUND: Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells. RESULTS: In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene. CONCLUSIONS: Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.


Assuntos
Agaricales/genética , Evolução Molecular , Genoma Mitocondrial/genética , Agaricales/classificação , Ascomicetos/classificação , Ascomicetos/genética , Basidiomycota/classificação , Basidiomycota/genética , DNA Mitocondrial/genética , Proteínas Fúngicas/genética , Ordem dos Genes , Variação Genética , Filogenia , Seleção Genética , Especificidade da Espécie
9.
Enzymes ; 45: 311-341, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31627882

RESUMO

Mitochondria play a central role in bioenergetics, and fulfill a plethora of functions in cell signaling, programmed cell death, and biosynthesis of key protein cofactors. Mitochondria harbor their own genomic DNA, which encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. Mitochondrial DNA (mtDNA) is essential for cellular and organismal functions, and defects in mitochondrial genome maintenance have been implicated in common human diseases and mitochondrial disorders. mtDNA repair and degradation are known pathways to cope with mtDNA damage; however, molecular factors involved in this process have remained unclear. Such knowledge is fundamental to the understanding of mitochondrial genomic maintenance and pathology, because mtDNA degradation may contribute to the etiology of mtDNA depletion syndromes and to the activation of the innate immune response by fragmented mtDNA. This article reviews the current literature regarding the importance of mitochondrial DNA degradation in mtDNA maintenance and stress response, and the recent progress in uncovering molecular factors involved in mtDNA degradation. These factors include key components of the mtDNA replication machinery, such as DNA polymerase γ, helicase Twinkle, and exonuclease MGME1, as well as a major DNA-packaging protein, mitochondrial transcription factor A (TFAM).


Assuntos
DNA Mitocondrial/metabolismo , Genoma Mitocondrial/genética , Estresse Fisiológico , Replicação do DNA , Humanos , Doenças Mitocondriais/genética , Doenças Mitocondriais/patologia
10.
Parasit Vectors ; 12(1): 490, 2019 Oct 17.
Artigo em Inglês | MEDLINE | ID: mdl-31623679

RESUMO

BACKGROUND: The monogenean Benedenia seriolae parasitizes fishes belonging to the genus Seriola, represents a species complex, and causes substantial impact on fish welfare in aquaculture systems worldwide. This study reports, for the first time, the complete mitochondrial genome of B. humboldti n. sp., a new cryptic species from the South-East Pacific (SEP). METHODS: The mitogenome of B. humboldti n. sp. was assembled from short Illumina 150 bp pair-end reads. The phylogenetic position of B. humboldti n. sp. among other closely related congeneric and confamiliar capsalids was examined using mitochondrial protein-coding genes (PCGs). Morphology of B. humboldti n. sp. was examined based on fixed and stained specimens. RESULTS: The AT-rich mitochondrial genome of B. humboldti is 13,455 bp in length and comprises 12 PCGs (atp8 was absent as in other monogenean genomes), 2 ribosomal RNA genes, and 22 transfer RNA genes. All protein-coding, ribosomal RNA, and transfer RNA genes are encoded on the H-strand. The gene order observed in the mitochondrial genome of B. humboldti n. sp. was identical to that of B. seriolae from Japan but different from that of B. seriolae from Australia. The genetic distance between B. humboldti n. sp. and B. seriolae from Japan was high. Minor but reliable differences in the shape of the penis were observed between Benedenia humboldti n. sp. and congeneric species. CONCLUSIONS: Phylogenetic analyses based on PCGs in association with differences in the shape of the penis permitted us to conclude that the material from the South-East Pacific represents a new species of Benedenia infecting S. lalandi off the coast of Chile. The discovery of this parasite represents the first step to improving our understanding of infestation dynamics and to develop control strategies for this pathogen infecting the farmed yellowtail kingfish, Seriola lalandi, in the South-East Pacific.


Assuntos
Doenças dos Peixes/parasitologia , Genoma Mitocondrial/genética , Platelmintos/genética , Dermatopatias Parasitárias/veterinária , Infecções por Trematódeos/veterinária , Animais , Doenças dos Peixes/epidemiologia , Peixes , Genes de RNAr , Anotação de Sequência Molecular , Oceano Pacífico/epidemiologia , Filogenia , Platelmintos/anatomia & histologia , Platelmintos/classificação , RNA de Transferência/química , RNA de Transferência/genética , Dermatopatias Parasitárias/epidemiologia , Dermatopatias Parasitárias/parasitologia , Sequências de Repetição em Tandem/genética , Infecções por Trematódeos/epidemiologia , Infecções por Trematódeos/parasitologia
11.
BMC Plant Biol ; 19(1): 448, 2019 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-31653201

RESUMO

BACKGROUND: Organelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome (mitogenome) sequences of Fabaceae have been published, all but four of which belong to the subfamily Papilionoideae, limiting the understanding of size variation and content across the family. To address this, four mitogenomes were sequenced and assembled from three different subfamilies (Cercidoideae, Detarioideae and Caesalpinioideae). RESULTS: Phylogenetic analysis based on shared mitochondrial protein coding regions produced a fully resolved and well-supported phylogeny that was completely congruent with the plastome tree. Comparative analyses suggest that two kinds of mitogenome expansions have occurred in Fabaceae. Size expansion of four genera (Tamarindus, Libidibia, Haematoxylum, and Leucaena) in two subfamilies (Detarioideae and Caesalpinioideae) occurred in relatively deep nodes, and was mainly caused by intercellular gene transfer and/or interspecific horizontal gene transfer (HGT). The second, more recent expansion occurred in the Papilionoideae as a result of duplication of native mitochondrial sequences. Family-wide gene content analysis revealed 11 gene losses, four (rps2, 7, 11 and 13) of which occurred in the ancestor of Fabaceae. Losses of the remaining seven genes (cox2, rpl2, rpl10, rps1, rps19, sdh3, sdh4) were restricted to specific lineages or occurred independently in different clades. Introns of three genes (cox2, ccmFc and rps10) showed extensive lineage-specific length variation due to large sequence insertions and deletions. Shared DNA analysis among Fabaceae mitogenomes demonstrated a substantial decay of intergenic spacers and provided further insight into HGT between the mimosoid clade of Caesalpinioideae and the holoparasitic Lophophytum (Balanophoraceae). CONCLUSION: This study represents the most exhaustive analysis of Fabaceae mitogenomes so far, and extends the understanding the dynamic variation in size and gene/intron content. The four newly sequenced mitogenomes reported here expands the phylogenetic coverage to four subfamilies. The family has experienced multiple mitogenome size fluctuations in both ancient and recent times. The causes of these size variations are distinct in different lineages. Fabaceae mitogenomes experienced extensive size fluctuation by recruitment of exogenous DNA and duplication of native mitochondrial DNA.


Assuntos
Fabaceae/genética , Tamanho do Genoma , Genoma Mitocondrial/genética , Mitocôndrias/genética
12.
Integr Comp Biol ; 59(4): 856-863, 2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31504533

RESUMO

Eukaryotes are the outcome of an ancient symbiosis and as such, eukaryotic cells fundamentally possess two genomes. As a consequence, gene products encoded by both nuclear and mitochondrial genomes must interact in an intimate and precise fashion to enable aerobic respiration in eukaryotes. This genomic architecture of eukaryotes is proposed to necessitate perpetual coevolution between the nuclear and mitochondrial genomes to maintain coadaptation, but the presence of two genomes also creates the opportunity for intracellular conflict. In the collection of papers that constitute this symposium volume, scientists working in diverse organismal systems spanning vast biological scales address emerging topics in integrative, comparative biology in light of mitonuclear interactions.


Assuntos
Coevolução Biológica , Núcleo Celular/fisiologia , Eucariotos/fisiologia , Genoma Mitocondrial/fisiologia , Adaptação Biológica , Núcleo Celular/genética , Eucariotos/genética , Genoma Mitocondrial/genética
13.
BMC Genomics ; 20(1): 691, 2019 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-31477008

RESUMO

BACKGROUND: Mitochondria perform many key roles in their eukaryotic hosts, from integrating signaling pathways through to modulating whole organism phenotypes. The > 1 billion years of nuclear and mitochondrial gene co-evolution has necessitated coordinated expression of gene products from both genomes that maintain mitochondrial, and more generally, eukaryotic cellular function. How mitochondrial DNA (mtDNA) variation modifies host fitness has proved a challenging question but has profound implications for evolutionary and medical genetics. In Drosophila, we have previously shown that recently diverged mtDNA haplotypes within-species can have more impact on organismal phenotypes than older, deeply diverged haplotypes from different species. Here, we tested the effects of mtDNA haplotype variation on gene expression in Drosophila under standardized conditions. Using the Drosophila Genetic Reference Panel (DGRP), we constructed a panel of mitonuclear genotypes that consists of factorial variation in nuclear and mtDNA genomes, with mtDNAs originating in D. melanogaster (2x haplotypes) and D. simulans (2x haplotypes). RESULTS: We show that mtDNA haplotype variation unequivocally alters nuclear gene expression in both females and males, and mitonuclear interactions are pervasive modifying factors for gene expression. There was appreciable overlap between the sexes for mtDNA-sensitive genes, and considerable transcriptional variation attributed to particular mtDNA contrasts. These genes are generally found in low-connectivity gene co-expression networks, occur in gene clusters along chromosomes, are often flanked by non-coding RNA, and are under-represented among housekeeping genes. Finally, we identify the giant (gt) transcription factor motif as a putative regulatory sequence associated with mtDNA-sensitive genes. CONCLUSIONS: There are predictive conditions for nuclear genes that are influenced by mtDNA variation.


Assuntos
Núcleo Celular/genética , Drosophila/genética , Redes Reguladoras de Genes/genética , Genoma Mitocondrial/genética , Motivos de Aminoácidos/genética , Animais , Núcleo Celular/metabolismo , Drosophila/crescimento & desenvolvimento , Feminino , Regulação da Expressão Gênica , Redes Reguladoras de Genes/fisiologia , Genes Essenciais/genética , Genes Essenciais/fisiologia , Variação Genética , Genótipo , Haplótipos , Masculino , Família Multigênica , Fenótipo , Mapas de Interação de Proteínas/genética , Mapas de Interação de Proteínas/fisiologia , RNA não Traduzido/genética , RNA não Traduzido/metabolismo , Transcriptoma
14.
DNA Cell Biol ; 38(11): 1257-1268, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31553224

RESUMO

Recent analyses suggest bacterial and/or mitochondrion-like ancestry for giant viruses (Megavirales sensu latu): amoeban mitochondrial gene arrangements resemble those of their candidate homologs in megaviral genomes. This presumed ancestral synteny decreases with genome size across megaviral families at large and within Poxviridae. In this study, analyses focus on Phycodnaviridae, a polyphyletic group of giant viruses infecting Haplophyta, Stramenopiles, and other algae, using syntenies between algal mitogene arrangements and chloroplast genomes and Rickettsia prowazekii as positive controls. Mitogene alignment qualities with Rickettsia are much higher than with viral genomes. Mitogenome synteny with some viruses is higher, for others lower than with Rickettsia, despite lower alignments qualities. In some algae, syntenies among cohosted chloroplast, virus, and mitochondrion are higher, in others lower than expected. This suggests gene order coevolution in cohosted genomes, different coregulations of organelle metabolisms for different algae, and viral mitogenome mimicry, to hijack organelle-committed cellular resources and/or escape cellular defenses/genetic immunity systems. This principle might explain high synteny between human mitochondria and the pathogenic endocellular alphaproteobacterium R. prowazekii beyond common ancestry. Results indicate that putative bacteria/mitochondrion-like genomic ancestors of Phycodnaviridae originated before or at the mitochondrion-bacteria split, and ulterior functional constraints on gene arrangements of cohosted genomes.


Assuntos
Cloroplastos/genética , Evolução Molecular , Mitocôndrias/genética , Mimetismo Molecular/fisiologia , Phycodnaviridae/genética , Sintenia/genética , Imunidade Adaptativa/genética , Genoma Mitocondrial/genética , Genoma Viral/genética , Interações Hospedeiro-Patógeno/genética , Interações Hospedeiro-Patógeno/imunologia , Evasão da Resposta Imune/genética , Organelas/genética , Filogenia , Análise de Sequência de DNA
15.
Parasitol Res ; 118(10): 3091-3097, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31418114

RESUMO

Echinostomes are important intestinal foodborne parasites. Despite their significance as pathogens, characterization of the molecular biology and phylogenetics of these parasites are limited. In the present study, we determined the entire mitochondrial (mt) genome of the echinostome Echinostoma miyagawai (Hunan isolate) and examined the phylogenetic relationship with selected members of the suborder Echinostomata. The complete mt genome of E. miyagawai (Hunan isolate) was 14,468 bp in size. This circular mt genome contained 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding region. The gene order and genomic content were identical with its congeners. Phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) based on the concatenated amino acid sequences of 12 protein-coding genes strongly supported monophyly for the genus Echinostoma; however, they rejected monophyly for the family Echinostomatidae and the genus Fasciola. The mt genomic data described in this study provides useful genetic markers for studying the population genetics, molecular biology, and phylogenetics of these echinostomes.


Assuntos
Echinostoma/classificação , Echinostoma/genética , Genoma Mitocondrial/genética , Filogenia , Sequência de Aminoácidos , Animais , DNA de Helmintos/genética , DNA Mitocondrial/genética , Ordem dos Genes , Proteínas de Helminto/química , Proteínas de Helminto/genética , Análise de Sequência de DNA
16.
PLoS Genet ; 15(8): e1008373, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31469821

RESUMO

Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held view across the broad community of life scientists that circular genome-sized molecules are the primary form of plant mitochondrial DNA, despite the understanding by plant mitochondrial researchers that this is an inaccurate and outdated concept. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sites for inter- or intramolecular recombination, leading to multiple alternative arrangements (isoforms). Most mitochondrial genomes have been assembled using methods unable to capture the complete spectrum of isoforms within a species, leading to an incomplete inference of their structure and recombinational activity. To document and investigate underlying reasons for structural diversity in plant mitochondrial DNA, we used long-read (PacBio) and short-read (Illumina) sequencing data to assemble and compare mitochondrial genomes of domesticated (Lactuca sativa) and wild (L. saligna and L. serriola) lettuce species. We characterized a comprehensive, complex set of isoforms within each species and compared genome structures between species. Physical analysis of L. sativa mtDNA molecules by fluorescence microscopy revealed a variety of linear, branched, and circular structures. The mitochondrial genomes for L. sativa and L. serriola were identical in sequence and arrangement and differed substantially from L. saligna, indicating that the mitochondrial genome structure did not change during domestication. From the isoforms in our data, we infer that recombination occurs at repeats of all sizes at variable frequencies. The differences in genome structure between L. saligna and the two other Lactuca species can be largely explained by rare recombination events that rearranged the structure. Our data demonstrate that representations of plant mitochondrial genomes as simple, circular molecules are not accurate descriptions of their true nature and that in reality plant mitochondrial DNA is a complex, dynamic mixture of forms.


Assuntos
Mapeamento Cromossômico/métodos , Genoma de Planta/genética , Mitocôndrias/genética , DNA Mitocondrial/genética , DNA de Plantas/genética , Genes de Plantas/genética , Genoma Mitocondrial/genética , Alface/genética , Recombinação Genética/genética , Análise de Sequência de DNA/métodos
17.
Mol Biol (Mosk) ; 53(4): 627-637, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31397436

RESUMO

The woolly mammoth mitochondrial genome (including the Malolyakhovsky mammoth) has been previously sequenced, followed by the annotation of all its genes (MF770243). In this study, based on the Malolyakhovsky mammoth, we describe for the first time the sites of functional significance in the control region of the woolly mammoth mitogenome.


Assuntos
DNA Mitocondrial/genética , Fósseis , Genoma Mitocondrial/genética , Região de Controle de Locus Gênico/genética , Mamutes/genética , Animais
18.
Int J Biol Macromol ; 138: 292-301, 2019 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-31319083

RESUMO

The subfamily Amphinemurinae has five genera in China, with each genus of similar morphology. To gain a better understanding of architecture and evolution of mitogenome in Amphinemurinae, mitogenomes of eight species representing four genera (Amphinemura, Indonemoura, Protonemura and Sphaeronemoura) in the subfamily Amphinemurinae were sequenced, and a comparative mitogenomic analysis of five genera (including a published stonefly genus, Mesonemoura) was carried out. By comparative analysis, we found highly conserved genome organization of ten Amphinemurinae species including genome contents, gene order, nucleotide composition, codon usage, amino acid composition, as well as genome asymmetry. GC content was the most significant factor in determining codon bias among organisms. The Ka/Ks values for all PCGs were far lower than 1, indicating that these genes were evolving under purifying selection. We also found some important conserved stem and loop in the cloverleaf structure of tRNAs, and found conserved helices and loops in each domain of the secondary structure of rRNAs. The presence of structural elements in the control region is also discussed. The phylogenetic analyses indicated that within Amphinemurinae, Sphaeronemoura was assigned the sister group of Mesonemoura. Our analyses inferred a relationship within Euholognatha: ((Nemouridae + Notonemouridae) + (Taeniopterygidae + Capniidae) + Scopuridae) + Leuctridae.


Assuntos
Sequência Conservada , Genoma Mitocondrial/genética , Genômica , Insetos/genética , Animais , Evolução Molecular , Filogenia , RNA Ribossômico/genética , RNA de Transferência/genética
19.
Int J Biol Macromol ; 137: 767-773, 2019 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-31269414

RESUMO

In this study, the mitochondrial genomes of three Stenogastrinae species, Eustenogaster scitula, Liostenogaster nitidipennis and Parishnogaster mellyi were sequenced and annotated, and a total of 16 vespid mtgenomes are comparatively analyzed. Our results indicate that codon usage bias is mainly dominated by mutational pressure, and affected only slightly by natural selection. Selective pressure analysis of protein-coding genes (PCGs) shows that the highest evolutionary rate is present in NADH complex I, and the lowest in cox1. Compared with the reported mtgenomes of other Vespidae, in Stenogastrinae, trnH is shifted to a new position. Phylogenetic analyses are performed using Bayesian method and Maximum Parsimony. Phylogenetic analysis further confirms that the Stenogastrinae is the sister group of all remaining Vespidae. Divergence time of Stenogastrinae from other Vespidae is estimated at ~ 166 Mya. Our results also support that eusociality evolved twice in the family Vespidae.


Assuntos
Genoma Mitocondrial/genética , Himenópteros/genética , Filogenia , Animais , Rearranjo Gênico , Genômica
20.
BMC Biol ; 17(1): 53, 2019 07 08.
Artigo em Inglês | MEDLINE | ID: mdl-31286943

RESUMO

Perturbed mitochondrial bioenergetics constitute a core pillar of cancer-associated metabolic dysfunction. While mitochondrial dysfunction in cancer may result from myriad biochemical causes, a historically neglected source is that of the mitochondrial genome. Recent large-scale sequencing efforts and clinical studies have highlighted the prevalence of mutations in mitochondrial DNA (mtDNA) in human tumours and their potential roles in cancer progression. In this review we discuss the biology of the mitochondrial genome, sources of mtDNA mutations, and experimental evidence of a role for mtDNA mutations in cancer. We also propose a 'metabolic licensing' model for mtDNA mutation-derived dysfunction in cancer initiation and progression.


Assuntos
DNA Mitocondrial/genética , Genoma Mitocondrial/genética , Mutação , Neoplasias/genética , Animais , Carcinogênese/genética , DNA Mitocondrial/metabolismo , Progressão da Doença , Humanos , Camundongos , Neoplasias/metabolismo
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