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1.
Mol Biol Rep ; 51(1): 390, 2024 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-38446255

RESUMO

BACKGROUD: Paecilomyces variotii has important economic value in stimulating crop growth, biodegradation, and other aspects. Up to now, there are no research reports on its mitochondrial genome. METHODS AND RESULTS: The mitochondrial genome of Paecilomyces variotii was determined with the next-generation sequencing method (Illumina, NovaSeq), and its characteristics were analyzed using various bioinformatics approaches. The length of complete mitochondrial genome sequence of P. variotii is 40,965 bp and consists of 14 protein-coding genes, 2 ribosomal RNA genes, 1 ribosomal protein S3 gene, 26 transport RNA genes. The results of phylogenetics analysis using Bayesian inference and Maximum likelihood methods showed that P. variotii belongs to the Eurotiales order in the Thermoascaceae family, and 9 genera within the Eurotiomycetes class were effectively distinguished with high support rates (bootstrap value > 92% and posterior probabilities > 99%). The analysis of synonymous substitution rates and nonsynonymous substitution rates indicated that the Ka/Ks values of the 14 PCGs in the mitochondrial genomes of the two orders in the Eurotiomycetes class ranged from 0 to 0.4333. CONCLUSIONS: This study revealed the structural and sequence information characteristics of the mitochondrial genome of P. variotii, and the phylogenetic results strongly support its classification within the family Thermoascaceae, consistent with traditional morphological taxonomy studies. The 14 PCGs in the mitochondrial genomes of the two orders in the Eurotiomycetes class are subject to strong purifying (negative) selection. The results of this research provides an important molecular basis for the development of genomics, evolutionary genetics and molecular markers of P. variotii in the future.


Assuntos
Byssochlamys , Genoma Mitocondrial , Genoma Mitocondrial/genética , Filogenia , Teorema de Bayes , Fungos
2.
J Helminthol ; 97: e69, 2023 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-37655787

RESUMO

New data on the complete mitochondrial genome of Azygia robusta (Azygiidae) were obtained by the next-generation sequencing (NGS) approach. The mitochondrial DNA (mtDNA) of A. robusta had a length of 13 857 bp and included 12 protein-coding genes, two ribosomal genes, 22 transfer RNA genes, and two non-coding regions. The nucleotide sequences of the complete mitochondrial genomes of two A. robusta specimens differed from each other by 0.12 ± 0.03%. Six of 12 protein-coding genes demonstrated intraspecific variation. The difference between the nucleotide sequences of the complete mitochondrial genomes of A. robusta and Azygia hwangtsiyui was 26.95 ± 0.35%; the interspecific variation of protein-coding genes between A. robusta and A. hwangtsiyui ranged from 20.5 ± 0.9% (cox1) to 30.7 ± 1.2% (nad5). The observed gene arrangement in the mtDNA sequence of A. robusta was identical to that of A. hwangtsiyui. Codon usage and amino acid frequencies were highly similar between A. robusta and A. hwangtsiyui. The results of phylogenetic analyses based on mtDNA protein-coding regions showed that A. robusta is closely related to A. hwangtsiyui (belonging to the same suborder, Azygiida) that formed a distinct early-diverging branch relative to all other Digenea. A preliminary morphological analysis of paratypes of the two azygiid specimens studied showed visible morphological differences between them. The specimen extracted from Sakhalin taimen (Parahucho perryi) was most similar to A. robusta. Thus, we here provide the first record of a new definitive host, P. perryi, for A. robusta and also molecular characteristics of the trematode specimens.


Assuntos
Salmonidae , Trematódeos , Filogenia , Salmonidae/parasitologia , Animais , DNA Mitocondrial/química , Análise de Sequência de DNA , Federação Russa , Trematódeos/anatomia & histologia , Trematódeos/classificação , Trematódeos/genética , Trematódeos/isolamento & purificação
3.
Mol Biol Rep ; 49(9): 9121-9127, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-35941414

RESUMO

BACKGROUND: The genus Trichoglossus belongs to the family Psittacidae and includes fourteen species distributed worldwide. According to the International Union for Conservation of Nature and Natural Resources (IUCN) Red List of Threatened Species, most Trichoglossus species have shown a decreasing population trend recently. In particular, Trichoglossus forsteni is listed as "Endangered" in the IUCN Red List of Threatened Species. Moreover, Trichoglossus haematodus and Trichoglossus moluccanus are one of the most traded and illegally traded parrots. However, only a few genetic studies have been conducted regarding the conservation of this genus. METHODS AND RESULTS: In the present study, complete mitochondrial genomes of three species (T. forsteni, T. haematodus, and T. moluccanus) were sequenced and compared with Trichoglossus rubritorquis, species whose mitochondrial genome is already reported. Results indicate that the complete mitochondrial genomes of the three species were similar in length (17,906 bp for T. haematodus to 17,909 bp for T. forsteni). Furthermore, the organization and order of these three mitochondrial genomes were identical, including thirteen protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and two control regions (CRs) categorized into three domains containing nine conserved motifs. In addition, the genus Trichoglossus formed a well-supported monophyletic lineage. CONCLUSIONS: The results of this study may be useful for future genetic studies toward the conservation of the genus Trichoglossus.


Assuntos
Genoma Mitocondrial , Papagaios , Animais , Sequência de Bases , Espécies em Perigo de Extinção , Genoma Mitocondrial/genética , Papagaios/genética , Filogenia , RNA de Transferência/genética
4.
Curr Issues Mol Biol ; 43(3): 1391-1418, 2021 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-34698117

RESUMO

The complete mitochondrial genomes (mitogenomes) of two DNA barcode-defined haplotypes of Metcalfa pruinosa and one of Salurnis marginella (Hemiptera: Flatidae) were sequenced and compared to those of other Fulgoroidea species. Furthermore, the mitogenome sequences were used to reconstruct phylogenetic relationships among fulgoroid families. The three mitogenomes, including that of the available species of Flatidae, commonly possessed distinctive structures in the 1702-1836 bp A+T-rich region, such as two repeat regions at each end and a large centered nonrepeat region. All members of the superfamily Fulgoroidea, including the Flatidae, consistently possessed a motiflike sequence (TAGTA) at the ND1 and trnS2 junction. The phylogenetic analyses consistently recovered the familial relationships of (((((Ricaniidae + Issidae) + Flatidae) + Fulgoridae) + Achilidae) + Derbidae) in the amino acid-based analysis, with the placement of Cixiidae and Delphacidae as the earliest-derived lineages of fulgoroid families, whereas the monophyly of Delphacidae was not congruent between tree-constructing algorithms.


Assuntos
Genoma Mitocondrial , Genômica , Hemípteros/classificação , Hemípteros/genética , Filogenia , Animais , Sequência de Bases , Biologia Computacional/métodos , Sequência Conservada , Código de Barras de DNA Taxonômico , DNA Espaçador Ribossômico , Rearranjo Gênico , Genes de Insetos , Genes Mitocondriais , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Motivos de Nucleotídeos
5.
Mol Biol Rep ; 48(2): 1995-2003, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33527322

RESUMO

The wild water buffalo (Bubalus arnee) is one of the most endangered and least studied large bovid in the Indian subcontinent. India retains 90% of the estimated global population of >4000 individuals as two fragmented populations in Assam and Chhattisgarh, both threatened by habitat loss and degradation, hunting, disease from livestock, and hybridization with the domestic buffalos. Small, fragmented population size and potential hybridisation pressures from co-occurring domestic buffalos are the major conservation challenges. For the first time, we sequenced the 16,357 bp long mitogenome of three opportunistically collected wild water buffalo samples from Assam (n = 1) and Chhattishgarh (n = 2). The annotated sequence has a base composition of 26.4% T, 26.6% C, 33.1% A and 13.9% G depicting an AT-rich mitogenome composition, including 13 protein-coding genes (11,361 bp), 22 transfer RNA (tRNA) (1514 bp), two ribosomal genes (2525 bp), and a non-coding control region (928 bp). The gene order is conserved with other bovid species. Comparative mitogenome analyses showed both populations are genetically similar but significantly different from domestic buffalo. We also identified structural differences in seven tRNA secondary structures between both species. The genetic distance between wild buffalo and other bovids varied between 0.103 and 0.122. Multiple Bayesian phylogenetic trees showed that both wild and domestic water buffalo formed sister clades which were paraphyletic to other potentially sympatric species of genus Bos. This study provides baseline information on wild buffalo mitogenome for further research on phylogeny, phylogeography and hybrid assessment and help conserving this endangered species.


Assuntos
Búfalos/genética , DNA Mitocondrial/genética , Espécies em Perigo de Extinção , Genoma Mitocondrial , Animais , Teorema de Bayes , Bovinos , Classificação , Genes de RNAr , Variação Genética , Índia , Proteínas Mitocondriais/genética , Filogenia , Filogeografia , Reação em Cadeia da Polimerase , RNA de Transferência/química , RNA de Transferência/genética , Análise de Sequência de DNA
6.
J Helminthol ; 94: e101, 2019 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-31679533

RESUMO

Tracheophilus cymbius (Trematoda: Cyclocoelidae) is a common tracheal fluke of waterfowl, causing serious loss in the poultry industry. However, taxonomic identification of T. cymbius remains controversial and confused. Mitochondrial (mt) genomes can provide genetic markers for the identification of closely related species. We determined the mt genome of T. cymbius and reconstructed phylogenies with other trematodes. The T. cymbius mt genome is 13,760 bp in size, and contains 12 protein-coding genes (cox 1-3, nad 1-6, nad 4L, cyt b and atp 6), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes and one non-coding region. All are transcribed in the same direction. The A + T content is 62.82%. ATG and TAG are the most common initiation and termination codons, respectively. Phylogenetic analyses of concatenated nucleotide sequences show T. cymbius grouping in suborder Echinostomata, and clustering together, with high statistical support, as a sister taxon with Echinochasmus japonicus (Echinochasmidae), the two forming a distinct branch rooted to the ancestor of all Echinostomatidae and Fasciolidae species. This is the first report of the T. cymbius mt genome, and the first reported mt genome within the family Cyclocoelidae. These data will provide a significant resource of molecular markers for studying the taxonomy, population genetics and systematics of trematodes.


Assuntos
Genoma Mitocondrial , Trematódeos/genética , Animais , Sequência de Bases , Genoma Helmíntico , Mitocôndrias/genética , Filogenia , Análise de Sequência de DNA , Trematódeos/classificação , Trematódeos/isolamento & purificação
7.
J Helminthol ; 93(5): 643-647, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-30132429

RESUMO

The parasite Cyathostomum pateratum, which occurs in the large intestine of equines, is a common species of the subfamily Cyathostominae. Cyathostominae nematodes are a complex nematode group for which only limited genetic information has been reported. To re-examine the phylogenetic relationships among Cyathostominae nematodes, we sequenced the complete mitochondrial (mt) genome of Cy. pateratum and compared it with the mt genome of the congeneric species Cyathostomum catinatum. The complete mtDNA sequence of Cy. pateratum was 13,822 bp in length, 16 bp shorter than that of Cy. catinatum. The mtDNA sequences of both species contained 12 protein-coding genes, two rRNA genes and 22 tRNA genes, and all 36 genes were transcribed in the same direction and in the same strand. Pairwise comparisons of the 12 predicted amino acid sequences between Cy. catinatum and Cy. pateratum revealed differences of 0.4-3.1%; the least conserved sequence was that of cytochrome c oxidase subunit 3 (cox3). Phylogenetic analysis of the concatenated amino acid sequences using Bayesian inference and maximum likelihood methods showed that Cy. catinatum and Cy. pateratum clustered together with very high nodal support, and Cylicostephanus goldi was closer to the Cyathostomum nematodes than to other Cyathostominae nematodes. The mtDNA sequence of Cy. pateratum is reported here for the first time. The study will shed some light on the genetic evolution among parasitic nematodes in Cyathostomum.


Assuntos
Evolução Molecular , Genoma Mitocondrial , Filogenia , Strongyloidea/classificação , Animais , Cavalos/parasitologia , Intestinos/parasitologia , Análise de Sequência de DNA
8.
Genetica ; 145(6): 559-573, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28942468

RESUMO

The complete mitochondrial genome sequences of Porzana fusca and Porzana pusilla were determined. The two avian species share a high degree of homology in terms of mitochondrial genome organization and gene arrangement. Their corresponding mitochondrial genomes are 16,935 and 16,978 bp and consist of 37 genes and a control region. Their PCGs were both 11,365 bp long and have similar structure. Their tRNA gene sequences could be folded into canonical cloverleaf secondary structure, except for tRNASer (AGY), which lost its "DHU" arm. Based on the concatenated nucleotide sequences of the complete mitochondrial DNA genes of 16 Rallidae species, reconstruction of phylogenetic trees and analysis of the molecular clock of P. fusca and P. pusilla indicated that these species from a sister group, which in turn are sister group to Rallina eurizonoides. The genus Gallirallus is a sister group to genus Lewinia, and these groups in turn are sister groups to genus Porphyrio. Moreover, molecular clock analyses suggested that the basal divergence of Rallidae could be traced back to 40.47 (41.46‒39.45) million years ago (Mya), and the divergence of Porzana occurred approximately 5.80 (15.16‒0.79) Mya.


Assuntos
Aves/genética , Genoma Mitocondrial , Animais , Evolução Biológica , Aves/classificação , China , DNA Mitocondrial , Filogenia , Análise de Sequência de DNA
9.
Exp Parasitol ; 172: 18-22, 2017 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-27915089

RESUMO

Cylicocyclus nassatus is a common and important parasite in the large intestine of equine. In this study, the complete mitochondrial (mt) genome sequence of C. nassatus was determined and comparatively analyzed with Cylicocyclus insigne. The mt genome size of C. nassatus was 13,846 bp, 18 bp longer than that of C. insigne. The circular mt genome includes 12 protein-coding genes, two rRNA genes, 22 tRNA genes and two non-coding regions. All the genes are transcribed in the same direction and gene arrangement is consistent with that of gene arrangement 3 (GA3). The overall sequence difference between the two complete mt genomes was 10.7%. For the 12 protein-coding genes, the comparison between C. nassatus and C. insigne revealed sequence divergence at both the nucleotide (6.3-13.0%) and amino acid (0.8-6.6%) levels. The nucleotide lengths of the 12 protein-coding genes were the same, except for cox3 which was longer in C. insigne. Phylogenetic analysis based on the concatenated amino acid sequence of the 12 protein-coding genes was performed using all the Strongylidae nematodes of the horse available in the GenBank. Phylogenetic analysis showed that C. nassatus and C. insigne clustered together with very high nodal support and the genus Cylicocyclus was closer to the genus Triodontophorus than to genus Strongylus. The mtDNA data determined in this study provides novel genetic markers for further studies on the identification, population genetics and molecular epidemiology of the genus Cylicocyclus.


Assuntos
Genoma Mitocondrial , Strongyloidea/genética , Animais , DNA de Helmintos/genética , DNA Mitocondrial/genética , Ordem dos Genes , Genes de Helmintos , Genoma Helmíntico , Doenças dos Cavalos/parasitologia , Cavalos , Filogenia , Análise de Sequência de DNA , Infecções por Strongylida/parasitologia , Infecções por Strongylida/veterinária , Strongyloidea/classificação
10.
Exp Parasitol ; 181: 88-93, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28803904

RESUMO

Triodontophorus serratus and Triodontophorus nipponicus are two of the most common nematodes inhabiting in the large intestine of horse. In the present study, the complete mitochondrial (mt) genome sequences of T. serratus and T. nipponicus have been determined. The mt genomes of T. serratus and T. nipponicus are circular molecules with 13,794 bp and 13,701 bp in size, respectively. These circular mt genomes encode 36 genes, including 12 protein-coding genes, two rRNA genes and 22 tRNA genes. All of these genes are transcribed in the same direction and gene arrangements are consistent with that of gene arrangement 3 (GA3-type). T. serratus and T. nipponicus had two non-coding regions, but T. brevicauda had three. Phylogenetic relationships were reconstructed using concatenated amino acid sequences of the 12 protein-coding genes with three methods, indicating that three species of Triodontophorus clustered together with strong statistical support. However, the genera of Strongylus and Triodontophorus belonged to Strongylinae do not cluster together, and Triodontophorus is more closely related to Cylicocyclus insigne, Cylicocyclus nassatus, Cylicostephanus goldi (Cyathostominae) than to Strongylus. The findings from the present study provide useful genetic markers for studying the molecular ecology, systematics, and population genetics of Triodontophorus in equine.


Assuntos
Genoma Mitocondrial , Doenças dos Cavalos/parasitologia , Infecções por Strongylida/veterinária , Strongyloidea/genética , Animais , Composição de Bases , Ceco/parasitologia , Colo/parasitologia , DNA de Helmintos/química , DNA Mitocondrial/química , Ordem dos Genes , Genoma Mitocondrial/genética , Cavalos , Filogenia , Infecções por Strongylida/parasitologia , Strongyloidea/classificação
11.
Breed Sci ; 67(4): 357-362, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29085245

RESUMO

The complete sequence of the mitochondrial genome was determined for two cultivars of Brassica rapa. After determining the sequence of a Chinese cabbage variety, 'Oushou hakusai', the sequence of a mizuna variety, 'Chusei shiroguki sensuji kyomizuna', was mapped against the sequence of Chinese cabbage. The precise sequences where the two varieties demonstrated variation were ascertained by direct sequencing. It was found that the mitochondrial genomes of the two varieties are identical over 219,775 bp, with a single nucleotide polymorphism (SNP) between the genomes. Because B. rapa is the maternal species of an amphidiploid crop species, Brassica juncea, the distribution of the SNP was observed both in B. rapa and B. juncea. While the mizuna type SNP was restricted mainly to cultivars of mizuna (japonica group) in B. rapa, the mizuna type was widely distributed in B. juncea. The finding that the two Brassica species have these SNP types in common suggests that the nucleotide substitution occurred in wild B. rapa before both mitotypes were domesticated. It was further inferred that the interspecific hybridization between B. rapa and B. nigra took place twice and resulted in the two mitotypes of cultivated B. juncea.

12.
Asian-Australas J Anim Sci ; 30(7): 930-937, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-28111450

RESUMO

OBJECTIVE: The I pig is a long nurtured longstanding breed in Vietnam, and contains excellent indigenous genetic resources. However, after 1970s, I pig breeds have become a small population because of decreasing farming areas and increasing pressure from foreign breeds with a high growth rate. Thus, there is now the risk of the disappearance of the I pigs breed. The aim of this study was to focus on classifying and identifying the I pig genetic origin and supplying molecular makers for conservation activities. METHODS: This study sequenced the complete mitochondrial genome and used the sequencing result to analyze the phylogenetic relationship of I pig with Asian and European domestic pigs and wild boars. The full sequence was annotated and predicted the secondary tRNA. RESULTS: The total length of I pig mitochondrial genome (accession number KX094894) was 16,731 base pairs, comprised two rRNA (12S and 16S), 22 tRNA and 13 mRNA genes. The annotation structures were not different from other pig breeds. Some component indexes as AT content, GC, and AT skew were counted, in which AT content (60.09%) was smaller than other pigs. We built the phylogenetic trees from full sequence and D loop sequence using Bayesian method. The result showed that I pig, Banna mini, wild boar (WB) Vietnam and WB Hainan or WB Korea, WB Japan were a cluster. They were a group within the Asian clade distinct from Chinese pigs and other Asian breeds in both phylogenetic trees (0.0004 and 0.0057, respectively). CONCLUSION: These results were similar to previous phylogenic study in Vietnamese pig and showed the genetic distinctness of I pig with other Asian domestic pigs.

13.
Curr Genet ; 62(4): 873-885, 2016 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-27016941

RESUMO

Cytoplasmic male-sterility (CMS) conferred by the CMS-S cytoplasm has been most commonly used for onion (Allium cepa L.) F1 hybrid seed production. We first report the complete mitochondrial genome sequence containing CMS-S cytoplasm in this study. Initially, seven contigs were de novo assembled from 150-bp paired-end raw reads produced from the total genomic DNA using the Illumina NextSeq500 platform. These contigs were connected into a single circular genome consisting of 316,363 bp (GenBank accession: KU318712) by PCR amplification. Although all 24 core protein-coding genes were present, no ribosomal protein-coding genes, except rps12, were identified in the onion mitochondrial genome. Unusual trans-splicing of the cox2 gene was verified, and the cox1 gene was identified as part of the chimeric orf725 gene, which is a candidate gene responsible for inducing CMS. In addition to orf725, two small chimeric genes were identified, but no transcripts were detected for these two open reading frames. Thirteen chloroplast-derived sequences, with sizes of 126-13,986 bp, were identified in the intergenic regions. Almost 10 % of the onion mitochondrial genome was composed of repeat sequences. The vast majority of repeats were short repeats of <100 base pairs. Interestingly, the gene encoding ccmFN was split into two genes. The ccmF N gene split is first identified outside the Brassicaceae family. The breakpoint in the onion ccmF N gene was different from that of other Brassicaceae species. This split of the ccmF N gene was also present in 30 other Allium species. The complete onion mitochondrial genome sequence reported in this study would be fundamental information for elucidation of onion CMS evolution.


Assuntos
Genes de Plantas , Genoma Mitocondrial , Genômica , Cebolas/genética , Sequência de Bases , Análise por Conglomerados , Biologia Computacional/métodos , Evolução Molecular , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Fases de Leitura Aberta , Filogenia , Transcrição Gênica
14.
Zoolog Sci ; 33(5): 566-574, 2016 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-27715413

RESUMO

The Mugilogobius group consists of brackish water gobionellines widely distributed in the Indo-West Pacific region. Complete mitochondrial genome and morphological evidence was collected to estimate their phylogenetic relationship and taxonomic status. A total of 11 genera were sampled, including Brachygobius, Calamiana, Hemigobius, Mugilogobius, Pandaka, Pseudogobiopsis, Pseudogobius, Redigobius, Rhinogobius, Stigmatogobius, and Wuhanlinigobius, five of which were sequenced for the first time. A morphological phylogenetic tree was also reconstructed based on 35 characters. The molecular phylogenetic trees reveal that the Mugilogobius group contains four major clades. The present study also reveals that the adult male mouth size and forked sensory papillae row d can be considered as synapomorphies, and that the head pores on inter-orbital, anterior oculoscapular, and preopercular regions can be regarded as derived features among the Mugilogobius group. Furthermore, the absence of posterior oculoscapular pores may provide a clue for understanding the evolutionary history of the Mugilogobius group.


Assuntos
DNA Mitocondrial/genética , Peixes/genética , Animais , Peixes/anatomia & histologia , Masculino , Filogenia , Águas Salinas
15.
Exp Parasitol ; 169: 22-7, 2016 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-27423970

RESUMO

Ticks are obligate blood-sucking ectoparasites of a wide range of vertebrates. They can transmit a range of pathogens that cause economic losses to livestock production as well as human disease. In the present study, the complete mitochondrial (mt) genome of Dermacentor silvarum was determined. The mt genome is 14,945 bp in length contains 37 genes, including 13 are protein-coding genes (cox1-3, nad1-6, nad4L, cytb, atp6 and atp8), two ribosomal RNA genes and 22 transfer RNA genes. The nucleotide composition of the D. silvarum mt genome was A + T biased at 78.78%; T was the most abundant nucleotide and G the least abundant. The mt genome of D. silvarum was 106 bp longer than that of Dermacentor nitens and the arrangements of two genomes were identical. For the 13 protein-coding genes, comparison between D. silvarum and D. nitens revealed sequence divergence at both the nucleotide (15.46-35.14%) and amino acid (6.05-48.98%) levels. Among them, cox1 was the most conserved gene, while atp8 was the least conserved. The lengths of the 13 protein-coding genes were the same or similar, except for cytb which was significantly longer in D. silvarum than in D. nitens. The mtDNA contained a variable repeat region consisting of a "similar to nad1" motif that was repeated three times, and the "Tick-box" motifs were also found. The overall difference between the nucleotide sequences of the two complete mt genomes was 21.4%. The mtDNA data presented in this study provide a rich resource for further studies on the phylogenetics, population genetics, and molecular epidemiology of ticks.


Assuntos
DNA Mitocondrial/química , Dermacentor/genética , Genoma Mitocondrial/genética , Animais , Composição de Bases , Sequência de Bases/genética , Bovinos , Dermacentor/classificação , Repetições Minissatélites , Anotação de Sequência Molecular , Reação em Cadeia da Polimerase , Proteínas/genética , RNA Ribossômico/genética , RNA de Transferência/genética
16.
Genome ; 57(11-12): 577-82, 2014 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-25767903

RESUMO

Crop species of Brassica (Brassicaceae) consist of three monogenomic species and three amphidiploid species resulting from interspecific hybridizations among them. Until now, mitochondrial genome sequences were available for only five of these species. We sequenced the mitochondrial genome of the sixth species, Brassica nigra (nuclear genome constitution BB), and compared it with those of Brassica oleracea (CC) and Brassica carinata (BBCC). The genome was assembled into a 232 145 bp circular sequence that is slightly larger than that of B. oleracea (219 952 bp). The genome of B. nigra contained 33 protein-coding genes, 3 rRNA genes, and 17 tRNA genes. The cox2-2 gene present in B. oleracea was absent in B. nigra. Although the nucleotide sequences of 52 genes were identical between B. nigra and B. carinata, the second exon of rps3 showed differences including an insertion/deletion (indel) and nucleotide substitutions. A PCR test to detect the indel revealed intraspecific variation in rps3, and in one line of B. nigra it amplified a DNA fragment of the size expected for B. carinata. In addition, the B. carinata lines tested here produced DNA fragments of the size expected for B. nigra. The results indicate that at least two mitotypes of B. nigra were present in the maternal parents of B. carinata.


Assuntos
Genoma Mitocondrial , Mostardeira/genética , Brassica/genética , Éxons , Genes Mitocondriais , Variação Genética , Análise de Sequência de DNA
17.
Mitochondrial DNA B Resour ; 9(1): 214-218, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38298223

RESUMO

The flightless intertidal beetle genus Aegialites (family Salpingidae) is distributed along the Northern Pacific coasts, from California to Alaska and from Northern Japan to Kamchatka. Systematics of Aegialites and its phylogenetic relationships to other members of Salpingidae are unclear, and little genetic information is available. We here present the first complete mitochondrial genome of this genus, represented by Aegialites californicus (Motchoulsky, 1845) from Sonoma County, California, U.S.A. The complete mitochondrial genome of A. californicus is 15,899 bp long and comprises 13 protein-coding (PCG), two ribosomal RNA (rRNA) and 22 transfer RNA (tRNA) genes. The phylogenetic analysis places A.californicus as sister to other members of family Salpingidae. The mitochondrial genome sequence of A. californicus will contribute to future phylogenetic and taxonomic studies of genus Aegialites, family Salpingidae and superfamily Tenebrionoidea.

18.
Mitochondrial DNA B Resour ; 9(9): 1218-1222, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39291128

RESUMO

Rattus tanezumi (Niethammer, 1975) is one of the commensal rodent species in South China. With the development of transportation and climate change, R. tanezumi has gradually migrated north and become the dominant rat species for the past few years. In this study, we assembled a complete mitochondrial genome of R. tanezumi, captured from North China. The mitogenome contains 16,307 nucleotide pairs, including 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, as well as one non-coding control region. Based on whole mitogenome phylogenetical analysis showed that R. tanezumi captured from North China had a close phylogenetic relationship with that from Japan and South Korea. These findings are valuable for further studies on the evolution, genetic diversity, and taxonomy of Asian commensal rodent.

19.
Mitochondrial DNA B Resour ; 9(6): 729-733, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38859914

RESUMO

The Sigara lateralis (Leach, 1817) is a small aquatic insect belonging to the family Corixidae. The study aims to reveal the genomic data of the mitochondrial genome of S. lateralis. The length of its circular mitochondrial genome is 15,725 bp long with an A + T bias (75.96%). The mitogenome comprises 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two rRNA genes. The phylogenetic analyses showed that the S. lateralis is the closest to S. septemlineata. These findings will help the conservation of Corixidae from the perspective of genetic evolution.

20.
Mitochondrial DNA B Resour ; 9(1): 178-181, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38288250

RESUMO

The complete mitochondrial genome of Tomocerus caputiviolaceus was sequenced and assembled. The complete mitochondrial genome is 15,519 bp in length. The mitogenome contained 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. In phylogenetic analysis based on the nucleotide sequences of 13 PCGs, T. caputiviolaceus is closely related to Tomocerus qinae Yu, Yao & Hu, 2016, both of which belong to the genus Tomocerus within the family Tomoceridae.

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