RESUMO
The age distribution of gene duplication events within the human genome exhibits two waves of duplications along with an ancient component. However, because of functional constraint differences, genes in different functional categories might show dissimilar retention patterns after duplication. It is known that genes in some functional categories are highly duplicated in the early stage of vertebrate evolution. However, the correlations of the age distribution pattern of gene duplication between the different functional categories are still unknown. To investigate this issue, we developed a robust pipeline to date the gene duplication events in the human genome. We successfully estimated about three-quarters of the duplication events within the human genome, along with the age distribution pattern in each Gene Ontology (GO) slim category. We found that some GO slim categories show different distribution patterns when compared to the whole genome. Further hierarchical clustering of the GO slim functional categories enabled grouping into two main clusters. We found that human genes located in the duplicated copy number variant regions, whose duplicate genes have not been fixed in the human population, were mainly enriched in the groups with a high proportion of recently duplicated genes. Moreover, we used a phylogenetic tree-based method to date the age of duplications in three signaling-related gene superfamilies: transcription factors, protein kinases and G-protein coupled receptors. These superfamilies were expressed in different subcellular localizations. They showed a similar age distribution as the signaling-related GO slim categories. We also compared the differences between the age distributions of gene duplications in multiple subcellular localizations. We found that the distribution patterns of the major subcellular localizations were similar to that of the whole genome. This study revealed the whole picture of the evolution patterns of gene functional categories in the human genome.
Assuntos
Evolução Molecular , Duplicação Gênica , Ontologia Genética , Genes , Família Multigênica , Distribuição por Idade , Genoma Humano , Humanos , Filogenia , Frações SubcelularesRESUMO
In this study, the complete mitochondrial genome of Parachaeturichthys polynema was reported. The mitochondrial genome was 16,620bp in length including 13 protein-coding genes, 23 tRNAs, 2 rRNAs, and a control region. The overall contents of A, T, G, and C were 28.56%, 26.34%, 16.22%, and 28.89%, respectively. Phylogenetic analysis of 18 species in the family Gobiidae showed that P. polynema was clustered into the subfamily Gobiinae. This information will contribute to future phylogenetic studies of P. polynema and Gobiidae.
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In this paper, we determined the complete mitochondrial DNA (mtDNA) sequence of Gobio coriparoides and analyzed its phylogenetic position. The complete mitogenome is 16,604 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. Among the 37 genes, 28 were encoded on the heavy strand, while 9 were encoded on the light strand. The overall base composition was 28.97% for A, 18.06% for G, 26.54% for T, and 26.43% for C, with a higher A + T content (55.51%). There are some overlaps existing in G. coriparoides mitochondrial genome. The neighbor-joining (NJ) phylogenetic tree based on whole mitogenome sequences supported that G. coriparoides is the closest to G. cynocephalus. This result will provide a basic reference for understanding the genetic structure, molecular evolution, and phylogeny of G. coriparoides and related species.
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Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light-strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA-Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination-associated sequence, six conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E, CSB-F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.
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In order to understand the genetic distinctness between four Coilia fishes,i.e., C. ectenes, C. e. taihuensis, C. mystus, and C. grayii, the combined cytochrome b (cytb), 12S rRNA and 16S rRNA gene sequences were obtained and analysed. The results are as follows: 1) neighbour-joining (NJ) and maximum parsimony (MP) trees were built with 1000 bootstrap replicates. They supported that Coilia fishes consisted of two clades: C. grayii form a monophyletic group, and the rest samples form the other monophyletic group; 2) the topological differences between the NJ tree and the MP tree are checked by Templeton test, indicating that their differences are insignificant (P > 0.05); and 3) Kimura-2-parameter distances between the samples of C. ectenes, C. e. taihuensis and C. mystus are all no bigger than 1.6%, and most of them are between 0.0% and 0.9%. C. ectenes, C. e. taihuensis and C. mystus are closely related and that their differences may be under subspecies.
Assuntos
DNA Mitocondrial/genética , Evolução Molecular , Peixes/genética , Variação Genética , Filogenia , AnimaisRESUMO
Half-fin anchovy (Setipinna tenuifilis) is one of the most important economic fishes around the world. In the present study, we determined the complete mitochondrial DNA sequence and organization of S. tenuifilis. The entire mitochondrial genome is a circular-molecule of 16,215 bp in length, which encodes 37 genes in all. These genes comprise 13 protein-coding genes (ATP6 and 8, COI-III, Cytb, ND1-6, and 4L), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (12S and 16S rRNAs), with gene arrangement and content basically identical to those of other species of Engraulidae. The result of phylogenetic analysis strongly supported that S. tenuifilis was first clustered together with Setipinna melanochir and formed a monophyly in the genus Coilia, and then they constituted a sister-group relationship with two genus Engraulis, and Stolephorus. It concluded that the S. tenuifilis should be classified into the genus Setipinna. The present study also revealed the phylogenetic relationship of this genus at molecular levels. The complete mitochondrial genome sequence of S. tenuifilis can provide basic information for the studies on molecular taxonomy and phylogeny of teleost fishes.
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Oyster reefs have important ecological functions and environmental service values, such as filtering water, providing fish habitats, maintaining biodiversity, and carbon sequestration. Oyster reef recovery has become one of the most important means for fishery resource conservation and ecosystems restoration of coastal regions. C. sikamea and C. ariakensis are two important reef oysters along the coast of China. However, it is very difficult to identify the larvae of these two oysters. To solve this problem, we developed two pairs of novel species-specific PCR primers for identifying these two oysters. The forward C. sikamea-specific primer is Cs-F: 5'-CGAAGAGGGGCATGATAAATGAGG-3', and the reverse primer is Cs-R: 5'-ATATGAACTTCTCCAACCTCCCC-3', both of them within the scope of mitochondrial ND5 gene. The forward C. ariakensis-specific primer is Ca-F: 5'-GGGCAAATAAAAGGCAAAACCC-3', located between tRNAser and tRNApro, and the reverse primer is Ca-R: 5'-CATAAACTTCTGCAAGACTCCC-3', lies between tRNApro and small subunit ribosomal RNA (ssrRNA). These two primers can identify the larvae of C. ariakensis and C. sikamea from other oysters rapidly and effectively, with extremely high accurate rate (=100%). This molecular identification method does not require prior sorting of larvae. These two specific primers are good contribution to molecular identification of C. sikamea, C. ariakensis and other oysters, and could be a useful tool for oyster larvae identification and ecological restoration.
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In this study, we obtained the complete mitochondrial genome sequence of Sphyraena jello and analyzed its phylogenetic position. The complete mitogenome of S. jello is 16 699 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Among the 37 genes, 28 were encoded on heavy strand, while 9 were encoded on light strand. The overall base composition was 28.97% for A, 16.14% for G, 29.64% for C, and 25.25% for T, with a higher A + T content (54.22%). The phylogenetic analysis based on 13 concatenated protein-coding genes suggested that S. jello is a sister species to Sphyraena barracuda in the family Sphyraenidae. This result should be useful for understanding the genetic structure, molecular evolution, and phylogeny of S. jello and related species.
Assuntos
Genoma Mitocondrial , Perciformes/genética , Animais , Composição de Bases , Códon de Iniciação , DNA Mitocondrial/química , DNA Mitocondrial/isolamento & purificação , DNA Mitocondrial/metabolismo , Proteínas de Peixes/química , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Fases de Leitura Aberta/genética , Perciformes/classificação , Filogenia , RNA Ribossômico/química , RNA Ribossômico/genética , RNA de Transferência/química , RNA de Transferência/genética , Análise de Sequência de DNARESUMO
The phylogeography history and contemporary agents of selection for many marine fisheries, characterized by widespread species distributions in the face of significant harvest, remains poorly understood. Chub mackerel (Scomber japonicus) are a widespread species in the Indo-Pacific and represent one of the top five commercially fished species in the world, yet their phylogeographic history remains unknown. We characterized the genetic diversity, structure and demographic history of S. japonicus throughout adjacent Chinese seas (from the Yellow Sea to the South China Sea). Using 220 individuals from 11 sites, we inferred 55 distinct haplotypes from complete mitochondrial cytochrome b gene sequences. Haplotype diversity ranged from 0.505 to 0.967 and nucleotide diversity ranged from 0.00056 to 0.01042. Genetic differentiation (Fst) statistics suggested that the highest level of differentiation existed between the SanYa and SanSha localities (Fst = 0.86977), while the lowest levels of differentiation occurred between the DongGang and ShiDao localities (Fst â¼ 0). Kimura's genetic distances ranged from 0.001 to 0.011 within and from 0.001 to 0.018 between populations. Hierarchical analysis of molecular variance, Neighbor-joining and median-joining network analyses identified significant phylogeographic structure with two localities (SanYa, Hainan of the South China Sea and LianYunGang, Jiangsu of the East China Sea) explaining most of the genetic variation observed, while the remaining populations were poorly differentiated.
Assuntos
Citocromos b/genética , Perciformes/genética , Animais , China , DNA Mitocondrial/química , DNA Mitocondrial/genética , Estruturas Genéticas , Variação Genética , Haplótipos , Mitocôndrias/genética , Proteínas Mitocondriais/genética , Oceanos e Mares , Filogeografia , Análise de Sequência de DNARESUMO
In this study, we sequenced and annotated the complete mitochondrial genome of Pampus argenteus (Perciformes: Stromateidae). The mitogenome is 17,098 bp in length, which contains 13 protein-coding genes, 2 rRNA genes, 23 tRNA genes and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The overall nucleotide base composition of P. argenteus mtDNA is A 30.35%, C 25.55%, G 15.28% and T 28.82%, with an A + T content of 59.17%. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. The mitochondrial genome of P. argenteus may be helpful to the studies on conservation genetics and stock evaluation of P. argenteus resource, as well as molecular phylogeny and species identification of Stromateidae.
Assuntos
Genoma Mitocondrial/genética , Perciformes/genética , Análise de Sequência de DNA , Animais , Genes de RNAr , Anotação de Sequência Molecular , Dados de Sequência Molecular , Fases de Leitura Aberta/genética , RNA de Transferência/genéticaRESUMO
Thunnus alalunga is an excellent food fish and is of great importance in recreational fisheries. In the study, the complete mitochondrial genome (mitogenome) of T. alalunga is sequenced and annotated, which is a circular DNA molecule with 16,527 bp in length. The overall nucleotide base composition of T. alalunga mitogenome is as follows: A, 28.37%; G, 16.69%; T, 25.46%; and C, 29.49%, with the A+T content of 53.83%, showing an obvious anti-G bias. The entire mitogenome encodes 37 genes in all, comprising 13 protein-coding genes (ATP6 and ATP8, COI-III, Cytb, ND1-6 and 4L), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (12S and 16S rRNAs). The complete mitochondrial genome sequence of T. alalunga can provide useful information for the studies on molecular systematics, stock evaluation, and conservation genetics of teleost fishes.
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Proteínas de Peixes/genética , Peixes/genética , Genoma Mitocondrial , Proteínas Mitocondriais/genética , RNA Ribossômico/genética , RNA de Transferência/genética , RNA/genética , Animais , RNA MitocondrialRESUMO
In this study, the complete mitochondrial genome of Pampus chinensis (Perciformes: Stromateidae) was determined. The mitogenome is 16,535 bp in length, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The overall mtDNA nucleotide base composition of P. chinensis is A 29.72%, C 28.10%, G 15.34%, and T 26.84%, with an A + T content of 56.56%. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. The mitochondrial genome of P. chinensis may be helpful to the studies on stock evaluation and conservation genetics of P. chinensis resource, as well as molecular phylogeny of Stromateidae.
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Genoma Mitocondrial/genética , Perciformes/genética , Análise de Sequência de DNA , Animais , DNA Mitocondrial/genética , Genes de RNAr/genética , Anotação de Sequência Molecular , Dados de Sequência Molecular , Fases de Leitura Aberta/genética , Filogenia , RNA de Transferência/genéticaRESUMO
Yellowfin tuna (Thunnus albacares) is one of the most important economic fishes around the world. In the present study, we determined the complete mitochondrial DNA sequence and organization of T. albacares. The entire mitochondrial genome is a circular-molecule of 16,528 bp in length, which encodes 37 genes in all. These genes comprise 13 protein-coding genes (ATP6 and 8, COI-III, Cytb, ND1-6 and 4 L), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (12S and 16S rRNAs). The complete mitochondrial genome sequence of T. albacares can provide basic information for the studies on molecular taxonomy and conservation genetics of teleost fishes.
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Genoma Mitocondrial , Genômica , Atum/classificação , Atum/genética , Animais , Composição de Bases , Códon , Genes Mitocondriais , Tamanho do Genoma , Genômica/métodos , Fases de Leitura Aberta , Análise de Sequência de DNA , Sequenciamento Completo do GenomaRESUMO
PURPOSE: Reduced expression of the transforming growth factor beta receptor type II (TGF beta RII), a key inhibitor of epithelial cell growth and tumor suppressor gene, was reported frequently in many types of tumors including non-small cell lung cancer (NSCLC). This study explored the significance of the TGF beta RII gene in NSCLC carcinogenesis. EXPERIMENTAL DESIGN: With 43 independent pairs of tumor and paracarcinoma tissue samples from patients with primary NSCLC, we carried out PCR-denaturing gradient gel electrophoresis screening for DNA variants over the coding sequence of the TGF beta RII gene, immunohistochemical assay of TGF beta RII expression, methylation-specific PCR analysis, and semiquantitative reverse transcription-PCR. RESULTS: The PCR-denaturing gradient gel electrophoresis did not detect variation in the whole coding sequence of the TGF beta RII gene, but the immunohistochemistry experiment revealed reduced or lost expression of the gene in 44% (19 of 43) of the tumor samples. The methylation analysis on the 19 pairs detected the frequent occurrence of methylated TGF beta RII promoter in tumor tissues, whereas most of the paracarcinoma tissues were free of methylation. The reduced TGF beta RII expression was highly significantly associated with the methylation event (P < 10(-4)). The reverse transcription-PCR analysis demonstrated a clear agreement between reduced TGF beta RII expression and decreased mRNA level of the gene in the tumor tissue samples. CONCLUSIONS: TGF beta RII plays an important role as a tumor suppressor in NSCLC carcinogenesis. The defective expression may serve as one of most important molecular mechanisms in explaining progression of the disease. In particular, aberrant 5' CpG methylation of the gene has explained the down-regulation of the gene at a transcriptional level.
Assuntos
Carcinoma Pulmonar de Células não Pequenas/genética , Ilhas de CpG , Metilação de DNA , Neoplasias Pulmonares/genética , Regiões Promotoras Genéticas , Receptores de Fatores de Crescimento Transformadores beta/biossíntese , Receptores de Fatores de Crescimento Transformadores beta/genética , Adulto , Idoso , Carcinoma Pulmonar de Células não Pequenas/metabolismo , DNA/química , Análise Mutacional de DNA , Regulação para Baixo , Éxons , Feminino , Humanos , Imuno-Histoquímica , Neoplasias Pulmonares/metabolismo , Masculino , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase , Proteínas Serina-Treonina Quinases , RNA Mensageiro/metabolismo , Receptor do Fator de Crescimento Transformador beta Tipo II , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Análise de Sequência de DNARESUMO
The complete mitochondrial DNA sequence of Gymnocypris namensis was determined and analyzed. The mitogenome of G. namensis is 16,674 bp long, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes and two non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The gene order of G. namensis mitogenome is identical to that observed in most other vertebrates. The complete mitogenome sequence information of G. namensis can provide useful data for further studies on molecular systematics, taxonomic status, stock evaluation and conservation genetics.
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Cyprinidae/genética , Genoma Mitocondrial/genética , Animais , Composição de Bases/genética , Sequência de Bases , Códon/genética , Ordem dos Genes/genética , Dados de Sequência Molecular , Análise de Sequência de DNA , Especificidade da Espécie , TibetRESUMO
Gymnocypris dobula is listed as Vulnerable (VU) status in the IUCN's Red List of Threatened Species. In this paper, complete mitochondrial DNA sequence of G. dobula was determined. The complete mitogenome is 16,720 bp in length, and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence information of G. dobula is conducive to futher studies on molecular systematics, stock evaluation and conservation genetics.
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Cyprinidae/genética , Genoma Mitocondrial/genética , Animais , Composição de Bases/genética , Sequência de Bases , China , Códon/genética , Ordem dos Genes/genética , Dados de Sequência Molecular , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
In this study, we determined the complete mitogenome sequence of Schizopygopsis thermalis. The complete mitogenome of S. thermalis is 16,676 bp in length, which contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mtDNA sequence of S. thermalis provides useful genetic markers for the studies on molecular systematic, population genetics and phylogeography.
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Cyprinidae/genética , Genoma Mitocondrial/genética , Animais , Composição de Bases/genética , Sequência de Bases , China , Códon/genética , Ordem dos Genes/genética , Dados de Sequência Molecular , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
Pelteobagrus fulvidraco (yellow catfish) is a small-sized species in the family Bagridae, order Siluriformes. In this study, we determined the complete mitogenome sequence of P. fulvidraco and performed phylogenetic analysis with closely related species. The complete mitochondrial genome of P. fulvidraco was 16,527 bp in length, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: control region (D-loop) and the origin of light-strand replication. We inferred that five markers in mitogenome, i.e. D-loop, ND5, 16SrRNA, COXI and ND1, may be suitable markers for studies on population genetics, phylogeny, conservation genetics and evolutionary adaptation mechanisms.
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Peixes-Gato/genética , Genoma Mitocondrial/genética , Filogenia , Animais , Composição de Bases/genética , Sequência de Bases , China , Análise por Conglomerados , Códon/genética , Evolução Molecular , Ordem dos Genes/genética , Marcadores Genéticos/genética , Modelos Genéticos , Dados de Sequência Molecular , Mutação/genética , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
In this paper, we determined complete mitochondrial DNA sequence of Schizopygopsis younghusbandi. The mitogenome is 16,674 bp in length, which includes 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes, and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence of S. younghusbandi is useful to the studies on taxonomic status, molecular systematics, stock evaluation, and conservation genetics.
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Cyprinidae/genética , DNA Mitocondrial/genética , Genes Mitocondriais/genética , Genoma Mitocondrial/genética , Animais , Composição de Bases/genética , Sequência de Bases , Ordem dos Genes/genética , Tamanho do Genoma/genética , Dados de Sequência Molecular , Análise de Sequência de DNARESUMO
In this study, we sequenced and annotated the complete mitochondrial genome of Schizothorax waltoni (Cypriniformes:Cyprinidae). The mitogenome is 16,587 bp in length, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (O(L)) and control region (D-loop). The overall nucleotide base composition of S. waltoni mtDNA is A 29.96%, C 27.07%, G 17.58%, and T 25.39%, with an A + T content of 55.35%. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. The mitochondrial genome of S. waltoni can contribute to the studies on conservation genetics and stock evaluation of S. waltoni resource, as well as molecular phylogeny and species identification of Cyprinidae.