Journal of phylogenetics & evolutionary biology最新文献

{"title":"Evolution of Vertebrate Solute Carrier Family 9B Genes and Proteins (<i>SLC9B</i>): Evidence for a Marsupial Origin for Testis Specific <i>SLC9B1</i> from an Ancestral Vertebrate <i>SLC9B2</i> Gene.","authors":"Roger S Holmes,&nbsp;Kimberly D Spradling-Reeves,&nbsp;Laura A Cox","doi":"10.4172/2329-9002.1000167","DOIUrl":"https://doi.org/10.4172/2329-9002.1000167","url":null,"abstract":"<p><p><i>SLC9B</i> genes and proteins are members of the sodium/lithium hydrogen antiporter family which function as solute exchangers within cellular membranes of mammalian tissues. <i>SLC9B2</i> and <i>SLC9B1</i> amino acid sequences and structures and <i>SLC9B</i>-like gene locations were examined using bioinformatic data from several vertebrate genome projects. Vertebrate <i>SLC9B2</i> sequences shared 56-98% identity as compared with ∼50% identities with mammalian <i>SLC9B1</i> sequences. Sequence alignments, key amino acid residues and conserved predicted transmembrane structures were also studied. Mammalian <i>SLC9B2</i> and <i>SLC9B1</i> genes usually contained 11 or 12 coding exons with differential tissue expression patterns: <i>SLC9B2,</i> broad tissue distribution; and <i>SLC9B1</i>, being testis specific. Transcription factor binding sites and CpG islands within the human <i>SLC9B2</i> and <i>SLC9B1</i> gene promoters were identified. Phylogenetic analyses suggested that <i>SLC9B1</i> originated in an ancestral marsupial genome from a <i>SLC9B2</i> gene duplication event.</p>","PeriodicalId":89991,"journal":{"name":"Journal of phylogenetics & evolutionary biology","volume":"4 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/2329-9002.1000167","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35371245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Causal Genomic and Epigenomic Network Analysis emerges as a New Generation of Genetic Studies of Complex Diseases","authors":"M. Xiong","doi":"10.4172/2329-9002.1000e113","DOIUrl":"https://doi.org/10.4172/2329-9002.1000e113","url":null,"abstract":"In the past decade, rapid advances in genomic technologies have dramatically changed the genetic studies of complex diseases. Genome-wide association studies (GWAS) have been widely used in dissecting genetic structure of complex diseases. As of December 18th, 2014, A Catalog of Published Genome-Wide Association Studies (GWAS) had reported significant association of 15,177 SNPs with more than 700 traits in 2,087 publications [1]. However, numerous studies reported that the genetic loci identified by GWAS collectively explain only < 10% of genetic variation across the population in most complex diseases. About 90% of the heritability of common diseases are unexplained by a large number of identified GWA loci. Each variant usually has weak effect and make small and mild contributions to the disease. More than 1,000 loci for many complex diseases have been identified [2]. Although extremely large number of samples are collected and whole genome sequencing studies will be conducted very soon, which will lead to reducing he fraction of missing heritability, a large proportion of heritability will be still missing under the paradigm of single trait genetic analysis. The methods for heritability estimation and single trait genetic study paradigm are questionable. \u0000 \u0000A biological system consists of multiple phenotypes. The multiple phenotypes are correlated. It has been reported that more than 4.6% of the SNPs and 16.9% of the genes in previous genome-wide association studies (GWAS) were significantly associated with more than one trait [3]. These results demonstrate that genetic pleiotropic effects likely play a crucial role in the molecular basis of correlated phenotype [4]. The heritability of individual phenotype cannot reveal complicated genotype-phenotype structure and is highly unlikely to fully capture the structure of heritability of multiple phenotypes. Furthermore, the estimation of heritability by a single trait approach might be inaccurate. The concept of heritability should be extended from a single trait to multiple traits. \u0000 \u0000Consider k traits. The breeding and phenotype values for k traits are denoted by a k dimensional vector \u0000 \u0000 \u0000A= [A1,…, Ak] and P= [P1,… P,k]T, respectively. A breeding equation is given by \u0000 \u0000 \u0000A=HP \u0000 \u0000(1) \u0000 \u0000 \u0000 \u0000 \u0000Where H is a heritability matrix and denoted by \u0000 \u0000 \u0000H=[h1⋯h1k⋮⋱⋮hk1⋯hk] \u0000 \u0000 \u0000 \u0000 \u0000Suppose that the phenotype can) be decomposed as a summation of additive effect, dominant effect and environment effect:k \u0000 \u0000 \u0000P=A+D+E,where \u0000 \u0000(2) \u0000 \u0000 \u0000 \u0000 \u0000A, D and E represent the genetic additive, dominant and environmental effect, respectively. Denote the covariance matrix between the breeding value and phenotype values by \u0000 \u0000 \u0000cov(A,P)=[cov(A1,P1)⋯cov(A1,Pk)⋮⋱⋮cov(Ak,P1)⋮cov(Ak,Pk)] \u0000 \u0000 \u0000and variance-covariance matrix of the phenotype P by \u0000 \u0000 \u0000var(P)=[var(P1)⋯cov(P1,Pk)⋮⋱⋮cov(Pk,P1)⋯var(Pk)] \u0000 \u0000 \u0000 \u0000 \u0000It is known that \u0000 \u0000 \u0000cov(Ai,Pj)=cov(Ai,Aj)+cov(Ai,Dj)+cov(Ai,Ej), \u0000 \u0000 \u0000which implies that \u0000 \u0000 \u0000cov(A,P)=[cov(A1,A1)+cov(","PeriodicalId":89991,"journal":{"name":"Journal of phylogenetics & evolutionary biology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/2329-9002.1000e113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70276887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ancient Origin of Chaperonin Gene Paralogs Involved in Ciliopathies.","authors":"Krishanu Mukherjee,&nbsp;Luciano Brocchieri","doi":"10.4172/2329-9002.1000107","DOIUrl":"https://doi.org/10.4172/2329-9002.1000107","url":null,"abstract":"<p><p>The Bardet-Biedl Syndrome (BBS) is a human developmental disorder that has been associated with fourteen <i>BBS</i> genes affecting the development of cilia. Three <i>BBS</i> genes are distant relatives of chaperonin proteins, a family of chaperones well known for the protein-folding role of their double-ringed complexes. Chaperonin-like <i>BBS</i> genes were originally thought to be vertebrate-specific, but related genes from different metazoan species have been identified as chaperonin-like <i>BBS</i> genes based on sequence similarity. Our phylogenetic analyses confirmed the classification of these genes in the chaperonin-like <i>BBS</i> gene family, and set the origin of the gene family earlier than the time of separation of Bilateria, Cnidaria, and Placozoa. By extensive searches of chaperonin-like genes in complete genomes representing several eukaryotic lineages, we discovered the presence of chaperonin-like <i>BBS</i> genes also in the genomes of <i>Phytophthora</i> and <i>Pythium</i>, belonging to the group of Oomycetes. This finding suggests that the chaperonin-like BBS gene family had already evolved before the origin of Metazoa, as early in eukaryote evolution as before separation of the lineages of Unikonts and Chromalveolates. The analysis of coding sequences indicated that chaperonin-like BBS proteins have evolved in all lineages under constraining selection. Furthermore, analysis of the predicted structural features suggested that, despite their high rate of divergence, chaperonin-like BBS proteins mostly conserve a typical chaperonin-like three-dimensional structure, but question their ability to assemble and function as chaperonin-like double-ringed complexes.</p>","PeriodicalId":89991,"journal":{"name":"Journal of phylogenetics & evolutionary biology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760595/pdf/nihms493880.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31712653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}