Genome最新文献

{"title":"Chromosomes in the African frog genus <i>Tomopterna</i> (Pyxicephalidae) and probing the origin of tetraploid <i>Tomopterna tandyi</i>.","authors":"James P Bogart,&nbsp;Abeda Dawood,&nbsp;François S Becker,&nbsp;Alan Channing","doi":"10.1139/gen-2022-0053","DOIUrl":"https://doi.org/10.1139/gen-2022-0053","url":null,"abstract":"<p><p>Speciation by polyploidization has been documented to have independently occurred in 12 families of anuran amphibians. <i>Tomopterna tandyi</i> was described as a South African allotetraploid species of sand frogs in the family Pyxicephalidae. Recent taxonomic revisions and new species descriptions in the genus present problems with respect to the evolution of this tetraploid species. Chromosomes, mitochondrial and nuclear gene sequences, isozymes, and male mating calls were examined for <i>T. tandyi</i> and for diploid species of <i>Tomopterna.</i> Mitochondrial sequences confirmed the diploid species, <i>T. adiastola,</i> to be the maternal ancestor that gave rise to the tetraploid about 5 mya. Nuclear sequences and isozymes reveal a complex reticulation of paternal ancestry that may be explained by occasional hybridization of <i>T. tandyi</i> with diploid species of <i>Tompoterna</i> at various times in sympatric populations. Interspecific diploid to tetraploid gene introgression is suspected to have also occurred in Australian and North American tetraploid species of frogs. Diploid to tetraploid introgression is facilitated through triploid hybrids that are more viable than diploid hybrids and produce unreduced triploid eggs.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"65 12","pages":"585-604"},"PeriodicalIF":3.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33501701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Autophagy in cell fate decisions: knowledge gained from <i>Drosophila</i>.","authors":"Camille Lacarrière-Keïta,&nbsp;Sonya Nassari,&nbsp;Steve Jean","doi":"10.1139/gen-2022-0069","DOIUrl":"https://doi.org/10.1139/gen-2022-0069","url":null,"abstract":"<p><p>Autophagy is an important process that maintains adult tissue homeostasis and functions by protecting cells in autonomous and non-cell-autonomous ways. By degrading toxic components or proteins involved in cell signaling pathways, autophagy preserves the balance among stem cells, progenitors, and differentiated cells in various tissues. In this minireview, we discuss recent studies performed in <i>Drosophila</i> that highlight new roles of autophagy in adult cell fate decisions, including quiescence, proliferation, differentiation, and death.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"65 12","pages":"573-584"},"PeriodicalIF":3.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33511157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miR-181a-5p is a potential candidate epigenetic biomarker in multiple sclerosis.","authors":"Tuba Gökdoğan Edgünlü,&nbsp;Şenay Görücü Yılmaz,&nbsp;Ufuk Emre,&nbsp;Bahar Taşdelen,&nbsp;Oktay Kuru,&nbsp;Gülnihal Kutlu,&nbsp;Mehmet Emin Erdal","doi":"10.1139/gen-2022-0040","DOIUrl":"https://doi.org/10.1139/gen-2022-0040","url":null,"abstract":"<p><p>Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) characterized by demyelination and axonal degeneration. Abnormal expression of microRNAs (miRNAs) plays an important role in MS pathology. In this cohort study, differential expression of the four miRNAs (<i>hsa-miR-155-5p</i>, <i>hsa-miR-9-5p</i>, <i>hsa-miR-181a-5p</i>, and <i>hsa-miR-125b-5p)</i> was investigated in 69 individuals, including 39 MS patients (relapsing-remitting MS (RRMS), <i>n</i> = 27; secondary progressive MS (SPMS), <i>n</i> = 12) and 30 healthy controls. In silico analyses revealed possible genes and pathways specific to miRNAs. Peripheral blood miRNA expressions were detected by quantitative real-time PCR (qPCR). <i>hsa-miR-181a-5p</i> was downregulated and associated with increased MS risk (<i>P</i> = 0.012). The other three miRNAs were upregulated and not associated with MS (<i>P</i> < 0.05). The area under the curve (AUC) is 0.779. In silico analyses showed that <i>hsa-miR-181a-5p</i> may participate in MS pathology by targeting <i>MAP2K1</i>, <i>CREB1</i>, <i>ATXN1</i>, and <i>ATXN3</i> genes in inflammation and neurodegeneration pathways. The circulatory <i>hsa-miR-181a-5p</i> can regulate target genes, reversing the mechanisms involved in MS pathologies such as protein uptake and processing, cell proliferation and survival, inflammation, and neurodegeneration. Thus, this miRNA could be used as an epigenomic-guided diagnostic tool and for therapeutic purpose.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"65 11","pages":"547-561"},"PeriodicalIF":3.1,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40356582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using telomeric length measurements and methylation to understand the karyotype diversification of <i>Ctenomys minutus</i> (a small fossorial mammal).","authors":"C A Matzenbacher,&nbsp;J Da Silva,&nbsp;A L H Garcia,&nbsp;R Kretschmer,&nbsp;M Cappetta,&nbsp;E H C de Oliveira,&nbsp;T R O de Freitas","doi":"10.1139/gen-2022-0018","DOIUrl":"https://doi.org/10.1139/gen-2022-0018","url":null,"abstract":"<p><p>The genus <i>Ctenomys</i> has been widely used in karyotype evolution studies due to the variation in their diploid numbers. <i>Ctenomys minutus</i> is characterized by intraspecific variation in diploid number (2<i>n</i> = 42, 46, 48, and 50), which makes it an interesting model to investigate genomic rearrangements mechanisms that could lead to different cytotypes in this species. Thereupon, it has been already shown that DNA methylation may participate in chromosome structure. Therefore, we aimed to investigate whether telomeres and global DNA methylation had a role in the genome rearrangements that led to this variation in <i>C. minutus</i>. We also realized an analysis for the presence of intrachromosomal telomeric repeats (ITRs) by fluorescence in situ hybridization. Our study demonstrated that neither telomere length nor DNA methylation had significant differences among the cytotypes. However, if only females were considered, there were significant differences for telomere length and methylation. Young individuals, regardless of their cytotypes, had the most methylated DNA. Regarding the ITRs, we found a signal on chromosome 1 in 2<i>n</i> = 50b. No evidence was found that telomere length or methylation could have influenced chromosomal rearrangements, although new cytotypes seem to have emerged within the distribution of parental cytotypes by the accumulation of different chromosomal rearrangements.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"65 11","pages":"563-572"},"PeriodicalIF":3.1,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40334923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of the 12-oxophytoeienoic acid reductase (<i>OPR</i>) gene family in pepper (<i>Capsicum annuum</i> L.) and functional characterization of <i>CaOPR6</i> in pepper fruit development and stress response.","authors":"Wen-Feng Nie,&nbsp;Yue Chen,&nbsp;Junjie Tao,&nbsp;Yu Li,&nbsp;Jianping Liu,&nbsp;Yong Zhou,&nbsp;Youxin Yang","doi":"10.1139/gen-2022-0037","DOIUrl":"https://doi.org/10.1139/gen-2022-0037","url":null,"abstract":"<p><p>The 12-oxophytoeienoic acid reductase (OPR) is a kind of enzyme in the octadecanoid biosynthesis pathway that determines the biosynthesis of jasmonic acid. Although the roles of OPRs have been extensively studied in several crop plants, little is known about the biological functions of OPR-encoding genes in <i>Capsicum annuum</i> plants. In this study, seven OPR family genes (<i>CaOPR1-7</i>) were identified from the <i>C. annuum</i> genome. The physical and chemical properties of <i>CaOPR1-7</i> were further analyzed, including gene expression patterns, promoter elements, and chromosomal locations. The results showed that the seven CaOPR homologues could be divided into two subgroups, and CaOPR6 was highly similar to AtOPR3 in <i>Arabidopsis</i>. The expression of <i>CaOPR6</i> was significantly induced by various stresses such as cold, salt, and pathogen infection, indicating that <i>CaOPR6</i> plays important roles in response to abiotic and biotic stresses. Overall, these findings improve the understanding of the biological functions of <i>CaOPR6</i> in the development of pepper fruit and stress response of pepper plants, and facilitate further studies on the molecular biology of OPR proteins in <i>Solanaceae</i> vegetables.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"65 11","pages":"537-545"},"PeriodicalIF":3.1,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40693140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Zebrafish optineurin: genomic organization and transcription regulation.","authors":"Iris A L Silva,&nbsp;Débora Varela,&nbsp;M Leonor Cancela,&nbsp;Natércia Conceição","doi":"10.1139/gen-2022-0019","DOIUrl":"https://doi.org/10.1139/gen-2022-0019","url":null,"abstract":"<p><p>Optineurin (OPTN) is involved in a variety of mechanisms, such as autophagy, vesicle trafficking, and nuclear factor kappa-B (NF-κB) signaling. Mutations in the <i>OPTN</i> gene have been associated with different pathologies, including glaucoma, amyotrophic lateral sclerosis, and Paget's disease of bone. Since the relationship between fish and mammalian OPTN is not well understood, the objective of the present work was to characterize the zebrafish <i>optn</i> gene and protein structure and to investigate its transcriptional regulation. Through a comparative in silico analysis, we observed that zebrafish <i>optn</i> presents genomic features similar to those of its human counterpart, including its neighboring genes and structure. A comparison of OPTN protein from different species revealed a high degree of conservation in its functional domains and three-dimensional structure. Furthermore, our in vitro transient-reporter analysis identified a functional promoter in the upstream region of the zebrafish <i>optn</i> gene, along with a region important for its transcription regulation. Site-directed mutagenesis revealed that the NF-κB motif is responsible for the activation of this region. In conclusion, with this study, we characterize zebrafish <i>optn</i> and our results indicate that zebrafish can be considered as an alternative model to study OPTN's biological role in bone-related diseases.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"65 10","pages":"513-523"},"PeriodicalIF":3.1,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33445757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Marsupial satellite DNA as faithful reflections of long-terminal repeat retroelement structure.","authors":"Sakura Hayashi,&nbsp;Yusuke Honda,&nbsp;Etsuko Kanesaki,&nbsp;Akihiko Koga","doi":"10.1139/gen-2022-0039","DOIUrl":"https://doi.org/10.1139/gen-2022-0039","url":null,"abstract":"<p><p>Long terminal repeat (LTR) retroelements, including endogenous retroviruses, are one of the origins of satellite DNAs. However, the vast majority of satellite DNAs originating from LTR retroelements consists of parts of the element. In addition, they frequently contain sequences unrelated to that element. Here we report a novel marsupial satellite DNA (named walbRep) that contains, and consists solely of, the entire sequence of an LTR retroelement (the <i>walb</i> element). As is common with LTR retroelements, <i>walb</i> copies exhibit length variation. We focused on the abundance of copies of a specific length (2.7 kb) in the genome of the red-necked wallaby. Cloning and analyses of long genomic DNA fragments revealed a satellite DNA in which the LTR sequence (0.4 kb) and the sequence of the internal region of a nonautonomous <i>walb</i> copy (2.3 kb) were repeated alternately. The junctions between these two components exhibited the same end-to-end arrangements as those in the <i>walb</i> element. This satellite organization could be accounted for by a simple formation model that includes slippage during chromosome pairing followed by homologous recombination but does not invoke any other types of rearrangements. We discuss the possible reasons why satellite DNAs having such structures are rarely found in mammals.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"65 9","pages":"469-478"},"PeriodicalIF":3.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40584689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enriched tandem repeats in chromosomal fusion points of <i>Rineloricaria latirostris</i> (Boulenger, 1900) (Siluriformes: Loricariidae).","authors":"Larissa Glugoski,&nbsp;Viviane Nogaroto,&nbsp;Geize Aparecida Deon,&nbsp;Matheus Azambuja,&nbsp;Orlando Moreira-Filho,&nbsp;Marcelo Ricardo Vicari","doi":"10.1139/gen-2022-0043","DOIUrl":"https://doi.org/10.1139/gen-2022-0043","url":null,"abstract":"<p><p>Cytogenetic data showed the enrichment of repetitive DNAs in chromosomal rearrangement points between closely related species in armored catfishes. Still, few studies integrated cytogenetic and genomic data aiming to identify their prone-to-break DNA sites. Here, we aimed to obtain the repetitive fraction in <i>Rineloricaria latirostris</i> to recognize the microsatellite and homopolymers flanking the regions previously described as chromosomal fusion points. The results indicated that repetitive DNAs in <i>R. latirostris</i> are predominantly DNA transposons, and considering the microsatellite and homopolymers, A/T-rich expansions were the most abundant. The in situ localization demonstrated the A/T-rich repetitive sequences were scattered on the chromosomes, while A/G-rich microsatellite units were accumulated in some regions. The DNA transposon <i>hAT</i>, the 5S rDNA, and 45S rDNA (previously identified in Robertsonian fusion points in <i>R. latirostris</i>) were clusterized with some microsatellites, especially (CA)<i>_n</i>, (GA)<i>_n</i>, and poly-A, which were also enriched in regions of chromosomal fusions. Our findings demonstrated that repetitive sequences such as rDNAs, <i>hAT</i> transposons, and microsatellite units flank probable evolutionary breakpoint regions in <i>R. latirostris</i>. However, due to the sequence unit homologies in different chromosomal sites, these repeat DNAs only may facilitate chromosome fusion events in <i>R. latirostris</i> rather than working as a double-strand breakpoint site.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"65 9","pages":"479-489"},"PeriodicalIF":3.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40595209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis and evaluation of different sequencing depths from 5 to 20 million reads in shotgun metagenomic sequencing, with optimal minimum depth being recommended.","authors":"Jin Liu,&nbsp;Xiaokai Wang,&nbsp;Hailiang Xie,&nbsp;Qinghua Zhong,&nbsp;Yan Xia","doi":"10.1139/gen-2021-0120","DOIUrl":"https://doi.org/10.1139/gen-2021-0120","url":null,"abstract":"<p><p>Our study was to analyze and evaluate the impact of different shotgun metagenomic sequencing depths from 5 to 20 million in metagenome-wide association studies (MWASs), and to determine the optimal minimum sequencing depth. We included a set of 200 previously published gut microbial shotgun metagenomic sequencing data on obesity (100 obese vs. 100 non-obese). The reads with original sequencing depths >20 million were downsized into seven experimental groups with depths from 5 to 20 million (interval 2.5 million). Using both integrated gene cluster (IGC) and metagenomic phylogenetic analysis 2 (MetaPhlAn2), we obtained and analyzed the read matching rates, gene count, species richness and abundance, diversity, and clinical biomarkers of the experimental groups with the original depth as the control group. An additional set of 100 published data from a colorectal cancer (CRC) study was included for validation (50 CRC vs. 50 CRC-free). Our results showed that more genes and species were identified following the increase in sequencing depths. When it reached 15 million or higher, the species richness became more stable with changing rate of 5% or lower, and the species composition more stable with ICC intraclass correlation coefficient (ICC) higher than 0.75. In terms of species abundance, 81% and 97% of species showed significant differences in IGC and MetaPhlAn2 among all groups with <i>p</i> < 0.05. Diversity showed significant differences across all groups, with decreasing differences of diversity between the experimental and the control groups following the increase in sequencing depth. The area under a receiver operating characteristic curve, AUC, of the obesity classifier for running the obesity testing samples showed an increasing trend following the increase in sequencing depth (<i>τ</i> = 0.29). The validation results were consistent with the above results. Our study found that the higher the sequencing depth is, the more the microbial information in structure and composition it provides. We also found that when sequencing depth was 15 million or higher, we obtained more stable species compositions and disease classifiers with good performance. Therefore, we recommend 15 million as the optimal minimum sequencing depth for an MWAS.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"65 9","pages":"491-504"},"PeriodicalIF":3.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40595207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association studies identified loci associated with both feed conversion ratio and residual feed intake in Yorkshire pigs.","authors":"Kai Wang, Shujie Wang, Xiang‐Fen Ji, Dong Chen, Qi Shen, Yang Yu, Wei-hang Xiao, Pingxian Wu, G. Tang","doi":"10.1139/gen-2021-0105","DOIUrl":"https://doi.org/10.1139/gen-2021-0105","url":null,"abstract":"Feed occupies a significant proportion in the production cost of pigs, and the feed efficiency (FE) in pigs are of utmost economic importance. Hence, the objective of this study is to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with FE related traits, including feed conversion ratio (FCR) and residual feed intake (RFI). A genome-wide association study (GWAS) was conducted for FCR and RFI in 169 Yorkshire pigs using whole-genome sequencing data. A total of 23 and 33 suggestive significant SNPs (P<1×10^(-6)) were detected for FCR and RFI, respectively. However, none of the SNPs achieved the genome-wide significance threshold (P<5×10^(-8)). Importantly, three common SNPs (SSC7:7987268, SSC13:42350250, and SSC13:42551718) were associated with both FCR and RFI. Additionally, the NEDD9 gene related to FCR and RFI traits was overlapped. This study detected novel SNPs on SSC7 and SSC13 common for FCR and RFI. These results provide new insights into the genetic mechanisms and candidate genes of FE-related traits in pigs.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2022-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46111269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}