Genetics and Molecular Biology最新文献_第10页

Revealing the expression profile of genes that encode the Subcortical Maternal Complex in human reproductive failures. 揭示人类生殖失败中编码皮层下母体复合体的基因表达谱。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2023-12-11 eCollection Date: 2023-01-01 DOI: 10.1590/1678-4685-GMB-2023-0141

Marília Körbes Rockenbach, Lucas Rosa Fraga, Thayne Woycinck Kowalski, Maria Teresa Vieira Sanseverino

{"title":"Revealing the expression profile of genes that encode the Subcortical Maternal Complex in human reproductive failures.","authors":"Marília Körbes Rockenbach, Lucas Rosa Fraga, Thayne Woycinck Kowalski, Maria Teresa Vieira Sanseverino","doi":"10.1590/1678-4685-GMB-2023-0141","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2023-0141","url":null,"abstract":"The Subcortical Maternal Complex (SCMC) is composed of maternally encoded proteins required for the early stages of embryo development. Here we aimed to investigate the expression profile of the genes that encode the individual members of the SCMC in human reproductive failures. To accomplish that, we selected three datasets in the Gene Expression Omnibus repository for differential gene expression (DGE) analysis, comprising human endometrial and placental tissues of patients with recurrent implantation failure (RIF) or recurrent pregnancy loss (RPL). The SCMC genes KHDC3L, NLRP2, NLRP4, NLRP5, OOEP, PADI6, TLE6, and ZBED3 were included in the DGE analysis, as well as CFL1 and CFL2 that connect the SCMC with the actin cytoskeleton. Additionally, differential co-expression analysis and systems biology analysis of gene-gene co-expression were performed for KHDC3L, NLRP5, OOEP, and TLE6, demonstrating gene pairs differentially correlated under the two conditions, and the co-expression with genes involved in immune response, cell cycle, DNA damage repair, embryo development, and male reproduction. Compared to control groups, NLRP5 demonstrated upregulation in the endometrium of RIF patients, and KHDC3L was upregulated in the fetal placental tissue of RPL patients, shedding light on the importance of considering SCMC genes in reproductive failures.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230141"},"PeriodicalIF":2.1,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10718294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138798810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Neonatal screening for spinal muscular atrophy: A pilot study in Brazil. 新生儿脊髓性肌萎缩症筛查：巴西试点研究。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2023-12-11 eCollection Date: 2023-01-01 DOI: 10.1590/1678-4685-GMB-2023-0126

Alice Brinckmann Oliveira Netto, Ana Carolina Brusius-Facchin, Júlia F Lemos, Fernanda B Pasetto, Carolina S Brasil, Franciele B Trapp, Jonas Alex Morales Saute, Karina Carvalho Donis, Michele Michelin Becker, Paloma Wiest, Vivian L S Coutinho, Simone Castro, Juliana Ferreira, Cynthia Silveira, Maria Fernanda R Bittar, Cristina Wang, Janaina M Lana, Marcondes Cavalcante França Junior, Roberto Giugliani

{"title":"Neonatal screening for spinal muscular atrophy: A pilot study in Brazil.","authors":"Alice Brinckmann Oliveira Netto, Ana Carolina Brusius-Facchin, Júlia F Lemos, Fernanda B Pasetto, Carolina S Brasil, Franciele B Trapp, Jonas Alex Morales Saute, Karina Carvalho Donis, Michele Michelin Becker, Paloma Wiest, Vivian L S Coutinho, Simone Castro, Juliana Ferreira, Cynthia Silveira, Maria Fernanda R Bittar, Cristina Wang, Janaina M Lana, Marcondes Cavalcante França Junior, Roberto Giugliani","doi":"10.1590/1678-4685-GMB-2023-0126","DOIUrl":"10.1590/1678-4685-GMB-2023-0126","url":null,"abstract":"Spinal muscular atrophy (SMA) is considered one of the most common autosomal recessive disorders, with an estimated incidence of 1 in 10,000 live births. Testing for SMA has been recommended for inclusion in neonatal screening (NBS) panels since there are several therapies available and there is evidence of greater efficacy when introduced in the pre/early symptomatic phases. In Brazil, the National Neonatal Screening Program tests for six diseases, with a new law issued in 2021 stating that it should incorporate more diseases, including SMA. In the present study, dried blood spot (DBS) samples collected by the Reference Services of Neonatal Screening of RS and SP, to perform the conventional test were also screened for SMA, using real-time PCR, with SALSA MC002 technique. A total of 40,000 samples were analyzed, enabling the identification of four positive cases of SMA, that were confirmed by MLPA. Considering our sampling, Brazil seems to have an incidence comparable to the described in other regions. This work demonstrated that the use of the MC002 technique in samples routinely collected for the conventional NBS program is suitable to screen for SMA in our conditions and can be included in the expansion of the neonatal screening programs.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230126"},"PeriodicalIF":2.1,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10718293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138798809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In vitro substrate reduction, chaperone and immunomodulation treatments reduce heparan sulfate in mucolipidosis III human fibroblasts. 体外底物还原、伴侣和免疫调节处理可降低III型粘脂症人成纤维细胞中的硫酸肝素。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2023-12-04 eCollection Date: 2023-01-01 DOI: 10.1590/1678-4685-GMB-2023-0117

Fernanda Sperb-Ludwig, Nataniel Floriano Ludwig, Gustavo Mottin Rizowy, Renata Voltolini Velho, Ida Vanessa Doederlein Schwartz

{"title":"In vitro substrate reduction, chaperone and immunomodulation treatments reduce heparan sulfate in mucolipidosis III human fibroblasts.","authors":"Fernanda Sperb-Ludwig, Nataniel Floriano Ludwig, Gustavo Mottin Rizowy, Renata Voltolini Velho, Ida Vanessa Doederlein Schwartz","doi":"10.1590/1678-4685-GMB-2023-0117","DOIUrl":"10.1590/1678-4685-GMB-2023-0117","url":null,"abstract":"Mucolipidosis II and III (MLII and MLIII) are autosomal recessive diseases caused by pathogenic variants in GNPTAB and GNPTG genes that lead to defects in GlcNAc-1-phosphotransferase. This enzyme adds mannose 6-phosphate residues to lysosomal hydrolases, which allows enzymes to enter lysosomes. Defective GlcNAc-1-phosphotransferase causes substrate accumulation and inflammation. These diseases have no treatment, and we hypothesized that the use of substrate reduction therapy and immunomodulation may be beneficial at the cell level and as a future therapeutic approach. Fibroblasts from two patients with MLIII alpha/beta and 2 patients with MLIII gamma as well as from one healthy control were treated with 10 µM miglustat, 20 µM genistein, and 20 µM thalidomide independently. ELISA assay and confocal immunofluorescence microscopy were used to evaluate the presence of heparan sulfate (HS) and the impact on substrate accumulation. ELISA assay showed HS reduction in all patients with the different treatments used (p=0.05). HS reduction was also observed by immunofluorescence microscopy. Our study produced encouraging results, since the reduction in substrate accumulation, even partial, may offer benefits to the phenotype of patients with inborn errors of metabolism.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230117"},"PeriodicalIF":2.1,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10694850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138477340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of a new anellovirus species infecting an ocelot (Leopardus pardalis) in Brazil. 巴西一只猫鼬感染的一种新型无肠病毒的特征。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2023-12-04 eCollection Date: 2023-01-01 DOI: 10.1590/1678-4685-GMB-2023-0015

Liliane T F Cavalcante, Matheus A C Cosentino, Mirela D'arc, Filipe R R Moreira, Ricardo Mouta, Anderson M Augusto, Fernando Troccoli, Marcelo A Soares, André F Santos

引用次数: 0

Genome-wide identification and evolutionary view of ALOG gene family in Solanaceae. 茄科植物ALOG基因家族的全基因组鉴定及进化观点。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2023-11-24 eCollection Date: 2023-01-01 DOI: 10.1590/1415-4757-GMB-2023-0142

Caroline Turchetto, Ariadne de Castro Silvério, Edgar Luis Waschburger, Maria Eduarda Gonçalves Lacerda, Isadora Vieira Quintana, Andreia Carina Turchetto-Zolet

{"title":"Genome-wide identification and evolutionary view of ALOG gene family in Solanaceae.","authors":"Caroline Turchetto, Ariadne de Castro Silvério, Edgar Luis Waschburger, Maria Eduarda Gonçalves Lacerda, Isadora Vieira Quintana, Andreia Carina Turchetto-Zolet","doi":"10.1590/1415-4757-GMB-2023-0142","DOIUrl":"10.1590/1415-4757-GMB-2023-0142","url":null,"abstract":"The ALOG gene family, which was named after its earliest identified members ( Arabidopsis LSH1 and Oryza G1), encodes a class of transcription factors (TF) characterized by the presence of a highly conserved ALOG domain. These proteins are found in various plant species playing regulatory roles in plant growth, development, and morphological diversification of inflorescence. The functional characterization of these genes in some plant species has demonstrated their involvement in floral architecture. In this study, we used a genome-wide and phylogenetic approach to gain insights into plants' origin, diversification, and functional aspects of the ALOG gene family. In total, 648 ALOG homologous genes were identified in 77 Viridiplantae species, and their evolutionary relationships were inferred using maximum likelihood phylogenetic analyses. Our results suggested that the ALOG gene family underwent several rounds of gene duplication and diversification during angiosperm evolution. Furthermore, we found three functional orthologous groups in Solanaceae species. The study provides insights into the evolutionary history and functional diversification of the ALOG gene family, which could aid in understanding the mechanisms underlying floral architecture in angiosperms.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230142"},"PeriodicalIF":2.1,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10695626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138482212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cranial morphological variation of Ctenomys lami (Rodentia: Ctenomyidae) in a restricted geographical distribution. 在有限的地理分布中，棘球绦虫(啮齿目:棘球绦虫科)的颅形态变异。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2023-11-13 eCollection Date: 2023-01-01 DOI: 10.1590/1678-4685-GMB-2023-0130

Rodrigo Fornel, Renan Maestri, Pedro Cordeiro-Estrela, Daniela Sanfelice, Thales Renato O de Freitas

{"title":"Cranial morphological variation of Ctenomys lami (Rodentia: Ctenomyidae) in a restricted geographical distribution.","authors":"Rodrigo Fornel, Renan Maestri, Pedro Cordeiro-Estrela, Daniela Sanfelice, Thales Renato O de Freitas","doi":"10.1590/1678-4685-GMB-2023-0130","DOIUrl":"10.1590/1678-4685-GMB-2023-0130","url":null,"abstract":"The relationship between chromosomal and morphological variation in mammals is poorly understood. We analyzed the cranial size and shape variation in Ctenomys lami concerning to the geographic variation in their chromosome numbers. This subterranean rodent occurs in a narrow range of sand-dunes in the Coastal Plain of southern Brazil. This species presents a high karyotypic variation with diploid numbers varying from 2n = 54 to 2n = 58, involving the fission and fusion of chromosome pairs 1 and 2. Due to different chromosome rearrangement frequencies along their geographic distribution, four karyotypic blocks were proposed. This study, explored cranium shape and size variation in geographical, chromosomal polymorphism, and chromosome rearrangements contexts to test whether the four karyotypic blocks reflect morphologically distinct units. For this, we measured 89 craniums using geometric morphometrics and used uni and multivariate statistics to discriminate the predicted groups and test for an association among chromosomal and morphological variation. Our results show the size and shape of sexual dimorphism, with males larger than females, and support the existence of four karyotypic blocks for Ctenomys lami based on morphological variation. However, our results do not support a direct relationship between chromosomal and cranial morphological variation in C. lami.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230130"},"PeriodicalIF":2.1,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10655944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"107590842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolution and diversification of the O-methyltransferase (OMT) gene family in Solanaceae. 茄科植物O-甲基转移酶（OMT）基因家族的进化和多样化。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2023-11-10 eCollection Date: 2023-01-01 DOI: 10.1590/1678-4685-GMB-2023-0121

Pedro Henrique Pezzi, Leonardo Tresoldi Gonçalves, Maríndia Deprá, Loreta Brandão de Freitas

{"title":"Evolution and diversification of the O-methyltransferase (OMT) gene family in Solanaceae.","authors":"Pedro Henrique Pezzi, Leonardo Tresoldi Gonçalves, Maríndia Deprá, Loreta Brandão de Freitas","doi":"10.1590/1678-4685-GMB-2023-0121","DOIUrl":"10.1590/1678-4685-GMB-2023-0121","url":null,"abstract":"O-methyltransferases (OMTs) are a group of enzymes involved in several fundamental biological processes in plants, including lignin biosynthesis, pigmentation, and aroma production. Despite the intensive investigation of the role of OMTs in plant secondary metabolism, the evolution and diversification of this gene family in Solanaceae remain poorly understood. Here, we conducted a genome-wide survey of OMT genes in six Solanaceae species, reconstructing gene phylogenetic trees, predicting the potential involvement in biological processes, and investigating the exon/intron structure and chromosomal location. We identified 57 caffeoyl-CoA OMTs (CCoAOMTs) and 196 caffeic acid OMTs (COMTs) in the studied species. We observed a conserved gene block on chromosome 2 that consisted of tandem duplicated copies of OMT genes. Our results suggest that the expansion of the OMT gene family in Solanaceae was driven by whole genome duplication, segmental duplication, and tandem duplication, with multiple genes being retained by neofunctionalization and subfunctionalization. This study represents an essential first step in unraveling the evolutionary history of OMTs in Solanaceae. Our findings deepen our understanding of the crucial role of OMTs in several biological processes and highlight their significance as potential biotechnological targets.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230121"},"PeriodicalIF":2.1,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10637433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72209045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phenotypic and molecular basis for genetic variation in jelly palms (Butia sp.): where are we now and where are we headed to? 果冻棕榈（Butia sp.）遗传变异的表型和分子基础：我们现在在哪里，我们将走向哪里？

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2023-11-10 eCollection Date: 2023-01-01 DOI: 10.1590/1678-4685-GMB-2023-0145

Camila Fritzen Cidón, Andreia Carina Turchetto-Zolet, Miklos Maximiliano Bajay, Maria Imaculada Zucchi, Enéas Ricardo Konzen

{"title":"Phenotypic and molecular basis for genetic variation in jelly palms (Butia sp.): where are we now and where are we headed to?","authors":"Camila Fritzen Cidón, Andreia Carina Turchetto-Zolet, Miklos Maximiliano Bajay, Maria Imaculada Zucchi, Enéas Ricardo Konzen","doi":"10.1590/1678-4685-GMB-2023-0145","DOIUrl":"10.1590/1678-4685-GMB-2023-0145","url":null,"abstract":"We compiled studies that addressed morphological and physicochemical traits, as well as population genetic studies involving jelly palms, genus Butia (Arecaceae). First, we conducted a bibliometric study with selected articles, by revising the fundamental contributions to unraveling phenotypic traits that have been used for describing the phenotypic variation within and among populations. Moreover, we sought to comprehend the patterns of genetic diversity and structure that have been presented so far, based on molecular markers. Finally, we conducted a review of the gene sequences registered to NCBI for Butia. Overall, morphological descriptors have been proposed to depict population-level variability, but the most significant results are available from chemical properties and characterization of metabolites, revealing important traits to being explored. Yet, limited information is available to describe population variation and their genetic components. On the molecular level, almost all studies so far provided results with classical molecular markers. The literature of SNP markers for Butia species is virtually non-existent. Given the current endangered state of Butia species, it is urgent that researchers pursue updated genomic technologies to invest in in-depth characterizations of the genetic diversity and structure of jelly palms. The current state of population fragmentation urges effective measures toward their conservation.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230145"},"PeriodicalIF":2.1,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10637346/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72209047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insights into the evolutionary history of the most skilled tool-handling platyrrhini monkey: Sapajus libidinosus from the Serra da Capivara National Park. 深入了解最熟练的工具处理鸭嘴猴的进化史：来自Serra da Capivara国家公园的Sapajus libidinosus。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2023-11-10 eCollection Date: 2023-01-01 DOI: 10.1590/1678-4685-GMB-2023-0165

Thaynara Lima, Bibiana Fam, Gustavo Medina Tavares, Tiago Falótico, Camila Cantele, Lucca Fanti, Luane Landau, Lucas Henriques Viscardi, Pedro Vargas-Pinilla, Ossman Barrientos-Diaz, Alcides Pissinatti, Vinicius A Sortica, Eduardo B Ottoni, Ana Lúcia A Segatto, Andreia Carina Turchetto-Zolet, Maria Cátira Bortolini

{"title":"Insights into the evolutionary history of the most skilled tool-handling platyrrhini monkey: Sapajus libidinosus from the Serra da Capivara National Park.","authors":"Thaynara Lima, Bibiana Fam, Gustavo Medina Tavares, Tiago Falótico, Camila Cantele, Lucca Fanti, Luane Landau, Lucas Henriques Viscardi, Pedro Vargas-Pinilla, Ossman Barrientos-Diaz, Alcides Pissinatti, Vinicius A Sortica, Eduardo B Ottoni, Ana Lúcia A Segatto, Andreia Carina Turchetto-Zolet, Maria Cátira Bortolini","doi":"10.1590/1678-4685-GMB-2023-0165","DOIUrl":"10.1590/1678-4685-GMB-2023-0165","url":null,"abstract":"Sapajus libidinosus members of the Pedra Furada group, living in the Serra da Capivara National Park, use stone tools in a wider variety of behaviors than any other living animal, except humans. To rescue the evolutionary history of the Caatinga S. libidinosus and identify factors that may have contributed to the emergence and maintenance of their tool-use culture, we conducted fieldwork seasons to obtain biological samples of these capuchin monkeys. UsingCYTBsequences, we show a discrete but constant population growth from the beginning of the Holocene to the present, overlapping the emergence of the Caatinga biome. Our habitat suitability reconstruction reports the presence of plants whose hard fruits, seeds, or roots are processed by capuchins using tools. TheS. libidinosusindividuals in the Caatinga were capable of dynamically developing and maintaining their autochthonous culture thanks to: a) cognitive capacity to generate and execute innovation under selective pressure; b) tolerance favoring learning and cultural inheritance; c) an unknown genetic repertoire that underpins the adaptive traits; d) a high degree of terrestriality; e) presence and abundance of natural resources, which makes some places \"hot spots\" for innovation, and cultural diversification within a relatively short time.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230165"},"PeriodicalIF":2.1,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10637428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72209046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species. 广义伯克霍尔德菌的基因组分类学：区分亲缘关系密切的物种。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2023-11-03 eCollection Date: 2023-01-01 DOI: 10.1590/1678-4685-GMB-2023-0122

Evelise Bach, Camila Gazolla Volpiano, Fernando Hayashi Sant'Anna, Luciane Maria Pereira Passaglia

{"title":"Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species.","authors":"Evelise Bach, Camila Gazolla Volpiano, Fernando Hayashi Sant'Anna, Luciane Maria Pereira Passaglia","doi":"10.1590/1678-4685-GMB-2023-0122","DOIUrl":"10.1590/1678-4685-GMB-2023-0122","url":null,"abstract":"The taxonomy of Burkholderia sensu lato (s.l.) has been revisited using genome-based tools, which have helped differentiate closely related species. Many species from this group are indistinguishable through phenotypic traits and 16S rRNA gene sequence analysis. Furthermore, they also exhibit whole-genome Average Nucleotide Identity (ANI) values in the twilight zone for species circumscription (95-96%), which may impair their correct classification. In this work, we provided an updated Burkholderia s.l. taxonomy focusing on closely related species and give other recommendations for those developing genome-based taxonomy studies. We showed that a combination of ANI and digital DNA-DNA hybridization (dDDH) applying the universal cutoff values of 95% and 70%, respectively, successfully discriminates Burkholderia s.l. species. Using genome metrics with this pragmatic criterion, we demonstrated that i) Paraburkholderia insulsa should be considered a later heterotypic synonym of Paraburkholderia fungorum; ii) Paraburkholderia steynii differs from P. terrae by harboring symbiotic genes; iii) some Paraburkholderia are indeed different species based on dDDH values, albeit sharing ANI values close to 95%; iv) some Burkholderia s.l. indeed represent new species from the genomic viewpoint; iv) some genome sequences should be evaluated with care due to quality concerns.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230122"},"PeriodicalIF":2.1,"publicationDate":"2023-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10629849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71480485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0