Milene Ferreira Barcellos, Laís Mara Santana Costa, Fernanda Bered
{"title":"Genetic diversity and conservation in Bromeliaceae based on SSR markers.","authors":"Milene Ferreira Barcellos, Laís Mara Santana Costa, Fernanda Bered","doi":"10.1590/1678-4685-GMB-2023-0135","DOIUrl":"10.1590/1678-4685-GMB-2023-0135","url":null,"abstract":"<p><p>Bromeliaceae has been used as a model Neotropical group to study evolutionary and diversification processes. Moreover, since large parts of the Neotropics are under anthropogenic pressure, a high percentage of possibly threatened species occurs. Despite this, concrete proposals for conservation based on genetic data are lacking. We compilated all genetic data obtained by nuclear microsatellites for Bromeliaceae and compared the levels of genetic diversity of subfamilies and their taxa, considering traits of life history and distribution in conservation and no conservation areas. We retrieved a total of 87 taxa (ca. 2.5% of the family size) and most present a mixed mating system, anemochoric dispersion, are ornithophilous, and were sampled outside Conservation Units, the majority occurring in the Atlantic Forest. Also, we found differences in some genetic indexes among taxa concerning seed dispersal mechanisms (e.g. Zoochoric taxa with higher diversity and lower inbreeding), mating systems (e.g. autogamous taxa showed higher inbreeding), outside/inside conservation units (allelic richness higher in not protected areas), and among different subfamilies (e.g. higher genetic diversity in Bromelioideae). The results obtained in this review can be useful for proposing conservation strategies, can facilitate the comparison of related taxa, and can help advance studies on the Bromeliaceae family.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11113272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141081184","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}
A. F. E. Silva, H. R. Antoniolli, E. Zefa, V. L. S. Valente, M. Deprá
{"title":"Phylomitogenomics of two Neotropical species of long-legged crickets Endecous Saussure, 1878 (Orthoptera: Phalangopsidae)","authors":"A. F. E. Silva, H. R. Antoniolli, E. Zefa, V. L. S. Valente, M. Deprá","doi":"10.1590/1678-4685-gmb-2023-0144","DOIUrl":"https://doi.org/10.1590/1678-4685-gmb-2023-0144","url":null,"abstract":"Abstract Mitochondrial genomes have provided significant insights into the evolution of several insects. A typical mitogenome contains 37 genes, and variations in gene order can indicate evolutionary relationships between species. In this study, we have assembled the first complete mitogenomes of Endecous chape and E. onthophagus and analyzed the phylogenetic implications for the Gryllidea infraorder. We performed DNA extractions and genome sequencing for both Endecous species. Subsequently, we searched for raw data in the Sequence Read Archive (SRA) in NCBI. Using the SRA data, we assembled the partial mitogenome of Dianemobius nigrofasciatus and annotated the protein-coding genes (PCGs) for nine species. Phylogenomic relationships were reconstructed using Maximum Likelihood (ML) and Bayesian Inference (BI), utilizing the PCGs from 49 Gryllidea species. The mitogenome lengths of E. chape and E. onthophagus are 16,266 bp and 16,023 bp, respectively, while D. nigrofasciatus has a length of 15,359 bp. Our results indicate that species within the infraorder exhibit four types of gene order arrangements that align with their phylogenetic relationships. Both phylogenomic trees displayed strong support, and the ML corroborated with the literature. Gryllidea species have significantly contributed to various fields, and studying their mitogenomes can provide valuable insights into this infraorder evolution.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140700749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. C. Batissoco, Dayane Bernardino Cruz, Thiago Geronimo Pires Alegria, Gerson Kobayashi, J. Oiticica, Luís Eduardo Soares Netto, M. Passos-Bueno, L. A. Haddad, R. C. Mingroni Netto
{"title":"GJB2 c.35del variant up-regulates GJA1 gene expression and affects differentiation of human stem cells","authors":"A. C. Batissoco, Dayane Bernardino Cruz, Thiago Geronimo Pires Alegria, Gerson Kobayashi, J. Oiticica, Luís Eduardo Soares Netto, M. Passos-Bueno, L. A. Haddad, R. C. Mingroni Netto","doi":"10.1590/1678-4685-GMB-2023-0170","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2023-0170","url":null,"abstract":"Abstract Pathogenic DNA alterations in GJB2 are present in nearly half of non-syndromic hearing loss cases with autosomal recessive inheritance. The most frequent variant in GJB2 causing non-syndromic hearing loss is the frameshifting c.35del. GJB2 encodes Cx26, a protein of the connexin family that assembles hemichannels and gap junctions. The expression of paralogous proteins is believed to compensate for the loss of function of specific connexins. As Cx26 has been involved in cell differentiation in distinct tissues, we employed stem cells derived from human exfoliated deciduous teeth (SHEDs), homozygous for the c.35del variant, to assess GJB2 roles in stem cell differentiation and the relationship between its loss of function and the expression of paralogous genes. Primary SHED cultures from patients and control individuals were compared. SHEDs from patients had significantly less GJB2 mRNA and increased amount of GJA1 (Cx43), but not GJB6 (Cx30) or GJB3 (Cx31) mRNA. In addition, they presented higher induced differentiation to adipocytes and osteocytes but lower chondrocyte differentiation. Our results suggest that GJA1 increased expression may be involved in functional compensation for GJB2 loss of function in human stem cells, and it may explain changes in differentiation properties observed in SHEDs with and without the c.35del variant.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140699920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Investigating the shared genetic architecture between breast and ovarian cancers","authors":"Xuezhong Shi, Anqi Bu, Yongli Yang, Yuping Wang, Chenyu Zhao, Jingwen Fan, Chaojun Yang, X. Jia","doi":"10.1590/1678-4685-GMB-2023-0181","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2023-0181","url":null,"abstract":"Abstract High heritability and strong correlation have been observed in breast and ovarian cancers. However, their shared genetic architecture remained unclear. Linkage disequilibrium score regression (LDSC) and heritability estimation from summary statistics (ρ-HESS) were applied to estimate heritability and genetic correlations. Bivariate causal mixture model (MiXeR) was used to qualify the polygenic overlap. Then, stratified-LDSC (S-LDSC) was used to identify tissue and cell type specificity. Meanwhile, the adaptive association test called MTaSPUsSet was performed to identify potential pleiotropic genes. The Single Nucleotide Polymorphisms (SNP) heritability was 13% for breast cancer and 5% for ovarian cancer. There was a significant genetic correlation between breast and ovarian cancers (rg=0.21). Breast and ovarian cancers exhibited polygenic overlap, sharing 0.4 K out 2.8 K of causal variants. Tissue and cell type specificity displayed significant enrichment in female breast mammary, uterus, kidney tissues, and adipose cell. Moreover, the 74 potential pleiotropic genes were identified between breast and ovarian cancers, which were related to the regulation of cell cycle and cell death. We quantified the shared genetic architecture between breast and ovarian cancers and shed light on the biological basis of the co-morbidity. Ultimately, these findings facilitated the understanding of disease etiology.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140701666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gabrielė Žukauskaitė, I. Domarkienė, Tautvydas Rančelis, Ingrida Kavaliauskienė, Karolis Baronas, V. Kučinskas, L. Ambrozaitytė
{"title":"Putative protective genomic variation in the Lithuanian population","authors":"Gabrielė Žukauskaitė, I. Domarkienė, Tautvydas Rančelis, Ingrida Kavaliauskienė, Karolis Baronas, V. Kučinskas, L. Ambrozaitytė","doi":"10.1590/1678-4685-GMB-2023-0030","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2023-0030","url":null,"abstract":"Abstract Genomic effect variants associated with survival and protection against complex diseases vary between populations due to microevolutionary processes. The aim of this study was to analyse diversity and distribution of effect variants in a context of potential positive selection. In total, 475 individuals of Lithuanian origin were genotyped using high-throughput scanning and/or sequencing technologies. Allele frequency analysis for the pre-selected effect variants was performed using the catalogue of single nucleotide polymorphisms. Comparison of the pre-selected effect variants with variants in primate species was carried out to ascertain which allele was derived and potentially of protective nature. Recent positive selection analysis was performed to verify this protective effect. Four variants having significantly different frequencies compared to European populations were identified while two other variants reached borderline significance. Effect variant in SLC30A8 gene may potentially protect against type 2 diabetes. The existing paradox of high rates of type 2 diabetes in the Lithuanian population and the relatively high frequencies of potentially protective genome variants against it indicate a lack of knowledge about the interactions between environmental factors, regulatory regions, and other genome variation. Identification of effect variants is a step towards better understanding of the microevolutionary processes, etiopathogenetic mechanisms, and personalised medicine.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140702039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nicolás Glison, Paola Gaiero, Eliana Monteverde, Pablo R Speranza
{"title":"Breeding for reduced seed dormancy to domesticate new grass species.","authors":"Nicolás Glison, Paola Gaiero, Eliana Monteverde, Pablo R Speranza","doi":"10.1590/1678-4685-GMB-2023-0262","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2023-0262","url":null,"abstract":"<p><p>Introducing new grass species into cultivation has long been proposed as beneficial to increase the sustainability and diversity of productive systems. However, wild species with potential tend to show high seed dormancy, causing slow, poor, and unsynchronized seedling emergence. Meanwhile, domesticated species, such as cereals, show lower seed dormancy, facilitating their successful establishment. In this work, we conduct a review of phenotypic variation on seed dormancy and its genetic and molecular basis. This quantitative and highly heritable trait shows phenotype plasticity which is modulated by environmental factors. The level of dormancy depends on the expression of genes associated with the metabolism and sensitivity to the hormones abscisic acid (ABA) and gibberellins (GA), along with other dormancy-specific genes. The genetic regulation of these traits is highly conserved across species. The low seed dormancy observed in cereals and some temperate forages was mostly unconsciously selected during various domestication processes. Emphasis is placed on selecting materials with low seed dormancy for warm-season forage grasses to improve their establishment and adoption. Finally, we review advances in the domestication of dallisgrass, where seed dormancy was considered a focus trait throughout the process.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11046443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140848585","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}
K. Donis, M. Kalil, F. Poswar, Fernando Kok, C. L. Kohem, Soraia Poloni, Taciane Borsatto, F. Vairo, Franciele Cabral Pinheiro, Ida Vanessa Doederlein Schwartz
{"title":"An adult with cystathionine beta-synthase deficiency, camptodactyly-arthropathy-coxa vara-pericarditis syndrome, and deafness: A case report","authors":"K. Donis, M. Kalil, F. Poswar, Fernando Kok, C. L. Kohem, Soraia Poloni, Taciane Borsatto, F. Vairo, Franciele Cabral Pinheiro, Ida Vanessa Doederlein Schwartz","doi":"10.1590/1678-4685-GMB-2022-0335","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2022-0335","url":null,"abstract":"Abstract Massive sequencing platforms allow the identification of complex clinical phenotypes involving more than one autosomal recessive disorder. In this study, we report on an adult patient, born to a related couple (third degree cousins), referred for genetic evaluation due to ectopia lentis, deafness and previous diagnosis of juvenile idiopathic arthritis. He was biochemically diagnosed as having Classic Homocystinuria (HCU); Sanger sequencing of the CBS gene showed the genotype NM_000071.2(CBS):c.[833T>C];[833T>C], compatible with the diagnosis of pyridoxine-responsive HCU. As he also had symptoms not usually associated with HCU, exome sequencing was performed. In addition to the variants found in the Sanger sequencing, the following variants were identified: NM_001256317.1(TMPRSS3):c.[413C>A];[413C>A]; and the NM_005807.6(PRG4):c.[3756dup]:[3756dup], confirming the diagnosis of autosomal recessive nonsyndromic deafness and Camptodactyly-Arthropathy-Coxa Vara-Pericarditis Syndrome (CACP), respectively. Genomic analysis allowed the refinement of the diagnosis of a complex case and improvement of the patient’s treatment.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140730999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
German Romero, Sandra González, Wendy Royero, Adriana González
{"title":"Morphological and transcriptional analysis of Colletotrichum lindemuthianum race 7 during early stages of infection in common bean","authors":"German Romero, Sandra González, Wendy Royero, Adriana González","doi":"10.1590/1678-4685-GMB-2022-0263","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2022-0263","url":null,"abstract":"Abstract The infection process of the hemibiotrophic fungus Colletotrichum lindemuthianum has been independently studied at the microscopic and genomic levels. However, the relationship between the morphological changes and the pathogenicity mechanisms of the fungus at the early stages of the infection remains uncharacterized. Therefore, this study attempts to bridge this gap by integrating microscopic and transcriptional approaches to understand the infection process of C. lindemuthianum. Fungal structures were followed by fluorescence microscopy for 120 hours. Simultaneously, the transcriptomic profile was made using RNAseq. Morphological characterization shows that appressoria, infective vesicles, and secondary hypha formation occur before 72 hours. Additionally, we assembled 38,206 transcripts with lengths between 201 and 3,548 bp. The secretome annotation revealed the expression of 1,204 CAZymes, of which 17 exhibited secretion domains and were identified as chitinases and β-1,3-glucanases, 27 were effector candidates, and 30 were transport proteins mostly associated with ABC-type. Finally, we confirmed the presence and expression of CAC1 role during the appressoria formation of Clr7. This result represents the first report of adenylate cyclase expression evaluated under three different approaches. In conclusion, C. lindemuthianum colonizes the host through different infection structures complemented with the expression of multiple enzymes, where CAC1 favors disease development.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140731617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jun Wang, Wenjia Liang, Xiangwen Wang, Zhao Chen, Lei Jiang
{"title":"LTBP2 regulates cisplatin resistance in GC cells via activation of the NF-κB2/BCL3 pathway","authors":"Jun Wang, Wenjia Liang, Xiangwen Wang, Zhao Chen, Lei Jiang","doi":"10.1590/1678-4685-GMB-2023-0231","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2023-0231","url":null,"abstract":"Abstract Gastric cancer (GC) often develops resistance to cisplatin treatment, but while latent transforming growth factor β-binding protein (LTBP2) is recognized as a potential regulator in GC, its specific role in cisplatin resistance is not fully understood. This study investigated LTBP2’s impact on cisplatin resistance in GC. LTBP2 expression was assessed in various GC cell lines, and its correlation with cisplatin sensitivity was determined through cell viability assays. Lentivirus-mediated LTBP2 silencing in HGC-27 cells demonstrated enhanced cisplatin sensitivity, reduced cell proliferation, and inhibition of the NF-κB2/Bcl-3/cyclin D1 pathway. Additionally, transient transfection overexpressed the NFκB2 gene in LTBP2-silenced HGC-27/DDPR cells, restoring cisplatin sensitivity and upregulating p52/Bcl-3/cyclin D1. In conclusion, silencing LTBP2 could effectively inhibit cell proliferation and mitigate cisplatin resistance via the NFKB noncanonical pathway NFKB2 p52/Bcl-3/cyclin D1. These findings propose LTBP2 as a potential therapeutic target for overcoming cisplatin resistance in GC patients.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140740743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Giovana Regina Weber Hoss, Fernanda Sperb-Ludwig, Tássia Tonon, Soraia Poloni, Sidney Behringer, Henk J. Blom, François Maillot, Ida Vanessa Doederlein Schwartz
{"title":"Homocysteine and methylmalonic acid in Phenylketonuria patients","authors":"Giovana Regina Weber Hoss, Fernanda Sperb-Ludwig, Tássia Tonon, Soraia Poloni, Sidney Behringer, Henk J. Blom, François Maillot, Ida Vanessa Doederlein Schwartz","doi":"10.1590/1678-4685-gmb-2023-0103","DOIUrl":"https://doi.org/10.1590/1678-4685-gmb-2023-0103","url":null,"abstract":"Abstract Hyperhomocysteinemia and vitamin B12 deficiency have been reported in patients with phenylketonuria. In this study, total homocysteine (tHcy) and methylmalonic acid (MMA) levels were analyzed in samples from 25 phenylketonuria (PKU) patients. Comparisons were made between pre- and post-treatment values (n= 3); on treatment values, between periods with high and normal/low phenylalanine (Phe) levels (n= 20); and in women before, during and after pregnancy (n= 3). THcy levels decreased after treating PKU with metabolic formula (p=0.014). Except for a pregnant woman before pregnancy, none of the patients had tHcy values above the normal range. In fact, tHcy was < 5 μmol/L in 34% of the samples. We observed a decrease in Phe, tHcy, and tyrosine levels during pregnancy. MMA levels did not differ significantly, with values remaining in the normal range. These data indicate that there was no B12 deficiency in patients who adhere to the diet. In conclusion, in PKU patients treated with metabolic formula, tHcy is frequently not elevated, remaining even in the lower normal range in some patients. Thus, clinical follow-up and adherence to dietary treatment are crucial to prevent B12 deficiency.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140739191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}