Genetics and Molecular Biology最新文献

Phylogenomic Analysis of Dichrocephala benthamii and Comparative Analysis within Tribe Astereae (Asteraceae). Dichrocephala benthamii 的系统发生组分析和菊科（Asteraceae）内的比较分析。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-10-21 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0340

Hui Chen, Tingyu Li, Xinyu Chen, Xinyi Zheng, Tianmeng Qu, Bo Li, Zhixi Fu

{"title":"Phylogenomic Analysis of Dichrocephala benthamii and Comparative Analysis within Tribe Astereae (Asteraceae).","authors":"Hui Chen, Tingyu Li, Xinyu Chen, Xinyi Zheng, Tianmeng Qu, Bo Li, Zhixi Fu","doi":"10.1590/1678-4685-GMB-2023-0340","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2023-0340","url":null,"abstract":"Dichrocephala benthamii C. B. Clarke has long been used as traditional Chinese medicine. However, the chloroplast (cp) genome of D. benthamii is poorly understood so far. In this study, we sequenced and analyzed the cp genome of D. benthamii. The results showed that the cp genome is 152,350 bp in length, with a pair of inverted repeat regions (IRa and IRb, each 24,982 bp), a large single-copy (LSC) region comprising 84,136 bp, and a small single-copy (SSC) region comprising 18,250 bp. The GC content of the cp genome was 37.3%. A total of 134 genes were identified, including 87 protein-coding genes (CDS), 38 tRNA genes, 8 rRNA genes, and 1 pseudogene (ycf1). Expansion or contraction of IR regions were detected in D. benthamii and other species of the tribe Astereae. Additionally, our analyses showed the types of sequence repeats and the highly variable regions discovered by analyzing the border regions, sequence divergence, and hot spots. The phylogenetic analysis revealed D. benthamii is the basal group of Astereae. The results of this study will be a significant contribution to the genetics and species identification related to D. benthamii.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11495966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498597","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

The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system. 具有 ZZ/ZW 性染色体系统的新热带鱼 Apareiodon sp.

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-10-11 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2024-0098

Ivan Rodrigo Wolf, Michelle Orane Schemberger, Matheus Azambuja, Fernanda Souza de Oliveira, Viviane Nogaroto, Guilherme Targino Valente, Cesar Martins, Marcelo Ricardo Vicari

{"title":"The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system.","authors":"Ivan Rodrigo Wolf, Michelle Orane Schemberger, Matheus Azambuja, Fernanda Souza de Oliveira, Viviane Nogaroto, Guilherme Targino Valente, Cesar Martins, Marcelo Ricardo Vicari","doi":"10.1590/1678-4685-GMB-2024-0098","DOIUrl":"10.1590/1678-4685-GMB-2024-0098","url":null,"abstract":"Neotropical fishes emerge as an extremely diverse group of vertebrates where genomic strategies to evaluate structural and functional features are still beginning. Here, we present a second draft genome of Apareiodon sp. (2n=54, ZZ/ZW), adding PacBio technology whole genome sequencing, and assembling by combining two technologies (long and short reads). Using a detailed strategy for genome assembly with fish genomes of Pygocentrus nattereri, Carassius auratus, and Astyanax mexicanus as references, the final assembly of the Apareiodon sp. genome generated 93 scaffolds, an N50 of 37,200,078 bases, and a size estimate considering 28 scaffolds (26 autosomes+ZW) of ~945 Mb. In Apareiodon sp., this second genome draft confirmed that ~36% of the genome is composed of repetitive DNA. Furthermore, the new draft genome has improved genomic quality assessments, allowing the annotation of 36,290 genes and 15,683 proteins, which presented similarities to reference genomes. The second draft genome of Apareiodon sp. will be useful for research on integrative cytogenetic and genomic data. It will open perspectives for analyzing sex-determining genes in Neotropical fish with a ZZ/ZW sex chromosome system.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11468460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406322","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

What we know so far and what we can expect next: A molecular investigation of plant parasitism. 我们目前所知道的和我们可以期待的下一步：植物寄生的分子研究。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-30 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2024-0051

Juliane Karine Ishida, Elaine Cotrim Costa

引用次数: 0

Genetic associations with disease in populations with Indigenous American ancestries. 美洲原住民血统人群中疾病的遗传关联。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-09 DOI: 10.1590/1678-4685-gmb-2023-0024

Lucas Vicuña

{"title":"Genetic associations with disease in populations with Indigenous American ancestries.","authors":"Lucas Vicuña","doi":"10.1590/1678-4685-gmb-2023-0024","DOIUrl":"https://doi.org/10.1590/1678-4685-gmb-2023-0024","url":null,"abstract":"The genetic architecture of complex diseases affecting populations with Indigenous American ancestries is poorly understood due to their underrepresentation in genomics studies. While most of the genetic diversity associated with disease trait variation is shared among worldwide populations, a fraction of this component is expected to be unique to each continental group, including Indigenous Americans. Here, I describe the current state of knowledge from genome-wide association studies on Indigenous populations, as well as non-Indigenous populations with partial Indigenous ancestries from the American continent, focusing on disease susceptibility and anthropometric traits. While some studies identified risk alleles unique to Indigenous populations, their effects on trait variation are mostly small. I suggest that the associations rendered by many inter-population studies are probably inflated due to the absence of socio-cultural-economic covariates in the association models. I encourage the inclusion of admixed individuals in future GWAS studies to control for inter-ancestry differences in environmental factors. I suggest that some complex diseases might have arisen as trade-off costs of adaptations to past evolutionary selective pressures. Finally, I discuss how expanding panels with Indigenous ancestries in GWAS studies is key to accurately assess genetic risk in populations from the American continent, thus decreasing global health disparities.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217263","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}

引用次数: 0

Expression profile of inflammasome genes in individuals with Down syndrome. 唐氏综合征患者炎症小体基因的表达谱。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-09 DOI: 10.1590/1678-4685-gmb-2023-0339

Juliana Vieira de Barros Arcoverde,Carla Fernandes Dos Santos,Maria Cecília Magalhães Luckwu,Raysa Samanta Moraes Laranjeira,Aldianne Milene Dos Santos Barbosa,Thays Maria Costa de Lucena,Jaqueline de Azevêdo Silva,Neide Santos

{"title":"Expression profile of inflammasome genes in individuals with Down syndrome.","authors":"Juliana Vieira de Barros Arcoverde,Carla Fernandes Dos Santos,Maria Cecília Magalhães Luckwu,Raysa Samanta Moraes Laranjeira,Aldianne Milene Dos Santos Barbosa,Thays Maria Costa de Lucena,Jaqueline de Azevêdo Silva,Neide Santos","doi":"10.1590/1678-4685-gmb-2023-0339","DOIUrl":"https://doi.org/10.1590/1678-4685-gmb-2023-0339","url":null,"abstract":"Down syndrome (DS), affecting 1 in 700 live births, is the most prevalent chromosomal disorder among newborns. Recognizable by classical clinical features, patients with DS are susceptible to various immunological misbalances. Inflammasome is (mis)activated in several immune-mediated diseases, however studies on individuals with DS are lacking. The present study evaluated the gene expression of NLRP1, NLRP3 and IL-1β in individuals with DS, aiming to understand their susceptibility to immune-mediated diseases. In addition, we assessed whether the individuals with DS present a differential inflammatory response after in vitro infection using PBMCs. For the gene expression assay, 20 individuals with DS and 15 healthy individuals for the control group (CT) were included, while the in vitro infection assay included 10 subjects. mRNA levels from individuals with DS group showed 1.9-fold change (FC) downregulation for NLRP1 (p=0.0001), but no differences for NLRP3 and IL1β. We did not observe significant differences between lipopolysaccharide (LPS)-treated and untreated cells in our in vitro assays. The differential expression of NLRP1 in individuals with DS suggests a potential association with susceptibility to the development of immune-mediated diseases, but further analysis is needed to confirm this relationship.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217262","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}

引用次数: 0

The complete chloroplast genome sequences of three Pedicularis species (Orobanchaceae). 三个 Pedicularis 物种（大戟科）的完整叶绿体基因组序列。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2024-0010

Mingcheng Wang, Shuqiao Zhang, Lei Zhang

{"title":"The complete chloroplast genome sequences of three Pedicularis species (Orobanchaceae).","authors":"Mingcheng Wang, Shuqiao Zhang, Lei Zhang","doi":"10.1590/1678-4685-GMB-2024-0010","DOIUrl":"https://doi.org/10.1590/1678-4685-GMB-2024-0010","url":null,"abstract":"Pedicularis L., a generally bothersome genus of hemiparasitic plants, is primarily native to southwestern China. The phylogenetic relationship and evolutionary history of this genus have not yet been fully resolved. In this study, we sequenced and assembled chloroplast genomes of three Pedicularis species, P. chinensis, P. melampyriflora, and P. striata using high-throughput Illumina sequencing. The assembled plastomes were 142,059 bp (P. chinensis) to 152,146 bp (P. striata) in size, containing 110 (P. chinensis) to 117 (P. striata) genes. Moreover, we identified 13-15 pseudogenes within the three plastomes, nine of which were pseudogenized in all three species. The three plastomes exhibited a similar codon usage pattern. Moreover, the plastomes contained abundant simple sequence repeats and long repeats, which showed slight variations between the three species. A maximum likelihood analysis was performed to elucidate the phylogenetic positions of the three species within the Pedicularis genus. The plastomes presented in our study can be used as valuable genomic resources for further genetic and genomic studies of the Pedicularis genus.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361410","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}

引用次数: 0

Pioneering role of RNA in the early evolution of life. RNA 在生命早期进化中的先锋作用。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2024-0028

Israel Muñoz-Velasco, Adrián Cruz-González, Ricardo Hernández-Morales, José Alberto Campillo-Balderas, Wolfgang Cottom-Salas, Rodrigo Jácome, Alberto Vázquez-Salazar

引用次数: 0

DNA copy number profiles and systems biology connect chromatin remodeling and DNA repair in high-risk neuroblastoma. DNA拷贝数图谱和系统生物学将高危神经母细胞瘤中的染色质重塑和DNA修复联系起来。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2024-0007

Thatyanne Gradowski F da C do Nascimento, Joice de Faria Poloni, Mateus Eduardo de Oliveira Thomazini, Luciane R Cavalli, Selene Elifio-Esposito, Bruno César Feltes

{"title":"DNA copy number profiles and systems biology connect chromatin remodeling and DNA repair in high-risk neuroblastoma.","authors":"Thatyanne Gradowski F da C do Nascimento, Joice de Faria Poloni, Mateus Eduardo de Oliveira Thomazini, Luciane R Cavalli, Selene Elifio-Esposito, Bruno César Feltes","doi":"10.1590/1678-4685-GMB-2024-0007","DOIUrl":"10.1590/1678-4685-GMB-2024-0007","url":null,"abstract":"Neuroblastoma (NB) is a solid tumor that accounts for 15% of all pediatric oncological deaths, and much is due to the low response to therapy in relapsed tumors. High-risk NB may present deletions in chromosome 11q, which may be associated with other chromosomal alterations and a poor response to therapy, but this association is still poorly understood. Using a systems biology network approach, we studied three patients with high-risk NB with deleted 11q stage 4 to highlight the connections between treatment resistance and copy number alterations in distinct cases. We built different protein-protein interaction networks for each patient based on protein-coding genes mapped at the cytobands pre- and post-chemotherapy from distinct copy number alterations data. In the post-chemotherapy networks, we identified five common regulatory nodes corresponding to the gained region located in ch17q:BIRC5, BRCA1, PRKCA, SUMO2, andGPS1. A crosslink between DNA damage and chromatin remodeling proteins was also found - a connection still poorly understood in NB. We identified a potential connection between XPB gain and chemoresistance of NB. The findings help elucidate the molecular profiles of high-risk NB with 11q deletion in pre- and post-chemotherapy tumor samples, which may reflect unique profiles in poor response to treatment.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361409","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}

引用次数: 0

Accuracy of genotype imputation of a low-density SNP array for the Amazon fish Colossoma macropomum. 低密度 SNP 阵列对亚马逊鱼类 Colossoma macropomum 基因型估算的准确性。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0364

John F G Agudelo, Vito A Mastrochirico-Filho, Baltasar F Garcia, Raquel B Ariede, José M Yáñez, Gustavo M R Valladão, Diogo T Hashimoto

{"title":"Accuracy of genotype imputation of a low-density SNP array for the Amazon fish Colossoma macropomum.","authors":"John F G Agudelo, Vito A Mastrochirico-Filho, Baltasar F Garcia, Raquel B Ariede, José M Yáñez, Gustavo M R Valladão, Diogo T Hashimoto","doi":"10.1590/1678-4685-GMB-2023-0364","DOIUrl":"10.1590/1678-4685-GMB-2023-0364","url":null,"abstract":"In South America, Tambaqui (Colossoma macropomum) stands as the primary target for aquaculture, yet breeding programs for this Amazon native species are in their early stages. While high-density single nucleotide polymorphism (SNP) arrays are pivotal for aquaculture breeding, their costs can be prohibitive for non- or semi-industrial species. To overcome this, a cost-effective approach involves developing low-density SNP arrays followed by genotype imputation to higher densities. In this study, a 1K SNP array for tambaqui was created and validated, offering a balance between SNP quantity and genome representativity. The imputation accuracy from various SNP densities to a medium-density array was evaluated, with the 1K density demonstrating the best trade-off (accuracy of 0.93). This subset was further utilized to construct a commercial array through Agriseq™ targeted genotyping-by-sequencing, validated in 192 DNA samples, affirming its high quality for genotyping tambaqui. The low-density SNP array, with genome-wide coverage and high polymorphism, emerges as an effective tool for exploring genetic variation within diverse populations. Population analyses using the 1K panel proved to be an efficient tool for genetic characterization of sampled broodstocks, making it a valuable resource for genetic improvement programs targeting this Amazon native species.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361408","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

Variability and functional characterization of the Phakopsora pachyrhizi Egh16-like effectors. Phakopsora pachyrhizi Egh16 类效应器的变异性和功能特征。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0192

Fernanda Machado Castanho, Beatriz Lorena Comin da Costa, Valéria Yukari Abe, Alessandra Yokoyama, Luana Mieko Darben, Liliane Santana Oliveira, Everton Geraldo Capote Ferreira, Ivani de Oliveira Negrão Lopes, Mayra Costa da Cruz Gallo de Carvalho, Maria Isabel Balbi-Peña, Francismar Corrêa Marcelino-Guimarães

{"title":"Variability and functional characterization of the Phakopsora pachyrhizi Egh16-like effectors.","authors":"Fernanda Machado Castanho, Beatriz Lorena Comin da Costa, Valéria Yukari Abe, Alessandra Yokoyama, Luana Mieko Darben, Liliane Santana Oliveira, Everton Geraldo Capote Ferreira, Ivani de Oliveira Negrão Lopes, Mayra Costa da Cruz Gallo de Carvalho, Maria Isabel Balbi-Peña, Francismar Corrêa Marcelino-Guimarães","doi":"10.1590/1678-4685-GMB-2023-0192","DOIUrl":"10.1590/1678-4685-GMB-2023-0192","url":null,"abstract":"Effector proteins in Phakopsora pachyrhizi (Pp), the causative agent of Asian Soybean rust, are involved in the infection process. A previous study identified a rust effector Egh16-like family based expression profile during the interaction with soybean. Herein, we scrutinized available the Pp genomes to validate the predicted Egh16-like family of Pp and identify new family members. We described 22 members of the Egh16-like gene family in the Pp MT2006 genome and 18 in the UFV02 and K8108 genomes, highlighting a family expansion. Family members have a small signal peptide, conserved cysteine-rich R/Y/FxC motifs in the C-terminal region, and a virulence-related Egh16-like domain and were able to suppress PTI related responses in Benthamiana. Phylogenetic analysis placed the family members into eight clusters, with members induced during the early stages of rust infection. Members of clusters VI and VII are present in different copy numbers in Pp genomes and suppressed PAMP-related responses.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11378017/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139796","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