IF 2.3 3区生物学

Genome Pub Date : 2024-10-01 Epub Date: 2024-09-03 DOI: 10.1139/gen-2024-0019

Kabwe Nkongolo, Paul Michael

{"title":"Reduced representation bisulfite sequencing (RRBS) analysis reveals variation in distribution and levels of DNA methylation in white birch (Betula papyrifera) exposed to nickel.","authors":"Kabwe Nkongolo, Paul Michael","doi":"10.1139/gen-2024-0019","DOIUrl":"10.1139/gen-2024-0019","url":null,"abstract":"Research in understanding the role of genetics and epigenetics in plant adaptations to environmental stressors such as metals is still in its infancy. The objective of the present study is to assess the effect of nickel on DNA methylation level and distribution in white birch (Betula papyrifera Marshall) using reduced representation bisulfite sequencing (RRBS). The distribution of methylated C sites of each sample revealed that the level of methylation was much higher in CG context varying between 54% and 65%, followed by CHG (24%-31.5%), and then CHH with the methylation rate between 3.3% and 5.2%. The analysis of differentially methylated regions (DMR) revealed that nickel induced both hypermethylation and hypomethylation when compared to water. Detailed analysis showed for the first time that nickel induced a higher level of hypermethylation compared to controls, while potassium triggers a higher level of hypomethylation compared to nickel. Surprisingly, the analysis of the distribution of DMRs revealed that 38%-42% were located in gene bodies, 20%-24% in exon, 19%-20% in intron, 16%-17% in promoters, and 0.03%-0.04% in transcription start site. RRBS was successful in detecting and mapping DMR in plants exposed to nickel.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"351-367"},"PeriodicalIF":2.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125507","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}

引用次数: 0

Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems. 不同性染色体系统鱼类可转座元件动态对比分析

IF 2.3 3区生物学

Genome Pub Date : 2024-10-01 Epub Date: 2024-05-13 DOI: 10.1139/gen-2023-0134

Carolina Crepaldi, Diogo Cavalcanti Cabral-de-Mello, Patricia Pasquali Parise-Maltempi

{"title":"Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems.","authors":"Carolina Crepaldi, Diogo Cavalcanti Cabral-de-Mello, Patricia Pasquali Parise-Maltempi","doi":"10.1139/gen-2023-0134","DOIUrl":"10.1139/gen-2023-0134","url":null,"abstract":"Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: Megaleporinus elongatus (Z1Z1Z2Z2/Z1W1Z2W2), Megaleporinus macrocephalus (ZZ/ZW) (both with highly differentiated W sex chromosomes), and Leporinus friderici (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with L. friderici having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both Megaleporinus recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, L. friderici showed the opposite pattern. Therefore, despite having similar TE compositions, Megaleporinus and Leporinus exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"339-350"},"PeriodicalIF":2.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140915974","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}

引用次数: 0

DNA barcoding of southern African mammal species and construction of a reference library for forensic application. 南部非洲哺乳动物物种的 DNA 条形码和法医应用参考文献库的构建。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-01 Epub Date: 2024-07-12 DOI: 10.1139/gen-2023-0050

J R Baxter, A Kotze, M de Bruyn, K Matlou, K Labuschagne, M Mwale

{"title":"DNA barcoding of southern African mammal species and construction of a reference library for forensic application.","authors":"J R Baxter, A Kotze, M de Bruyn, K Matlou, K Labuschagne, M Mwale","doi":"10.1139/gen-2023-0050","DOIUrl":"10.1139/gen-2023-0050","url":null,"abstract":"Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"378-391"},"PeriodicalIF":2.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141599107","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}

引用次数: 0

Specific amino acid changes correlate with pathogenic flavobacteria. 特定氨基酸的变化与致病性黄杆菌有关。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-01 Epub Date: 2022-09-05 DOI: 10.1139/gen-2024-0018

Vincent Gélinas, Valérie E Paquet, Maude F Paquet, Steve J Charette, Antony T Vincent

{"title":"Specific amino acid changes correlate with pathogenic flavobacteria.","authors":"Vincent Gélinas, Valérie E Paquet, Maude F Paquet, Steve J Charette, Antony T Vincent","doi":"10.1139/gen-2024-0018","DOIUrl":"10.1139/gen-2024-0018","url":null,"abstract":"Flavobacterium is a genus of microorganisms living in a variety of hosts and habitats across the globe. Some species are found in fish organs, and only a few, such as Flavobacterium psychrophilum and Flavobacterium columnare, cause severe disease and losses in fish farms. The evolution of flavobacteria that are pathogenic to fish is unknown, and the protein changes accountable for the selection of their colonization to fish have yet to be determined. A phylogenetic tree was constructed with the complete genomic sequences of 208 species of the Flavobacterium genus using 861 softcore genes. This phylogenetic analysis revealed clade CII comprising nine species, including five pathogenic species, and containing the most species that colonize fish. Thirteen specific amino acid changes were found to be conserved across 11 proteins within the CII clade compared with other clades, and these proteins were enriched in functions related to replication, recombination, and repair. Several of these proteins are known to be involved in pathogenicity and fitness adaptation in other bacteria. Some of the observed amino acid changes can be explained by preferential selection for certain codons and tRNA frequency. These results could help explain how species belonging to the CII clade adapt to fish environments.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"67 10","pages":"368-377"},"PeriodicalIF":2.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345157","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}

引用次数: 0

Chromosome mapping of retrotransposon AviRTE in a neotropical bird species: Trogon surrucura (Trogoniformes; Trogonidae). 新热带鸟类逆转录转座子 AviRTE 的染色体图谱：Trogon surrucura (Trogoniformes; Trogonidae)。

IF 2.3 3区生物学

Genome Pub Date : 2024-09-01 Epub Date: 2024-05-09 DOI: 10.1139/gen-2023-0075

Nairo Farias de Farias, Ricardo José Gunski, Analía Del Valle Garnero, Andrés Delgado Cañedo, Edivaldo Herculano Correa de Oliveira, Fábio Augusto Oliveira Silva, Fabiano Pimentel Torres

{"title":"Chromosome mapping of retrotransposon AviRTE in a neotropical bird species: Trogon surrucura (Trogoniformes; Trogonidae).","authors":"Nairo Farias de Farias, Ricardo José Gunski, Analía Del Valle Garnero, Andrés Delgado Cañedo, Edivaldo Herculano Correa de Oliveira, Fábio Augusto Oliveira Silva, Fabiano Pimentel Torres","doi":"10.1139/gen-2023-0075","DOIUrl":"10.1139/gen-2023-0075","url":null,"abstract":"Avian genomes are characterized as being more compact than other amniotes, with less diversity and density of transposable elements (TEs). In addition, birds usually show bimodal karyotypes, exhibiting a great variation in diploid numbers. Some species present unusually large sex chromosomes, possibly due to the accumulation of repetitive sequences. Avian retrotransposon-like element (AviRTE) is a long interspersed nuclear element (LINE) recently discovered in the genomes of birds and nematodes, and it is still poorly characterized in terms of chromosomal mapping and phylogenetic relationships. In this study, we mapped AviRTE isolated from the Trogon surrucura genome into the T. surrucura (TSU) karyotype. Furthermore, we analyzed the phylogenetic relationships of this LINE in birds and other vertebrates. Our results showed that the distribution pattern of AviRTE is not restricted to heterochromatic regions, with accumulation on the W chromosome of TSU, yet another species with an atypical sex chromosome and TE hybridization. The phylogenetic analysis of AviRTE sequences in birds agreed with the proposed phylogeny of species in most clades, and allowed the detection of this sequence in other species, expanding the distribution of the element.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"307-315"},"PeriodicalIF":2.3,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897920","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}

引用次数: 0

Chromosomal and genomic analysis suggests single origin and high molecular differentiation of the B chromosome of Abracris flavolineata. 染色体和基因组分析表明，Abracris flavolineata 的 B 染色体起源单一，分子分化程度较高。

IF 2.3 3区生物学

Genome Pub Date : 2024-09-01 Epub Date: 2024-05-09 DOI: 10.1139/gen-2023-0122

Diogo Milani, Ana Elisa Gasparotto, Vilma Loreto, Dardo A Martí, Diogo C Cabral-de-Mello

{"title":"Chromosomal and genomic analysis suggests single origin and high molecular differentiation of the B chromosome of Abracris flavolineata.","authors":"Diogo Milani, Ana Elisa Gasparotto, Vilma Loreto, Dardo A Martí, Diogo C Cabral-de-Mello","doi":"10.1139/gen-2023-0122","DOIUrl":"10.1139/gen-2023-0122","url":null,"abstract":"Supernumerary chromosomes (B chromosomes) have been an intriguing subject of study. Our understanding of the molecular differentiation of B chromosomes from an interpopulation perspective remains limited, with most analyses involving chromosome banding and mapping of a few sequences. To gain insights into the molecular composition, origin, and evolution of B chromosomes, we conducted cytogenetic and next-generation sequencing analysis of the repeatome in the grasshopper Abracris flavolineata across various populations. Our results unveiled the presence of B chromosomes in two newly investigated populations and described new satellite DNA sequences. While we observed some degree of genetic connection among A. flavolineata populations, our comparative analysis of genomes with and without B chromosomes provided evidence of two new B chromosome variants. These variants exhibited distinct compositions of various repeat classes, including transposable elements and satellite DNAs. Based on shared repeats, their chromosomal location, and the C-positive heterochromatin content on the B chromosome, these variants likely share a common origin but have undergone distinct molecular differentiation processes, resulting in varying degrees of heterochromatinization. Our data serve as a detailed example of the dynamic and differentiated nature of B chromosome molecular content at the interpopulation level, even when they share a common origin.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"327-338"},"PeriodicalIF":2.3,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897855","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}

引用次数: 0

Expression of defensin genes across house fly (Musca domestica) life history gives insight into immune system subfunctionalization. 家蝇（Musca domestica）生命史中防御素基因的表达深入揭示了免疫系统的亚功能化。

IF 2.3 3区生物学

Genome Pub Date : 2024-09-01 Epub Date: 2024-05-09 DOI: 10.1139/gen-2024-0016

Danial Asgari, Tanya Purvis, Victoria Pickens, Christopher Saski, Richard P Meisel, Dana Nayduch

{"title":"Expression of defensin genes across house fly (Musca domestica) life history gives insight into immune system subfunctionalization.","authors":"Danial Asgari, Tanya Purvis, Victoria Pickens, Christopher Saski, Richard P Meisel, Dana Nayduch","doi":"10.1139/gen-2024-0016","DOIUrl":"10.1139/gen-2024-0016","url":null,"abstract":"Animals encounter diverse microbial communities throughout their lifetime, which exert varying selection pressures. Antimicrobial peptides (AMPs), which lyse or inhibit microbial growth, are a first line of defense against some of these microbes. Here we examine how developmental variation in microbial exposure has affected the evolution of expression and amino acid sequences of Defensins (an ancient class of AMPs) in the house fly (Musca domestica). The house fly is a well-suited model for this work because it trophically associates with varying microbial communities throughout its life history and its genome contains expanded families of AMPs, including Defensins. We identified two subsets of house fly Defensins: one expressed in larvae or pupae, and the other expressed in adults. The amino acid sequences of these two Defensin subsets form distinct monophyletic clades, and they are located in separate gene clusters in the genome. The adult-expressed Defensins evolve faster than larval/pupal Defensins, consistent with different selection pressures across developmental stages. Our results therefore suggest that varied microbial communities encountered across life history can shape the evolutionary trajectories of immune genes.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"316-326"},"PeriodicalIF":2.3,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897921","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}

引用次数: 0

Fragments derived from non-coding RNAs: how complex is genome regulation? 非编码 RNA 片段：基因组调控有多复杂？

IF 2.3 3区生物学

Genome Pub Date : 2024-09-01 Epub Date: 2024-04-29 DOI: 10.1139/gen-2023-0136

Miguel Ángel Velázquez-Flores, Ruth Ruiz Esparza-Garrido

引用次数: 0

Understanding microchromosomal organization and evolution in four representative woodpeckers (Picidae, Piciformes) through BAC-FISH analysis. 通过 BAC-FISH 分析了解四种代表性啄木鸟（啄木鸟科、啄木鸟属）的微染色体组织和进化。

IF 2.3 3区生物学

Genome Pub Date : 2024-07-01 Epub Date: 2024-05-14 DOI: 10.1139/gen-2023-0096

Suziane Alves Barcellos, Rafael Kretschmer, Marcelo Santos de Souza, Victoria Tura, Luciano Cesar Pozzobon, Thales Renato Ochotorena de Freitas, Darren K Griffin, Rebecca O'Connor, Ricardo José Gunski, Analía Del Valle Garnero

{"title":"Understanding microchromosomal organization and evolution in four representative woodpeckers (Picidae, Piciformes) through BAC-FISH analysis.","authors":"Suziane Alves Barcellos, Rafael Kretschmer, Marcelo Santos de Souza, Victoria Tura, Luciano Cesar Pozzobon, Thales Renato Ochotorena de Freitas, Darren K Griffin, Rebecca O'Connor, Ricardo José Gunski, Analía Del Valle Garnero","doi":"10.1139/gen-2023-0096","DOIUrl":"10.1139/gen-2023-0096","url":null,"abstract":"The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species (Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus, and Picumnus nebulosus) was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from Gallus gallus and Taeniopygia guttata. Findings suggest that P. nebulosus (2n = 110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for V. spilogaster (2n = 88) and demonstrated microchromosomal rearrangements involving C. campestris plus a single, unique hitherto undescribed rearrangement in V. spilogaster. This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of M. candidus is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"223-232"},"PeriodicalIF":2.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140922037","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}

引用次数: 0

Genomic prediction in Brassica napus: evaluating the benefit of imputed whole-genome sequencing data. 甘蓝型油菜的基因组预测：评估估算全基因组测序数据的益处。

IF 2.3 3区生物学

Genome Pub Date : 2024-07-01 Epub Date: 2024-05-06 DOI: 10.1139/gen-2023-0126

Sven E Weber, Lennard Roscher-Ehrig, Tobias Kox, Amine Abbadi, Andreas Stahl, Rod J Snowdon

{"title":"Genomic prediction in Brassica napus: evaluating the benefit of imputed whole-genome sequencing data.","authors":"Sven E Weber, Lennard Roscher-Ehrig, Tobias Kox, Amine Abbadi, Andreas Stahl, Rod J Snowdon","doi":"10.1139/gen-2023-0126","DOIUrl":"10.1139/gen-2023-0126","url":null,"abstract":"Advances in sequencing technology allow whole plant genomes to be sequenced with high quality. Combining genotypic and phenotypic data in genomic prediction helps breeders to select crossing partners in partially phenotyped populations. In plant breeding programs, the cost of sequencing entire breeding populations still exceeds available genotyping budgets. Hence, the method for genotyping is still mainly single nucleotide polymorphism (SNP) arrays; however, arrays are unable to assess the entire genome- and population-wide diversity. A compromise involves genotyping the entire population using an SNP array and a subset of the population with whole-genome sequencing. Both datasets can then be used to impute markers from whole-genome sequencing onto the entire population. Here, we evaluate whether imputation of whole-genome sequencing data enhances genomic predictions, using data from a nested association mapping population of rapeseed (Brassica napus). Employing two cross-validation schemes that mimic scenarios for the prediction of close and distant relatives, we show that imputed marker data do not significantly improve prediction accuracy, likely due to redundancy in relationship estimates and imputation errors. In simulation studies, only small improvements were observed, further corroborating the findings. We conclude that SNP arrays are already equipped with the information that is added by imputation through relationship and linkage disequilibrium.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"210-222"},"PeriodicalIF":2.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140850004","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}

引用次数: 0

Genome最新文献