IF 2.3 3区生物学

Genome Pub Date : 2024-10-21 DOI: 10.1139/gen-2023-0110

Nayyer Abdollahi Sisi, Eva Herzog, Amine Abbadi, Rod J Snowdon, Agnieszka A Golicz

{"title":"Analysis of the winter oilseed rape recombination landscape suggests maternal-paternal bias.","authors":"Nayyer Abdollahi Sisi, Eva Herzog, Amine Abbadi, Rod J Snowdon, Agnieszka A Golicz","doi":"10.1139/gen-2023-0110","DOIUrl":"https://doi.org/10.1139/gen-2023-0110","url":null,"abstract":"Recombination, the reciprocal exchange of DNA between homologous chromosomes, is a mandatory step necessary for meiosis progression. Crossovers between homologous chromosomes generate new combinations of alleles and maintain genetic diversity. Due to genetic, epigenetic, and environmental factors, the recombination landscape is highly heterogeneous along the chromosomes and it also differs between populations and between sexes. Here, we investigated recombination characteristics across the 19 chromosomes of the model allopolyploid crop species oilseed rape (Brassica napus L.), using two unique multiparental populations derived from two genetically divergent founder pools, each of which comprised 50 genetically diverse founder accessions. A fully balanced, pairwise chain-crossing scheme was utilized to create each of the two populations. A total of 3213 individuals, spanning five successive generations, were genotyped using a 15K SNP array. We observed uneven distribution of recombination along chromosomes, with some genomic regions undergoing substantially more frequent recombination in both populations. In both populations, maternal recombination events were more frequent than paternal recombination. This study provides unique insight into the recombination landscape at chromosomal level and reveals a maternal-paternal bias for recombination number with implications for breeding.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463225","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

Mapping of quantitative trait loci (QTL) in Brassica napus L. for tolerance to water stress. 绘制甘蓝型油菜对水分胁迫耐受性的数量性状位点（QTL）图。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-17 DOI: 10.1139/gen-2023-0127

Samadhi B Jayarathna, Harmeet S Chawla, Mohammed M Mira, Robert W Duncan, Claudio Stasolla

{"title":"Mapping of quantitative trait loci (QTL) in Brassica napus L. for tolerance to water stress.","authors":"Samadhi B Jayarathna, Harmeet S Chawla, Mohammed M Mira, Robert W Duncan, Claudio Stasolla","doi":"10.1139/gen-2023-0127","DOIUrl":"https://doi.org/10.1139/gen-2023-0127","url":null,"abstract":"Brassica napus L. plants are sensitive to water stress conditions throughout their life cycle from seed germination to seed setting. This study aims at identifying quantitative trait loci (QTL) linked to B. napus tolerance to water stress mimicked by applications of 10% polyethylene glycol-6000 (PEG-6000). Two doubled haploid populations, each consisting of 150 genotypes, were used for this research. Plants at the two true leaf stage of development were grown in the absence (control) or presence (stress) of PEG-6000 under controlled environmental conditions for 48 h, and the drought stress index was calculated for each genotype. All genotypes, along with their parents, were genotyped using the Brassica Infinium 90K SNP BeadChip Array. Inclusive composite interval mapping was used to identify QTL. Six QTL and 12 putative QTL associated with water stress tolerance were identified across six chromosomes (A2, A3, A4, A9, C3, and C7). Collectively, 2154 candidate genes for water stress tolerance were identified for all the identified QTL. Among them, 213 genes were identified as being directly associated with water stress (imposed by PEG-6000) tolerance based on nine functional annotations. These results can be incorporated into future breeding initiatives to select plant material with the ability to cope effectively with water stress.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463228","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

Heat shock responsive genes in Brassicaceae: genome-wide identification, phylogeny, and evolutionary associations within and between genera. 十字花科植物的热休克反应基因：全基因组鉴定、系统发育以及属内和属间的进化关联。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-16 DOI: 10.1139/gen-2024-0061

Aldrin Y Cantila, Sheng Chen, Kadambot H M Siddique, Wallace A Cowling

{"title":"Heat shock responsive genes in Brassicaceae: genome-wide identification, phylogeny, and evolutionary associations within and between genera.","authors":"Aldrin Y Cantila, Sheng Chen, Kadambot H M Siddique, Wallace A Cowling","doi":"10.1139/gen-2024-0061","DOIUrl":"https://doi.org/10.1139/gen-2024-0061","url":null,"abstract":"Heat stress affects the growth and development of Brassicaceae crops. Plant breeders aim to mitigate the effects of heat stress by selecting for heat stress tolerance, but the genes responsible for heat stress in Brassicaceae remain largely unknown. During heat stress, heat shock proteins (HSPs) function as molecular chaperones to aid in protein folding, and heat shock transcription factors (HSFs) serve as transcriptional regulators of HSP expression. We identified 5002 heat shock related genes, including HSPs and HSFs, across 32 genomes in Brassicaceae. Among these, 3347 genes were duplicated, with segmented duplication primarily contributing to their expansion. We identified 466 physical gene clusters, including 240 homogenous clusters and 226 heterogeneous clusters, shedding light on the organization of heat shock related genes. Notably, 37 genes were co-located with published thermotolerance quantitative trait loci, which supports their functional role in conferring heat stress tolerance. This study provides a comprehensive resource for the identification of functional Brassicaceae heat shock related genes, elucidates their clustering and duplication patterns and establishes the genomic foundation for future heat tolerance research. We hypothesise that genetic variants in HSP and HSF genes in certain species have potential for improving heat stress tolerance in Brassicaceae crops.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463227","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

Association mapping identifies stable loci containing novel genes for developmental and reproductive traits in sorghum. 关联图谱确定了含有高粱发育和生殖性状新基因的稳定位点。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-16 DOI: 10.1139/gen-2024-0030

Hari D Upadhyaya, Lihua Wang, Andrew H Paterson, C L L Gowda, Rajendra Kumar, Jieqin Li, Yi-Hong Wang

引用次数: 0

Reduced representation bisulfite sequencing (RRBS) analysis reveals variation in distribution and levels of DNA methylation in white birch (Betula papyrifera) exposed to nickel. 还原表征亚硫酸氢盐测序（RRBS）分析揭示了暴露于镍的白桦树（Betula papyrifera）DNA甲基化分布和水平的变化。

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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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

Distinct patterns of satDNA distribution in holocentric chromosomes of spike-sedges (Eleocharis, Cyperaceae). 穗花杉（Eleocharis，茜草科）全中心染色体中 satDNA 分布的不同模式。

IF 2.3 3区生物学

Genome Pub Date : 2024-09-16 DOI: 10.1139/gen-2024-0089

Thaíssa Boldieri de Souza, Letícia Maria Parteka, Yi-Tzu Kuo, Thiago Henrique do Nascimento, Veit Schubert, Andrea Pedrosa-Harand, André Marques, Andreas Houben, André Laforga Vanzela

{"title":"Distinct patterns of satDNA distribution in holocentric chromosomes of spike-sedges (Eleocharis, Cyperaceae).","authors":"Thaíssa Boldieri de Souza, Letícia Maria Parteka, Yi-Tzu Kuo, Thiago Henrique do Nascimento, Veit Schubert, Andrea Pedrosa-Harand, André Marques, Andreas Houben, André Laforga Vanzela","doi":"10.1139/gen-2024-0089","DOIUrl":"https://doi.org/10.1139/gen-2024-0089","url":null,"abstract":"Eleocharis R. Br. (Cyperaceae) species are known for having holocentric chromosomes, which enable rapid karyotype differentiation. High intra- and interspecific variations in chromosome numbers and genome sizes are documented for different Eleocharis species, frequently accompanied by fluctuations in the repetitive DNA fraction. However, a lack of detailed analysis has hampered a better understanding of the interplay between holocentricity and repetitive DNA evolution in this genus. In our study, we confirmed the holocentricity of Eleocharis chromosomes by immunostaining against the kinetochore protein KNL1 and the cell-cycle dependent posttranslational modifications histone H2AThr121ph and H3S10ph. We further studied the composition and chromosomal distribution of the main satellite DNA repeats found in the newly sequenced species E. maculosa, E. geniculata, E. parodii, E. elegans, and E. montana. Five of the six satellites discovered were arranged in clusters, while EmaSAT14 was distributed irregularly along the chromatid length in a line-like manner. EmaSAT14 monomers were present in a few copies in few species across the Eleocharis phylogenetic tree. Nonetheless, they were accumulated within a restricted group of Maculosae series, subgenus Eleocharis. The data indicates that the amplification and line-like distribution of EmaSAT14 along chromatids may have occurred recently within a section of the genus.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142284426","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 diversity in Crematogaster Lund, 1831 (Formicidae: Myrmicinae) from the Amazon rainforest. 亚马逊雨林中 Crematogaster Lund, 1831 (Formicidae: Myrmicinae) 的染色体多样性。

IF 2.3 3区生物学

Genome Pub Date : 2024-09-03 DOI: 10.1139/gen-2023-0130

Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Dergam, Hilton Jeferson Alves Cardoso Aguiar

{"title":"Chromosomal diversity in Crematogaster Lund, 1831 (Formicidae: Myrmicinae) from the Amazon rainforest.","authors":"Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Dergam, Hilton Jeferson Alves Cardoso Aguiar","doi":"10.1139/gen-2023-0130","DOIUrl":"https://doi.org/10.1139/gen-2023-0130","url":null,"abstract":"Crematogaster Lund, 1831 is a speciose ant genus globally distributed and easily recognizable. Although biogeographical theories explain some variation among Neotropical Crematogaster, several taxonomical issues remain unresolved. While cytogenetic approaches can help to delimit species, cytogenetic data are only available for 18 taxa. In this study, classical and molecular cytogenetic analyses were performed on five Crematogaster species from the Brazilian Amazon to identify species-specific patterns. Two different cytotypes, both with 2n=22 chromosomes were observed in Crematogaster erecta Mayr, 1866, suggesting the presence of cryptic species, although with different karyotypic formulas. Crematogaster aff. erecta had 2n=28, while C. limata Smith, 1858, C. tenuicula Forel, 1904 and Crematogaster sp. had 2n = 38. The telomeric motif (TTAGG)n was found in all five species, and the (TCAGG)n motif was detected in the telomeres of C. limata. This peculiar motif was also detected in the centromeric regions of C. erecta cytotype I. The microsatellite (GA)n was dispersed in the chromosomes of all species studied which also had a single intrachromosomal rDNA site. The cytogenetic results revealed notable interspecific and intraspecific variation, which suggests different chromosomal rearrangements involved in the origin of these variations, also highlighting the taxonomic value of cytogenetic data on Crematogaster.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125506","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