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Satellitome analysis on Microtus thomasi (Arvicolinae) genome, a mammal species with high karyotype and sex chromosome variations. 对具有高度核型和性染色体变异的哺乳动物--Microtus thomasi（Arvicolinae）基因组进行卫星组分析。

IF 2.3 3区生物学

Genome Pub Date : 2025-02-11 DOI: 10.1139/gen-2024-0141

Gael Aleix Mata, Eugenia E Montiel, Pablo Mora-Ruiz, Alona Yurchenko, José M Rico-Porras, Francisco Anguita, Fátima Palomo, Juan Alberto Marchal, Michail Rovatsos, Antonio Sánchez Baca

{"title":"Satellitome analysis on Microtus thomasi (Arvicolinae) genome, a mammal species with high karyotype and sex chromosome variations.","authors":"Gael Aleix Mata, Eugenia E Montiel, Pablo Mora-Ruiz, Alona Yurchenko, José M Rico-Porras, Francisco Anguita, Fátima Palomo, Juan Alberto Marchal, Michail Rovatsos, Antonio Sánchez Baca","doi":"10.1139/gen-2024-0141","DOIUrl":"https://doi.org/10.1139/gen-2024-0141","url":null,"abstract":"The voles of the Microtus thomasi / M. atticus species complex (Arvicolinae) display extensive karyotypic variation, in the number of autosomes and the morphology of sex chromosomes. We analysed the satellitome of M. thomasi and identified 17 satDNA families, corresponding to 6.704% of the genome. Homogenization and divergence analyses showed that some satDNA families are more homogeneous, indicative of recent amplification, while others displayed higher variation, suggesting ancient amplification. Twelve of satDNA families are conserved across Arvicolinae with a substantial variation in the abundance and the composition. These results supports the \"library\" hypothesis, where a shared collection of satDNAs exists across related species, with differential amplification driving species-specific genomic profiles. Localization analysis demonstrated that an increased number of satDNA families are localized in the pericentromeric and the heterochromatic regions of autosomes and sex chromosomes. Our results suggest that the heterochromatin of the X and Y chromosomes co-evolved and that satDNA families might have contributed to the chromosomal rearrangements involved in the karyotypic variation and sex chromosome polymorphism of the chromosomal races. Our study contribute to a deeper understanding of the evolutionary mechanisms underlying karyotype diversification in Microtus species, which exhibit some of the highest rates of karyotypic variation among mammals.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398732","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

The nuclear and mitochondrial genomes of the bellicose bumblebee (Bombus bellicosus, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape.

IF 2.3 3区生物学

Genome Pub Date : 2025-02-11 DOI: 10.1139/gen-2024-0166

Leonardo Tresoldi Gonçalves, Pedro Henrique Pezzi, Flávia Regina Girardi Montagner, Wellington Vasconcelos de Souza, Elaine Françoso, Maríndia Deprá

{"title":"The nuclear and mitochondrial genomes of the bellicose bumblebee (Bombus bellicosus, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape.","authors":"Leonardo Tresoldi Gonçalves, Pedro Henrique Pezzi, Flávia Regina Girardi Montagner, Wellington Vasconcelos de Souza, Elaine Françoso, Maríndia Deprá","doi":"10.1139/gen-2024-0166","DOIUrl":"https://doi.org/10.1139/gen-2024-0166","url":null,"abstract":"We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (Bombus bellicosus). This is an endemic species in southern South America facing local extinction due to habitat loss and climate change. During the COVID-19 social distancing in Brazil, we launched a citizen science initiative via social media to locate remaining bellicose bumblebee populations, leading to the collection of a specimen for genome sequencing. Analysis of the novel genome revealed lower genetic diversity in the bellicose bumblebee compared to a widespread related species (B. pascuorum). However, the absence of extensive runs of homozygosity indicated a lack of recent inbreeding, offering a promising perspective for the conservation of this species. Furthermore, demographic history analysis indicates population expansion during past glacial periods, in contrast to Palearctic bumblebees which suffered a stark decline during glaciations. Our findings provide invaluable information for the conservation of this species and for further studies about its biology and evolution, particularly under a scenario of rapid environmental change.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398740","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

The repetitive DNA landscape in the 'brizantha' agamic complex of Urochloa P. Beauv.

IF 2.3 3区生物学

Genome Pub Date : 2025-01-31 DOI: 10.1139/gen-2024-0096

Caio Túlio Rodrigues Corrêa, Magdalena Vaio, Sanzio Carvalho Lima Barrios, Cacilda Borges do Valle, Giovana Augusta Torres, Vania Helena Techio

{"title":"The repetitive DNA landscape in the 'brizantha' agamic complex of Urochloa P. Beauv.","authors":"Caio Túlio Rodrigues Corrêa, Magdalena Vaio, Sanzio Carvalho Lima Barrios, Cacilda Borges do Valle, Giovana Augusta Torres, Vania Helena Techio","doi":"10.1139/gen-2024-0096","DOIUrl":"https://doi.org/10.1139/gen-2024-0096","url":null,"abstract":"Urochloa P. Beauv. (formerly classified as Brachiaria (Trin.) Griseb.) is a genus of African perennial grasses that is extensively cultivated in tropical countries for cattle nutrition. Three of the most economically relevant species, Urochloa brizantha, U. decumbens, and U. ruziziensis, form the 'brizantha' agamic complex, which includes allopolyploid series with distinct subgenomes. Investigating the composition and organization of repetitive DNA, a major component of grass genomes, can provide insights into their genomic relationships and evolutionary history. This study aimed to characterize the repetitive DNA landscape of selected Urochloa species belonging to the 'brizantha' agamic complex; identify and compare major repeat classes across species and evaluate their potential as cytogenetic markers on mitotic chromosomes using fluorescent in situ hybridization (FISH). Clustering analysis revealed that repetitive DNA constitutes 56-65% of the genomes, with Ty3/Gypsy retrotransposons, particularly the Athila and Retand lineages, representing the most abundant repeat class. U. decumbens exhibited the highest proportion of Ty3/Gypsy retrotransposons, while U. ruziziensis had the highest satellite DNA content. The chromosomal location of representative satellites (UroSat-1a, UroSat-2a, and UroSat-3) was determined in all three species via FISH. UroSat-1a was detected in all centromeres, while UroSat-2a and UroSat-3 signals varied in number and position. Our findings validate the use of satDNA as cytogenetic markers in the Urochloa 'brizantha' agamic complex and revealed genomic relationships among different species and ploidy levels.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070848","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

Karyotype Evolution of Suliformes and Description of a ♂Z1Z1Z2Z2/♀Z1Z2W Multiple Sex Chromosome System in boobies (Sula spp.).

IF 2.3 3区生物学

Genome Pub Date : 2025-01-30 DOI: 10.1139/gen-2024-0165

Luciano Pozzobon, Gustavo Akira Toma, Marcelo Bello Cioffi, Edivaldo Herculano Correa de Oliveira, Rafael Kretschmer, Thales Renato Ochotorena de Freitas

{"title":"Karyotype Evolution of Suliformes and Description of a ♂Z1Z1Z2Z2/♀Z1Z2W Multiple Sex Chromosome System in boobies (Sula spp.).","authors":"Luciano Pozzobon, Gustavo Akira Toma, Marcelo Bello Cioffi, Edivaldo Herculano Correa de Oliveira, Rafael Kretschmer, Thales Renato Ochotorena de Freitas","doi":"10.1139/gen-2024-0165","DOIUrl":"https://doi.org/10.1139/gen-2024-0165","url":null,"abstract":"Our comprehension of avian karyotypes still needs to be improved, especially for Suliform birds. To enhance understanding of chromosomal evolution in this order, we conducted conventional and molecular cytogenetic analysis in five species, named Sula dactylatra, S. leucogaster, S. sula (Sulidae), Fregata magnificens (Fregatidae), and Nannopterum brasilianum (Phalacrocoracidae). The diploid chromosome number for S. dactylatra and S. leucogaster was established as 2n = 76 in males, and 2n = 75 in females, but S. sula displayed a karyotype of 2n = 76 chromosomes in males. The disparity in diploid chromosome numbers between male and female Sula is due to a multiple sex chromosome system of the Z1Z1Z2Z2/Z1Z2W type. We propose that the emergence of this multiple-sex chromosome system resulted from a Robertsonian translocation involving the W chromosome and the smallest microchromosome. F. magnificens exhibited a diploid number 76 (2n = 76), while N. brasilianum displayed a diploid number of 74 (2n = 74) in both sexes. The ribosomal cluster was located in one microchromosome pair in S. dactylatra, S. leucogaster, S. sula, and F. magnificens and in four pairs in N. brasilianum. Our findings provide evidence of a conserved multiple-sex chromosome system within the Sula genus, shedding light on the high karyotype diversity in Suliformes.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064945","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

Sequence-based Identification of Polyamine Oxidase Genes in Sorghum bicolor L.

IF 2.3 3区生物学

Genome Pub Date : 2025-01-29 DOI: 10.1139/gen-2024-0143

Heba Ebeed, Mohamed El-Zonkorany, Eman Habib, Esraa Ali, Ahmed Zahran, Aya Hamdy Ragab

引用次数: 0

Comparative analysis of Aegilops speltoides and wheat repetitive elements and development of S genome-specific FISH painting.

IF 2.3 3区生物学

Genome Pub Date : 2025-01-29 DOI: 10.1139/gen-2024-0090

Tatiana Danilova, Alina R Akhunova, Xiwen Cai

{"title":"Comparative analysis of Aegilops speltoides and wheat repetitive elements and development of S genome-specific FISH painting.","authors":"Tatiana Danilova, Alina R Akhunova, Xiwen Cai","doi":"10.1139/gen-2024-0090","DOIUrl":"https://doi.org/10.1139/gen-2024-0090","url":null,"abstract":"Aegilops speltoides (2n=2x=14, genome SS) is a wild relative of wheat and a donor of useful traits for wheat improvement. Several whole-genome studies compared genic regions of Aegilops from the Sitopsis section and wheat and found that Ae. speltoides is most closely related to the wheat B subgenome but is not its direct progenitor. The results showed that a B subgenome ancestor diverged from Ae. speltoides more than 4 MYA and either has not yet been discovered, or is extinct. To further explore the evolutionary relationship between wheat and Ae. speltoides and develop Ae. speltoides chromosome paints, we performed comparative analysis of repetitive fractions of the S genome and three subgenomes of hexaploid wheat. The low coverage sequence data was analyzed with RepeatExplorer pipeline to annotate repeats and estimate their content. The LTR-retrotransposons comprised about 80% of repeats in Ae. speltoides and wheat datasets and about two-third of them were LTR/Ty3-Gypsy. Ae. speltoides had 1.5 times more LTR/Ty-Copia repeats and 1.5 times less DNA transposons than wheat subgenomes. Several S genome-specific dispersed repeats were found and annotated. Their sequences were used to develop S genome-specific paints for detecting Ae. speltoides chromatin in the wheat background using fluorescent in situ hybridization.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064944","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

The typical and the atypical filamins of Drosophila.

IF 2.3 3区生物学

Genome Pub Date : 2025-01-27 DOI: 10.1139/gen-2024-0159

Tiara Mulder, Jennifer Johnson, Nicanor Gonzalez Morales

引用次数: 0

Empowering canine genomics: Design and validation of a High-Density SNP array for Indian dogs.

IF 2.3 3区生物学

Genome Pub Date : 2025-01-27 DOI: 10.1139/gen-2024-0094

Raja Kolandanoor Nachiappan, Reena Arora, Ramesh Kumar Vijh, Upasana Sharma, Meenal Raheja, Manisha Sharma, Mehak Maggon, Sonika Ahlawat

{"title":"Empowering canine genomics: Design and validation of a High-Density SNP array for Indian dogs.","authors":"Raja Kolandanoor Nachiappan, Reena Arora, Ramesh Kumar Vijh, Upasana Sharma, Meenal Raheja, Manisha Sharma, Mehak Maggon, Sonika Ahlawat","doi":"10.1139/gen-2024-0094","DOIUrl":"https://doi.org/10.1139/gen-2024-0094","url":null,"abstract":"India harbours a substantial population of 9.43 million dogs, showcasing diverse phenotypes and utility. Initiatives focusing on awareness, conservation and informed breeding can greatly enhance the recognition and welfare of the unique Indian canine heritage. This study describes the design and development of a high density SNP array for genomic characterization of Indian dogs. Paired-end (150bp) DNA sequences from four diverse dog populations were generated with 10X coverage, following the standard pipeline of Axiom Array technology for chip design. More than 23 million raw SNPs were initially identified, with 629,597 SNP markers ultimately tiled on the Indian canine array (Axiom_Shwaan) after stringent filtering and processing. With an inter-marker distance of 3.8 kb the Axiom_Shwaan greatly increases the canine genome coverage. The array was validated by genotyping 186 samples representing 11 dog breeds/populations from India. The high call rate (99%) of SNPs on the designed chip indicates its suitability for use in Indian dog populations, reflecting sufficient genetic diversity. The principal component and phylogenetic analyses delineated the native dog breeds into discrete groups. This high-density SNP array will empower future applications in population genetics, breed/selection signature identification, development of trait-specific biomarkers and genome-wide data mining for various canine abilities.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051636","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

Whole Genome Sequencing and Analysis of Benzo(a)pyrene Degrading Bacteria Bacillus cereus M72-4. 全基因组测序和苯并（a）芘降解细菌蜡样芽孢杆菌 M72-4 的分析。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-27 DOI: 10.1139/gen-2024-0114

Aofei Jin, Dilbar Tursun, Lirong Tan, Zhuonan Yang, Zhixian Duo, Yanan Qin, Rui Zhang

{"title":"Whole Genome Sequencing and Analysis of Benzo(a)pyrene Degrading Bacteria Bacillus cereus M72-4.","authors":"Aofei Jin, Dilbar Tursun, Lirong Tan, Zhuonan Yang, Zhixian Duo, Yanan Qin, Rui Zhang","doi":"10.1139/gen-2024-0114","DOIUrl":"https://doi.org/10.1139/gen-2024-0114","url":null,"abstract":"Benzo (a) pyrene produced by food during high-temperature process enters the body through ingestion, which causes food safety issues to the human body. In order to alleviate the harm of foodborne benzo (a) pyrene to human health, a strain that can degrade benzo (a) pyrene was screened from Kefir, a traditional fermented product in Xinjiang. Bacillus cereus M72-4 is a Gram-positive bacteria sourced from Xinjiang traditional fermented product Kefir, under Benzo(a)pyrene stress conditions, there was 69.39% degradation rate of 20 mg/L Benzo(a)pyrene by strain M72-4 after incubation for 72 h. The whole genome of M72-4 sequenced using PacBio sequencing technology in this study. The genome size was 5754801 bp and a GC content was 35.24%, a total of 5719 coding genes were predicted bioinformatically. Through functional database annotation, it was found that the strain has a total of 219 genes involved in the transportation and metabolism of hydrocarbons, a total of 9 metabolic pathways related to the degradation and metabolism of exogenous substances, and a total of 67 coding genes.According to the KEGG database annotation results, a key enzyme related to Benzo(a)pyrene degradation, catechol 2,3-dioxygenase, was detected in the genome data of Bacillus cereus M72-4, encoding genes dmpB and xylE, respectively; There are also monooxygenases and dehydrogenases. Therefore, it can be inferred that this strain mainly degrades Benzo(a)pyrene through Benzoate metabolic.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051854","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

Peroxisome inter-organelle cooperation in Drosophila. 果蝇的过氧物酶体细胞器间合作

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-10-29 DOI: 10.1139/gen-2024-0082

Andy Y Cheng, Andrew J Simmonds

{"title":"Peroxisome inter-organelle cooperation in Drosophila.","authors":"Andy Y Cheng, Andrew J Simmonds","doi":"10.1139/gen-2024-0082","DOIUrl":"10.1139/gen-2024-0082","url":null,"abstract":"Many cellular functions are compartmentalized within the optimized environments of organelles. However, processing or storage of metabolites from the same pathway can occur in multiple organelles. Thus, spatially separated organelles need to cooperate functionally. Coordination between organelles in different specialized cells is also needed, with shared metabolites passed via circulation. Peroxisomes are membrane-bounded organelles responsible for cellular redox and lipid metabolism in eukaryotic cells. Peroxisomes coordinate with other organelles including mitochondria, endoplasmic reticulum, lysosomes, and lipid droplets. This functional coordination requires, or is at least enhanced by, direct contact between peroxisomes and other organelles. Peroxisome dysfunction in humans leads to multiorgan effects including neurological, metabolic, developmental, and age-related diseases. Thus, increased understanding of peroxisome coordination with other organelles, especially cells in various organs is essential. Drosophila melanogaster (fruit fly) has emerged recently as an effective animal model for understanding peroxisomes. Here we review current knowledge of pathways regulating coordination between peroxisomes with other organelles in flies, speculating about analogous roles for conserved Drosophila genes encoding proteins with known organelle coordinating roles in other species.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545118","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