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Chromosomal and molecular perspectives on Potamotrygon motoro (Müller & Henle, 1841) from central Amazon.
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0153
Alex M V Ferreira, Patrik F Viana, Leandro Marajó, Eliana Feldberg
{"title":"Chromosomal and molecular perspectives on <i>Potamotrygon motoro</i> (Müller & Henle, 1841) from central Amazon.","authors":"Alex M V Ferreira, Patrik F Viana, Leandro Marajó, Eliana Feldberg","doi":"10.1139/gen-2024-0153","DOIUrl":"https://doi.org/10.1139/gen-2024-0153","url":null,"abstract":"<p><p>Cytogenetic studies on <i>Potamotrygon motoro</i> (Müller & Henle, 1841) are limited to classical cytogenetic techniques, but they do reveal great karyotypic variation. The main differences are related to the karyotypic formula and the absence/presence of sex chromosome systems. Thus, this study aimed to expand knowledge of the karyotypic composition of <i>Potamotrygon motoro</i> from different locations of the Central Amazon using Fluorescence in situ Hybridization to investigate the distribution of ribosomal DNAs (rDNA) and microsatellites sequences (SSRs). In addition, we used the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) to perform neighbor-joining analysis to investigate the relationships among the individuals sampled. In our study, <i>Potamotrygon motoro</i> presented 2n = 66 chromosomes, with 18m + 12sm + 10st + 26a and heterochromatic blocks on centromeric region of all chromosomes. The 18S rDNA is present in three chromosomal pairs and 5S rDNA is located in the pair 16, which is a feature shared among freshwater stingray species. Regarding the mapping of SSRs, dinucleotide sequences showed a greater number of sites, usually on terminal regions of chromosomal pairs, with an accumulation throughout the long arms of the pair 17. Our molecular analyses did not reveal differences between the sequences used. In general, the karyotypic differences previously reported for <i>Potamotrygon motoro</i> indicate the presence of different cytotypes within the species.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-9"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499364","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
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 : 2025-01-01 DOI: 10.1139/gen-2024-0141
Gaël Aleix-Mata, Eugenia E Montiel, Pablo Mora, Alona Yurchenko, José M Rico-Porras, Francisco Anguita, Fátima Palomo, Juan Alberto Marchal, Michail Rovatsos, Antonio Sánchez
{"title":"Satellitome analysis on <i>Microtus thomasi</i> (Arvicolinae) genome, a mammal species with high karyotype and sex chromosome variations.","authors":"Gaël Aleix-Mata, Eugenia E Montiel, Pablo Mora, Alona Yurchenko, José M Rico-Porras, Francisco Anguita, Fátima Palomo, Juan Alberto Marchal, Michail Rovatsos, Antonio Sánchez","doi":"10.1139/gen-2024-0141","DOIUrl":"10.1139/gen-2024-0141","url":null,"abstract":"<p><p>The voles of the <i>Microtus thomasi</i>/<i>Microtus atticus</i> species complex (Arvicolinae) display extensive karyotypic variation, in the number of autosomes and the morphology of sex chromosomes. We analyzed the satellitome of <i>Microtus thomasi</i> and identified 17 satellite DNA (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 the satDNA families are conserved across Arvicolinae with a substantial variation in the abundance and the composition. These results support 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 contributes to a deeper understanding of the evolutionary mechanisms underlying karyotype diversification in <i>Microtus</i> species, which exhibit some of the highest rates of karyotypic variation among mammals.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","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
Resistance genes against yellow rust pathogen in Triticum spelta: a possible new Yr resistance gene in accession IARI276 and Yr5 presence confirmed in PI348764.
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0171
Lovely Arya, Malavika N Shal, M Niranjana, S K Jha, Madhu Patial, M S Saharan, N Mallick, K Raghunandan, A Priyanka, D P Walia, S M S Tomar, Vinod
{"title":"Resistance genes against yellow rust pathogen in <i>Triticum spelta</i>: a possible new <i>Yr</i> resistance gene in accession IARI276 and <i>Yr5</i> presence confirmed in PI348764.","authors":"Lovely Arya, Malavika N Shal, M Niranjana, S K Jha, Madhu Patial, M S Saharan, N Mallick, K Raghunandan, A Priyanka, D P Walia, S M S Tomar, Vinod","doi":"10.1139/gen-2024-0171","DOIUrl":"https://doi.org/10.1139/gen-2024-0171","url":null,"abstract":"<p><p>Yellow/stripe rust caused by <i>Puccinia striiformis</i> f. sp. <i>tritici</i> is a major biotic stress in global wheat production. Introgression lines derived from the <i>Triticum spelta</i> accessions PI348764 and IARI276 showed high levels of yellow rust resistance at seedling and adult plant stage. The <i>Yr5</i> gene located on 2B chromosome was previously the only stripe rust resistance gene described in <i>T. spelta</i> gene pool. By genotyping parental and introgressed material with markers linked with the <i>Yr5</i> gene, we demonstrate that PI348764 likely carries <i>Yr5</i>, and that it appears to be absent from IARI276. By employing a combination of methods, including screening for adult plant resistance and seedling resistance at multiple field trials, bulked segregant analysis (BSA) on F<sub>5</sub> families, and genotyping using wheat Breeders' 35K array, we show that <i>Yr<sup>IARI276</sup></i> is a novel stripe rust resistance gene with putative chromosomal locations on 1BL, 1DL, 5AL, or 7BL. Furthermore, genetic analysis revealed that <i>Yr<sup>IARI276</sup></i> showed a goodness of fit to Mendelian ratios for a single dominant gene. As the gene is distinct from <i>Yr5</i> and the chromosomal location is unique from earlier reported <i>Yr</i> genes, it will be useful in improving diversity of <i>Yr</i> gene repertoire in disease resistance breeding programmes.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-11"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604688","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
AVITI as an alternative to Illumina for low-cost genome-wide genotyping.
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0068
Maxime de Ronne, Brian Boyle, Davoud Torkamaneh
{"title":"AVITI as an alternative to Illumina for low-cost genome-wide genotyping.","authors":"Maxime de Ronne, Brian Boyle, Davoud Torkamaneh","doi":"10.1139/gen-2024-0068","DOIUrl":"10.1139/gen-2024-0068","url":null,"abstract":"<p><p>Advancements in sequencing technologies have dramatically transformed genomics research by enabling the analysis of genetic information with unprecedented scale and efficiency. Next-generation sequencing, renowned for its high-throughput capabilities, has significantly reduced costs and expanded the scope of sequencing applications. Among these, sequencing by synthesis on Illumina systems is predominant, favored for its accuracy and cost-effectiveness. However, emerging technologies like Element Biosciences' sequencing by Avidity (AVITI) are beginning to challenge this dominance. In this study, we sequenced and genotyped a library of 40 <i>Cannabis</i> samples using both the AVITI and Illumina NovaSeq systems. After filtering out low-quality variants, both technologies showed an 81.2% overlap with 98.9% concordance in genotype calls. AVITI stands out for its flexibility and reduced per-base costs, presenting a viable option particularly for mid-sized laboratories. As the scientific community continues to seek ways to lower genotyping expenses, the combination of the AVITI system with NanoGBS library preparation offers a cost-effective solution adaptable to a wide range of project sizes.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-4"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457576","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 : 2025-01-01 Epub Date: 2024-09-03 DOI: 10.1139/gen-2023-0130
Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Abdala Dergam, Hilton Jeferson Alves Cardoso de Aguiar
{"title":"Chromosomal diversity in <i>Crematogaster</i> Lund, 1831 (Formicidae: Myrmicinae) from the Amazon rainforest.","authors":"Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Abdala Dergam, Hilton Jeferson Alves Cardoso de Aguiar","doi":"10.1139/gen-2023-0130","DOIUrl":"10.1139/gen-2023-0130","url":null,"abstract":"<p><p><i>Crematogaster</i> Lund, 1831 is a speciose ant genus globally distributed and easily recognizable. Although biogeographical theories explain some variation among Neotropical <i>Crematogaster</i>, 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 <i>Crematogaste</i>r species from the Brazilian Amazon to identify species-specific patterns. Two different cytotypes, both with 2<i>n</i> = 22 chromosomes were observed in <i>Crematogaster erecta</i> Mayr, 1866, suggesting the presence of cryptic species, although with different karyotypic formulas. <i>Crematogaster</i> aff. <i>erecta</i> had 2<i>n</i> = 28, while <i>Crematogaster limata</i> Smith, 1858, <i>Crematogaster tenuicula</i> Forel, 1904, and <i>Crematogaster</i> sp. had 2<i>n</i> = 38. The telomeric motif (TTAGG) <i><sub>n</sub></i> was found in all five species, and the (TCAGG) <i><sub>n</sub></i> motif was detected in the telomeres of <i>C. limata</i>. This peculiar motif was also detected in the centromeric regions of <i>C. erecta</i> cytotype I. The microsatellite (GA) <i><sub>n</sub></i> 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 <i>Crematogaster</i>.</p>","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":"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
Asp/ASPM phospho-regulation throughout the cell cycle. Asp/ASPM在整个细胞周期中的磷酸化调控。
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 Epub Date: 2024-10-29 DOI: 10.1139/gen-2024-0111
Maria C Burns, Lori Borgal
{"title":"Asp/ASPM phospho-regulation throughout the cell cycle.","authors":"Maria C Burns, Lori Borgal","doi":"10.1139/gen-2024-0111","DOIUrl":"10.1139/gen-2024-0111","url":null,"abstract":"<p><p>In mammals and <i>Drosophila melanogaster</i>, Asp/ASPM proteins contribute to cell proliferation and spindle formation. Recent evidence also suggests interphase roles for Asp/ASPM proteins, but little is known about the regulation allowing distinct roles in different cell cycle phases. In this review, we consider a cross-species comparison of Asp/ASPM protein sequences in light of cyclin-CDK literature, and suggest Asp/ASPM proteins to be prime candidates for cyclin-CDK regulation. Conserved regulatory features include an N-terminal proline directed serine/threonine (S/T-P) \"supershift\" phosphorylation domain common to proteins with bistable interphase and mitotic roles, as well as putative cyclin-binding sites positioned to allow multisite phosphorylation by cyclin-CDK complexes. Human, mouse, and <i>Drosophila</i> Asp/ASPM protein structural predictions show that multisite phosphorylation of the N-term supershift domain could alter the availability of CH-domains and HEAT-motifs, which can contribute to microtubule binding and protein aggregation likely required for spindle formation. Structural predictions of the smallest reported microcephaly patient truncation also emphasize the importance of the arrangement of these motifs. We position this <i>in silico</i> analysis within recent literature to build new hypotheses for Asp/ASPM regulation in interphase and mitosis, as well as de-regulation in microcephaly and cancer. We also highlight the utility of comparing structural/functional differences between human ASPM and <i>Drosophila</i> Asp to gain further insight.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-10"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545115","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 : 2025-01-01 DOI: 10.1139/gen-2024-0143
Heba T Ebeed, Mohamed El-Zonkorany, Eman Habib, Esraa Ali, Ahmed Zahran, Aya Hamdy Ragab
{"title":"Sequence-based identification of polyamine oxidase genes in <i>Sorghum bicolor</i> L.","authors":"Heba T Ebeed, Mohamed El-Zonkorany, Eman Habib, Esraa Ali, Ahmed Zahran, Aya Hamdy Ragab","doi":"10.1139/gen-2024-0143","DOIUrl":"10.1139/gen-2024-0143","url":null,"abstract":"<p><p>Polyamine oxidases (PAOs) are enzymes associated with polyamine catabolism and play important roles in growth and development and stress tolerance of plants. In the present study, genome-wide discovery and analysis of the PAO family in sorghum was done utilizing model PAO of Arabidopsis. Six PAO genes were found using publicly available genomic data. Sorghum has the PAO gene representatives distributed throughout four chromosomes (chr1, chr3, chr6, and chr7), and most members have eight to nine exons. The molecular weights of PAO proteins range from 53 to 63 kDa. PAO proteins have a theoretical PI between 5.2 and 8.1. The identification and characterization of PAO gene members in sorghum lay the foundation for further experimental studies elucidating their roles in growth, development, and stress responses, ultimately contributing to our understanding of plant biology, with significant implications for plant breeding by providing valuable insights into potential targets for enhancing stress tolerance and improving crop performance.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-5"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064946","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 homologies and polymorphisms in a Neotropical species complex of frogs revealed by the U2 snRNA gene.
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0131
Lucas Henrique Bonfim Souza, Bruno Cansanção Silva, Jennifer Nunes Pompeo, Kaleb Pretto Gatto, Luciana Bolsoni Lourenço
{"title":"Chromosome homologies and polymorphisms in a Neotropical species complex of frogs revealed by the U2 snRNA gene.","authors":"Lucas Henrique Bonfim Souza, Bruno Cansanção Silva, Jennifer Nunes Pompeo, Kaleb Pretto Gatto, Luciana Bolsoni Lourenço","doi":"10.1139/gen-2024-0131","DOIUrl":"https://doi.org/10.1139/gen-2024-0131","url":null,"abstract":"<p><p>The <i>Physalaemus cuvieri-Physalaemus ephippifer</i> species complex is a Neotropical frog group that encompasses seven well-supported major clades. Although very similar morphologically, the five lineages previously karyotyped show notorious cytogenetic signatures. There is also evidence of ancient secondary contact between <i>P. ephippifer</i>, which has heteromorphic sex chromosomes, and the lineage known as L1B, which lacks sex chromosome heteromorphism. Here, to aid comparative analysis within this complex, we mapped the U2 small nuclear RNA (snRNA) gene using fluorescent in situ hybridization (FISH). All samples presented a U2 snRNA gene cluster terminally in the short arm of chromosome 6. Additional small FISH signals were also revealed, particularly in one lineage with previously noted polymorphism of nucleolar organizer regions. Moreover, one additional site contributed for the analysis of sex chromosomes, since the Z chromosome of <i>P. ephippifer</i> harbors a small FISH signal, which is absent in the W chromosome. In lineage L1B, chromosome 9-which is homologous to the sex chromosomes of <i>P. ephippifer-</i>is polymorphic for a small FISH signal, as did the Z chromosome in the group derived from the contact between these lineages. Finally, nucleotide sequence analysis revealed some truncated gene sequences, suggesting the presence of pseudogenes of the U2 snRNA gene in these frogs.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-11"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482787","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 identification of Medicago polymorpha by oligonucleotide-based FISH.
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0136
Min Cheng, Jia Xu, Ying Li, Yaling Jian, Feng Yu
{"title":"Chromosome identification of <i>Medicago polymorpha</i> by oligonucleotide-based FISH.","authors":"Min Cheng, Jia Xu, Ying Li, Yaling Jian, Feng Yu","doi":"10.1139/gen-2024-0136","DOIUrl":"https://doi.org/10.1139/gen-2024-0136","url":null,"abstract":"<p><p><i>Medicago polymorpha</i> (2<i>n</i> = 2<i>x</i> = 14) is a valuable forage legume, but the identification of its somatic chromosomes has been challenging due to a lack of distinctive chromosome morphological features. With appropriate probes, oligonucleotide-based FISH is a highly effective method for chromosome identification. However, there are no available probes for <i>M. polymorpha</i>. In this study, we isolated five tandem repeats from the <i>M. polymorpha</i> genome, named Mp51, Mp139, Mp167, Mp179, and Mp497. Mp51 showed two pairs of signals located at the pericentromere. Mp139 exhibited four pairs of signals, located at the pericentromere and short arm of chromosomes. Mp167 and Mp179 showed seven pairs of signals, respectively, concentrated in the pericentromere. Mp497 exhibited three pairs of signals, distributed across the pericentromere and proximal position of the chromosomes. The combined FISH results of Mp51 and Mp139 oligo probes with 5S rDNA and 18S-26S rDNA probes demonstrated distinct signal patterns for each chromosome, enabling the precise identification of all chromosome pairs. Finally, the visual identification of <i>M. polymorpha</i> chromosomes was resolved. This will provide useful cytological information for studying the chromosomal structure and behavior of <i>M. polymorpha</i>.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-8"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143515477","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
Runs of homozygosity assessment using reduced representation sequencing highlight the evidence of random mating in emu (Dromaius novaehollandiae). 使用减少代表性测序的纯合子评估突出了鸸鹋(新荷兰Dromaius novaehollandiae)随机交配的证据。
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 Epub Date: 2024-12-12 DOI: 10.1139/gen-2024-0084
Rangasai Chandra Goli, Karan Mahar, Kiyevi G Chishi, Sonu Choudhary, Pallavi Rathi, Chandana Chinnareddyvari Sree, Pala Haritha, Nidhi Sukhija, K K Kanaka
{"title":"Runs of homozygosity assessment using reduced representation sequencing highlight the evidence of random mating in emu (<i>Dromaius novaehollandiae</i>).","authors":"Rangasai Chandra Goli, Karan Mahar, Kiyevi G Chishi, Sonu Choudhary, Pallavi Rathi, Chandana Chinnareddyvari Sree, Pala Haritha, Nidhi Sukhija, K K Kanaka","doi":"10.1139/gen-2024-0084","DOIUrl":"10.1139/gen-2024-0084","url":null,"abstract":"<p><p>The domestication of emu (<i>Dromaius novaehollandiae)</i> began in the 1970s, but their productive characteristics have not undergone significant genetic enhancement. This study investigated the inbreeding and genetic diversity of 50 emus from various farms in Japan using Double digest restriction-site associated DNA sequencing (ddRAD-seq) markers. Single nucleotide polymorphism (SNP) calling revealed 171 975 high-quality SNPs while runs of homozygosity (ROH) analysis identified 1843 homozygous segments, with an average of 36.86 ROH per individual and a mean genome length of 27 Mb under ROH. The majority (86%) of ROH were short (0.5-1 Mb), indicating ancient or remote inbreeding. The average genomic inbreeding coefficient (<i>F</i><sub>ROH</sub>) was 0.0228, suggesting nearly no inbreeding. Overlapping ROH regions were identified, with top consensus regions found on chromosomes 8 and Z. Seven candidate genes related to egg production, feather development, and energy metabolism were annotated in these regions. The findings highlight the prevalence of genetic diversity and low inbreeding levels in the studied emu population. This research highlights the potentiality of random mating in genetic management and conservation of emus. Further studies should focus on enhancing productive traits through selective breeding while preserving genetic diversity to ensure the sustainable growth of the emu farming.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-8"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817788","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
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