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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":"<p><p>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 <i>cytochrome c oxidase subunit 1</i> and <i>cytochrome b</i> 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.</p>","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":"<p><p><i>Flavobacterium</i> 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 <i>Flavobacterium psychrophilum</i> and <i>Flavobacterium columnare</i>, 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 <i>Flavobacterium</i> 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.</p>","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
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 Nascimento, Veit Schubert, Andrea Pedrosa-Harand, André Marques, Andreas Houben, André Luís Laforga Vanzela
{"title":"Distinct patterns of satDNA distribution in holocentric chromosomes of spike-sedges (<i>Eleocharis</i>, Cyperaceae).","authors":"Thaíssa Boldieri de Souza, Letícia Maria Parteka, Yi-Tzu Kuo, Thiago Nascimento, Veit Schubert, Andrea Pedrosa-Harand, André Marques, Andreas Houben, André Luís Laforga Vanzela","doi":"10.1139/gen-2024-0089","DOIUrl":"10.1139/gen-2024-0089","url":null,"abstract":"<p><p><i>Eleocharis</i> 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 <i>Eleocharis</i> 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 <i>Eleocharis</i> 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 <i>Eleocharis maculosa, Eleocharis</i> <i>geniculata, Eleocharis parodii, Eleocharis elegans</i>, and <i>Eleocharis</i> <i>montana</i>. 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 <i>Eleocharis</i> phylogenetic tree. Nonetheless, they were accumulated within a restricted group of Maculosae series, subgenus <i>Eleocharis</i>. The data indicates that the amplification and line-like distribution of EmaSAT14 along chromatids may have occurred recently within a section of the genus.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"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 4.6 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 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":""},"PeriodicalIF":4.6,"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
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: <i>Trogon surrucura</i> (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":"<p><p>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 <i>Trogon surrucura</i> genome into the <i>T. surrucura</i> (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.</p>","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 <i>Abracris flavolineata</i>.","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":"<p><p>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 <i>Abracris flavolineata</i> 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 <i>A. flavolineata</i> 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.</p>","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 (<i>Musca domestica</i>) 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":"<p><p>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 (<i>Musca domestica</i>). 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.</p>","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
{"title":"Fragments derived from non-coding RNAs: how complex is genome regulation?","authors":"Miguel Ángel Velázquez-Flores, Ruth Ruiz Esparza-Garrido","doi":"10.1139/gen-2023-0136","DOIUrl":"10.1139/gen-2023-0136","url":null,"abstract":"<p><p>The human genome is highly dynamic and only a small fraction of it codes for proteins, but most of the genome is transcribed, highlighting the importance of non-coding RNAs on cellular functions. In addition, it is now known the generation of non-coding RNA fragments under particular cellular conditions and their functions have revealed unexpected mechanisms of action, converging, in some cases, with the biogenic pathways and action machineries of microRNAs or Piwi-interacting RNAs. This led us to the question why the cell produces so many apparently redundant molecules to exert similar functions and regulate apparently convergent processes? However, non-coding RNAs fragments can also function similarly to aptamers, with secondary and tertiary conformations determining their functions. In the present work, it was reviewed and analyzed the current information about the non-coding RNAs fragments, describing their structure and biogenic pathways, with special emphasis on their cellular functions.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"292-306"},"PeriodicalIF":2.3,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140864971","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
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":"<p><p>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 (<i>Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus</i>, and <i>Picumnus nebulosus)</i> was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from <i>Gallus gallus</i> and <i>Taeniopygia guttata</i>. Findings suggest that <i>P. nebulosus</i> (2<i>n</i> = 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 <i>V. spilogaster</i> (2<i>n</i> = 88) and demonstrated microchromosomal rearrangements involving <i>C. campestris</i> plus a single, unique hitherto undescribed rearrangement in <i>V. spilogaster</i>. 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 <i>M. candidus</i> is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.</p>","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 <i>Brassica napus</i>: 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":"<p><p>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 (<i>Brassica napus</i>). 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.</p>","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
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