BMC genomic dataPub Date : 2024-07-10DOI: 10.1186/s12863-024-01252-8
Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Younes Miar
{"title":"Identification of consensus homozygous regions and their associations with growth and feed efficiency traits in American mink.","authors":"Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Younes Miar","doi":"10.1186/s12863-024-01252-8","DOIUrl":"10.1186/s12863-024-01252-8","url":null,"abstract":"<p><p>The recent chromosome-based genome assembly and the newly developed 70K single nucleotide polymorphism (SNP) array for American mink (Neogale vison) facilitate the identification of genetic variants underlying complex traits in this species. The objective of this study was to evaluate the association between consensus runs of homozygosity (ROH) with growth and feed efficiency traits in American mink. A subsample of two mink populations (n = 2,986) were genotyped using the Affymetrix Mink 70K SNP array. The identified ROH segments were included simultaneously, concatenated into consensus regions, and the ROH-based association studies were carried out with linear mixed models considering a genomic relationship matrix for 11 growth and feed efficiency traits implemented in ASReml-R version 4. In total, 298,313 ROH were identified across all individuals, with an average length and coverage of 4.16 Mb and 414.8 Mb, respectively. After merging ROH segments, 196 consensus ROH regions were detected and used for genome-wide ROH-based association analysis. Thirteen consensus ROH regions were significantly (P < 0.01) associated with growth and feed efficiency traits. Several candidate genes within the significant regions are known for their involvement in growth and body size development, including MEF2A, ADAMTS17, POU3F2, and TYRO3. In addition, we found ten consensus ROH regions, defined as ROH islands, with frequencies over 80% of the population. These islands harbored 12 annotated genes, some of which were related to immune system processes such as DTX3L, PARP9, PARP14, CD86, and HCLS1. This is the first study to explore the associations between homozygous regions with growth and feed efficiency traits in American mink. Our findings shed the light on the effects of homozygosity in the mink genome on growth and feed efficiency traits, that can be utilized in developing a sustainable breeding program for mink.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"68"},"PeriodicalIF":1.9,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11234557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC genomic dataPub Date : 2024-07-08DOI: 10.1186/s12863-024-01251-9
Shulei Ren, Wook Lee, Byungkyu Park, Kyungsook Han
{"title":"Constructing lncRNA-miRNA-mRNA networks specific to individual cancer patients and finding prognostic biomarkers.","authors":"Shulei Ren, Wook Lee, Byungkyu Park, Kyungsook Han","doi":"10.1186/s12863-024-01251-9","DOIUrl":"10.1186/s12863-024-01251-9","url":null,"abstract":"<p><strong>Background: </strong>The competitive endogenous RNA (ceRNA) hypothesis suggests that microRNAs (miRNAs) mediate a regulatory relation between long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) which share similar miRNA response elements (MREs) to bind to the same miRNA. Since the ceRNA hypothesis was proposed, several studies have been conducted to construct a network of lncRNAs, miRNAs and mRNAs in cancer. However, most cancer-related ceRNA networks are intended for representing a general relation of RNAs in cancer rather than for a patient-specific relation. Due to the heterogeneous nature of cancer, lncRNA-miRNA-mRNA interactions can vary in different patients.</p><p><strong>Results: </strong>We have developed a new method for constructing a ceRNA network of lncRNAs, miRNAs and mRNAs, which is specific to an individual cancer patient and for finding prognostic biomarkers consisting of lncRNA-miRNA-mRNA triplets. We tested our method on extensive data sets of three types of cancer (breast cancer, liver cancer, and lung cancer) and obtained potential prognostic lncRNA-miRNA-mRNA triplets for each type of cancer.</p><p><strong>Conclusions: </strong>Analysis of expression patterns of the RNAs involved in the triplets and survival rates of cancer patients revealed several interesting findings. First, even for the same cancer type, prognostic lncRNA-miRNA-mRNA triplets can be different depending on whether lncRNA and mRNA show opposite or similar expression patterns. Second, prognostic lncRNA-miRNA-mRNA triplets are often more predictive of survival rates than RNA pairs or individual RNAs. Our approach will be useful for constructing patient-specific lncRNA-miRNA-mRNA networks and for finding prognostic biomarkers from the networks.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 Suppl 1","pages":"67"},"PeriodicalIF":1.9,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11232193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141560440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC genomic dataPub Date : 2024-07-03DOI: 10.1186/s12863-024-01250-w
Haleh Hayatgheibi, Henrik R Hallingbäck, Sven-Olof Lundqvist, Thomas Grahn, Gerhard Scheepers, Peter Nordström, Zhi-Qiang Chen, Katri Kärkkäinen, Harry X Wu, M Rosario García-Gil
{"title":"Correction: Implications of accounting for marker-based population structure in the quantitative genetic evaluation of genetic parameters related to growth and wood properties in Norway spruce.","authors":"Haleh Hayatgheibi, Henrik R Hallingbäck, Sven-Olof Lundqvist, Thomas Grahn, Gerhard Scheepers, Peter Nordström, Zhi-Qiang Chen, Katri Kärkkäinen, Harry X Wu, M Rosario García-Gil","doi":"10.1186/s12863-024-01250-w","DOIUrl":"10.1186/s12863-024-01250-w","url":null,"abstract":"","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"66"},"PeriodicalIF":1.9,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11223410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141499800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC genomic dataPub Date : 2024-07-02DOI: 10.1186/s12863-024-01249-3
Juhee Kim, Tong Geon Lee
{"title":"Genome sequence data of the contemporary fresh-market tomatoes.","authors":"Juhee Kim, Tong Geon Lee","doi":"10.1186/s12863-024-01249-3","DOIUrl":"10.1186/s12863-024-01249-3","url":null,"abstract":"<p><strong>Objective: </strong>The fresh-market tomato (Solanum lycopersicum) is bred for direct human consumption. It is selected for specific traits to meet market demands and production systems, and unique genetic variations underlying fresh-market tomato yields have been recently identified. However, DNA sequence variant-trait associations are not yet fully examined even for major traits. To provide a rich genome sequence resource for various genetics and breeding goals for fresh-market tomato traits, we report whole genome sequence data of a pool of contemporary U.S. fresh-market tomatoes.</p><p><strong>Data description: </strong>Eighty-one tomatoes were nominated by academic tomato breeding programs in the U.S. Of the 81 tomatoes, 68 were contemporary fresh-market tomatoes, whereas the remaining 13 were relevant fresh-market tomato breeding and germplasm accessions. Whole genome sequencing (WGS) of the 81 tomatoes was conducted using the Illumina next-generation sequencing technology. The polymerase chain reaction (PCR)-free, paired-end sequencing libraries were sequenced on an average depth per sequenced base of 24 × for each tomato. This data note enhances visibility and potential for use of the more diverse, freely accessible whole genome sequence data of contemporary fresh-market tomatoes.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"65"},"PeriodicalIF":1.9,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11221115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141494518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC genomic dataPub Date : 2024-06-22DOI: 10.1186/s12863-024-01245-7
Luca Bianco, Paolo Fontana, Alexis Marchesini, Sara Torre, Mirko Moser, Stefano Piazza, Sara Alessandri, Vera Pavese, Paola Pollegioni, Cristiano Vernesi, Mickael Malnoy, Daniela Torello Marinoni, Sergio Murolo, Luca Dondini, Claudia Mattioni, Roberto Botta, Federico Sebastiani, Diego Micheletti, Luisa Palmieri
{"title":"The de novo, chromosome-level genome assembly of the sweet chestnut (Castanea sativa Mill.) Cv. Marrone Di Chiusa Pesio.","authors":"Luca Bianco, Paolo Fontana, Alexis Marchesini, Sara Torre, Mirko Moser, Stefano Piazza, Sara Alessandri, Vera Pavese, Paola Pollegioni, Cristiano Vernesi, Mickael Malnoy, Daniela Torello Marinoni, Sergio Murolo, Luca Dondini, Claudia Mattioni, Roberto Botta, Federico Sebastiani, Diego Micheletti, Luisa Palmieri","doi":"10.1186/s12863-024-01245-7","DOIUrl":"10.1186/s12863-024-01245-7","url":null,"abstract":"<p><strong>Objectives: </strong>The sweet chestnut Castanea sativa Mill. is the only native Castanea species in Europe, and it is a tree of high economic value that provides appreciated fruits and valuable wood. In this study, we assembled a high-quality nuclear genome of the ancient Italian chestnut variety 'Marrone di Chiusa Pesio' using a combination of Oxford Nanopore Technologies long reads, whole-genome and Omni-C Illumina short reads.</p><p><strong>Data description: </strong>The genome was assembled into 238 scaffolds with an N50 size of 21.8 Mb and an N80 size of 7.1 Mb for a total assembled sequence of 750 Mb. The BUSCO assessment revealed that 98.6% of the genome matched the embryophyte dataset, highlighting good completeness of the genetic space. After chromosome-level scaffolding, 12 chromosomes with a total length of 715.8 and 713.0 Mb were constructed for haplotype 1 and haplotype 2, respectively. The repetitive elements represented 37.3% and 37.4% of the total assembled genome in haplotype 1 and haplotype 2, respectively. A total of 57,653 and 58,146 genes were predicted in the two haplotypes, and approximately 73% of the genes were functionally annotated using the EggNOG-mapper. The assembled genome will be a valuable resource and reference for future chestnut breeding and genetic improvement.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"64"},"PeriodicalIF":1.9,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11193896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC genomic dataPub Date : 2024-06-19DOI: 10.1186/s12863-024-01246-6
Beenish Sarfraz, Jean Tuyisabe, Louis De Montfort, Abdulrahman Ibrahim, Shamma Z Abdulkreem Almansoori, Haya Alajami, Asma Almeqbaali, Biduth Kundu, Vishnu Sukumari Nath, Esam Eldin Saeed, Ajay Kumar Mishra, Khaled Michel Hazzouri, Raja Almaskari, Abhishek Kumar Sharma, Naganeeswaran Sudalaimuthuasari, Khaled M A Amiri
{"title":"High-quality genome assembly and annotation of five bacteria isolated from the Abu Dhabi sabkha-shore region.","authors":"Beenish Sarfraz, Jean Tuyisabe, Louis De Montfort, Abdulrahman Ibrahim, Shamma Z Abdulkreem Almansoori, Haya Alajami, Asma Almeqbaali, Biduth Kundu, Vishnu Sukumari Nath, Esam Eldin Saeed, Ajay Kumar Mishra, Khaled Michel Hazzouri, Raja Almaskari, Abhishek Kumar Sharma, Naganeeswaran Sudalaimuthuasari, Khaled M A Amiri","doi":"10.1186/s12863-024-01246-6","DOIUrl":"10.1186/s12863-024-01246-6","url":null,"abstract":"<p><strong>Objectives: </strong>Sabkhas represent polyextreme environments characterized by elevated salinity levels, intense ultraviolet (UV) radiation exposure, and extreme temperature fluctuations. In this study, we present the complete genomes of five bacterial isolates isolated from the sabkha-shore region and investigate their genomic organization and gene annotations. A better understanding of the bacterial genomic organization and genetic adaptations of these bacteria holds promise for engineering microbes with tailored functionalities for diverse industrial and agricultural applications, including bioremediation and promotion of plant growth under salinity stress conditions.</p><p><strong>Data description: </strong>We present a comprehensive genome sequencing and annotation of five bacteria (kcgeb_sa, kcgeb_sc, kcgeb_sd, kcgeb_S4, and kcgeb_S11) obtained from the shores of the Abu Dhabi Sabkha region. Initial bacterial identification was conducted through 16 S rDNA amplification and sequencing. Employing a hybrid genome assembly technique combining Illumina short reads (NovaSeq 6000) and Oxford Nanopore long reads (MinION), we obtained complete annotated high-quality gap-free genome sequences. The genome sizes of the kcgeb_sa, kcgeb_sc, kcgeb_sd, kcgeb_S4, and kcgeb_S11 isolates were determined to be 2.4 Mb, 4.1 Mb, 2.9 Mb, 5.05 Mb, and 4.1 Mb, respectively. Our analysis conclusively assigned the bacterial isolates as Staphylococcus capitis (kcgeb_sa), Bacillus spizizenii (kcgeb_sc and kcgeb_S11), Pelagerythrobacter marensis (kcgeb_sd), and Priestia aryabhattai (kcgeb_S4).</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"63"},"PeriodicalIF":1.9,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11188155/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141428436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC genomic dataPub Date : 2024-06-18DOI: 10.1186/s12863-024-01244-8
Haoming Wu, Wenxin Li, Chi Zeng, Jiaxin Li, Huan Wu
{"title":"Complete genome of a novel mycobacteriophage WXIN isolated in Wuhan, China.","authors":"Haoming Wu, Wenxin Li, Chi Zeng, Jiaxin Li, Huan Wu","doi":"10.1186/s12863-024-01244-8","DOIUrl":"10.1186/s12863-024-01244-8","url":null,"abstract":"<p><strong>Objectives: </strong>The rising of antibiotic resistance has sparked a renewed interest in mycobacteriophage as alternative therapeutic strategies against mycobacterial infections. So far, the vast majority of mycobacteriophages have been isolated using the model species Mycobacterium smegmatis, implying an overwhelming majority of mycobacteriophages in the environment remain uncultured, unclassified, and their specific hosts and infection strategies are still unknown. This study was undertaken to isolate and characterize novel mycobacteriophages targeting Mycobacterium septicum.</p><p><strong>Data description: </strong>Here a novel mycobacteriophage WXIN against M. septicum was isolated from soil samples in Wuhan, China. Whole genome analysis indicates that the phage genome consists of 115,158 bp with a GC content of 61.9%. Of the 260 putative open reading frames, 46 may be associated with phage packaging, structure, lysis, lysogeny, genome modification/replication, and other functional roles. The limited genome-wide similarity, along with phylogenetic trees constructed based on viral proteome and orthologous genes show that phage WXIN represents a novel cluster distantly related to cluster J mycobacteriophages (genus Omegavirus). Overall, these results provide novel insights into the genomic properties of mycobacteriophages, highlighting the great genetic diversity of mycobacteriophages in relation to their hosts.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"62"},"PeriodicalIF":1.9,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11186097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC genomic dataPub Date : 2024-06-14DOI: 10.1186/s12863-024-01242-w
Chunju Liu, Zhaohui Guo, Lei Zhang, Jiahong Dong, Xiahong He, Heng Li, Bin Qiu
{"title":"Genome sequence of Fusarium oxysporum strain ByF01, the causal agent of root rot of Knoxia roxburghii in China.","authors":"Chunju Liu, Zhaohui Guo, Lei Zhang, Jiahong Dong, Xiahong He, Heng Li, Bin Qiu","doi":"10.1186/s12863-024-01242-w","DOIUrl":"10.1186/s12863-024-01242-w","url":null,"abstract":"<p><strong>Objectives: </strong>Knoxia roxburghii is a member of the madder (Rubiaceae) family. This plant is cultivated in different areas of China and recognized for its medicinal properties, which leads to its use in traditional Chinese medicine. The incidence of root rot was 10-15%. In June 2023, the causal agent of root rot on K. roxburghii was identified as Fusarium oxysporum. To the best of our knowledge, this is the first report of the complete genome of F. oxysporum strain ByF01 that is the causal agent of root rot of K. roxburghii in China. The results will provide effective resources for pathogenesis on K. roxburghii and the prevention and control of root rot on this host in the future.</p><p><strong>Data description: </strong>To understand the molecular mechanisms used by F. oxysporum to cause root rot on K. roxburghii, strain ByF01 was isolated from diseased roots and identified by morphological and molecular methods. The complete genome of strain ByF01 was then sequenced using a combination of the PacBio Sequel IIe and Illumina sequencing platforms. We obtained 54,431,725 bp of nucleotides, 47.46% GC content, and 16,705 coding sequences.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"59"},"PeriodicalIF":1.9,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11177468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141322143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC genomic dataPub Date : 2024-06-14DOI: 10.1186/s12863-024-01241-x
Haleh Hayatgheibi, Henrik R Hallingbäck, Sven-Olof Lundqvist, Thomas Grahn, Gerhard Scheepers, Peter Nordström, Zhi-Qiang Chen, Katri Kärkkäinen, Harry X Wu, M Rosario García-Gil
{"title":"Implications of accounting for marker-based population structure in the quantitative genetic evaluation of genetic parameters related to growth and wood properties in Norway spruce.","authors":"Haleh Hayatgheibi, Henrik R Hallingbäck, Sven-Olof Lundqvist, Thomas Grahn, Gerhard Scheepers, Peter Nordström, Zhi-Qiang Chen, Katri Kärkkäinen, Harry X Wu, M Rosario García-Gil","doi":"10.1186/s12863-024-01241-x","DOIUrl":"10.1186/s12863-024-01241-x","url":null,"abstract":"<p><strong>Background: </strong>Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B).</p><p><strong>Results: </strong>Our results indicate that models incorporating population structure significantly reduce estimates of additive genetic variance, resulting in substantial reduction of narrow-sense heritability. However, these models considerably improve prediction accuracies. This was particularly significant for growth and solid-wood properties, which showed to have the highest population genetic differentiation (Q<sub>ST</sub>) among the studied traits. Additionally, although the pattern of correlations remained similar across the models, their magnitude was slightly lower for models that included population structure as a fixed effect. This suggests that selection, consistently performed within populations, might be less affected by unfavourable genetic correlations compared to mass selection conducted without pedigree restrictions.</p><p><strong>Conclusion: </strong>We conclude that the results of models properly accounting for population structure are more accurate and less biased compared to those neglecting this effect. This might have practical implications for breeders and forest managers where, decisions based on imprecise selections can pose a high risk to economic efficiency.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"60"},"PeriodicalIF":1.9,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11177499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141322044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BMC genomic dataPub Date : 2024-06-12DOI: 10.1186/s12863-024-01234-w
Aisha Fong, Christina M Rochus, Umesh K Shandilya, Maria M M Muniz, Ankita Sharma, Flavio S Schenkel, Niel A Karrow, Christine F Baes
{"title":"The role of interleukin-10 receptor alpha (IL10Rα) in Mycobacterium avium subsp. paratuberculosis infection of a mammary epithelial cell line.","authors":"Aisha Fong, Christina M Rochus, Umesh K Shandilya, Maria M M Muniz, Ankita Sharma, Flavio S Schenkel, Niel A Karrow, Christine F Baes","doi":"10.1186/s12863-024-01234-w","DOIUrl":"10.1186/s12863-024-01234-w","url":null,"abstract":"<p><strong>Background: </strong>Johne's disease is a chronic wasting disease caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP). Johne's disease is highly contagious and MAP infection in dairy cattle can eventually lead to death. With no available treatment for Johne's disease, genetic selection and improvements in management practices could help reduce its prevalence. In a previous study, the gene coding interleukin-10 receptor subunit alpha (IL10Rα) was associated with Johne's disease in dairy cattle. Our objective was to determine how IL10Rα affects the pathogenesis of MAP by examining the effect of a live MAP challenge on a mammary epithelial cell line (MAC-T) that had IL10Rα knocked out using CRISPR/cas9. The wild type and the IL10Rα knockout MAC-T cell lines were exposed to live MAP bacteria for 72 h. Thereafter, mRNA was extracted from infected and uninfected cells. Differentially expressed genes were compared between the wild type and the IL10Rα knockout cell lines. Gene ontology was performed based on the differentially expressed genes to determine which biological pathways were involved.</p><p><strong>Results: </strong>Immune system processes pathways were targeted to determine the effect of IL10Rα on the response to MAP infection. There was a difference in immune response between the wild type and IL10Rα knockout MAC-T cell lines, and less difference in immune response between infected and not infected IL10Rα knockout MAC-T cells, indicating IL10Rα plays an important role in the progression of MAP infection. Additionally, these comparisons allowed us to identify other genes involved in inflammation-mediated chemokine and cytokine signalling, interleukin signalling and toll-like receptor pathways.</p><p><strong>Conclusions: </strong>Identifying differentially expressed genes in wild type and ILR10α knockout MAC-T cells infected with live MAP bacteria provided further evidence that IL10Rα contributes to mounting an immune response to MAP infection and allowed us to identify additional potential candidate genes involved in this process. We found there was a complex immune response during MAP infection that is controlled by many genes.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"58"},"PeriodicalIF":1.9,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11167801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141312380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}