BMC genomic data最新文献

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Transcriptomic analysis of developing sorghum grains to detect genes related to cell wall biosynthesis and remodelling. 对发育中的高粱籽粒进行转录组分析,检测与细胞壁生物合成和重塑有关的基因。
BMC genomic data Pub Date : 2024-02-07 DOI: 10.1186/s12863-024-01198-x
Camille Costes, Sergi Navarro Sanz, Caroline Calatayud, Alexandre Soriano, Hamza Mameri, Nancy Terrier, Mathilde Francin-Allami
{"title":"Transcriptomic analysis of developing sorghum grains to detect genes related to cell wall biosynthesis and remodelling.","authors":"Camille Costes, Sergi Navarro Sanz, Caroline Calatayud, Alexandre Soriano, Hamza Mameri, Nancy Terrier, Mathilde Francin-Allami","doi":"10.1186/s12863-024-01198-x","DOIUrl":"10.1186/s12863-024-01198-x","url":null,"abstract":"<p><strong>Objective: </strong>Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important grain produced in the world. Interest for cultivating sorghum is increasing all over the world in the context of climate change, due to its low input and water requirements. Like other cultivated cereals, sorghum has significant nutritional value thanks to its protein, carbohydrate and dietary fiber content, these latter mainly consisting of cell wall polysaccharides. This work describes for the first time a transcriptomic analysis dedicated to identify the genes involved in the biosynthesis and remodelling of cell walls both in the endosperm and outer layers of sorghum grain during its development. Further analysis of these transcriptomic data will improve our understanding of cell wall assembly, which is a key component of grain quality.</p><p><strong>Data description: </strong>This research delineates the steps of our analysis, starting with the cultivation conditions and the grain harvest at different stages of development, followed by the laser microdissection applied to separate the endosperm from the outer layers. It also describes the procedures implemented to generate RNA libraries and to obtain a normalized and filtered table of transcript counts, and finally determine the number of putative cell wall-related genes already listed in literature.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10848504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139698948","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}
引用次数: 0
Genomic characterization of Listeria monocytogenes and Listeria innocua isolated from milk and dairy samples in Ethiopia. 从埃塞俄比亚牛奶和乳制品样本中分离出的单核细胞增生李斯特菌和无核李斯特菌的基因组特征。
IF 1.9
BMC genomic data Pub Date : 2024-01-31 DOI: 10.1186/s12863-024-01195-0
Xiaoyuan Wei, Anwar Hassen, Karen McWilliams, Karen Pietrzen, Taejung Chung, Marysabel Méndez Acevedo, Tyler Chandross-Cohen, Edward G Dudley, Jessie Vipham, Hassen Mamo, Tesfaye Sisay Tessema, Ashagrie Zewdu, Jasna Kovac
{"title":"Genomic characterization of Listeria monocytogenes and Listeria innocua isolated from milk and dairy samples in Ethiopia.","authors":"Xiaoyuan Wei, Anwar Hassen, Karen McWilliams, Karen Pietrzen, Taejung Chung, Marysabel Méndez Acevedo, Tyler Chandross-Cohen, Edward G Dudley, Jessie Vipham, Hassen Mamo, Tesfaye Sisay Tessema, Ashagrie Zewdu, Jasna Kovac","doi":"10.1186/s12863-024-01195-0","DOIUrl":"10.1186/s12863-024-01195-0","url":null,"abstract":"<p><p>Listeriosis caused by Listeria monocytogenes often poses a significant threat to vulnerable populations. Dairy products have been implicated in outbreaks of listeriosis worldwide. In Ethiopia, studies have identified Listeria spp. and L. monocytogenes in various dairy products, but the genetic diversity and phylogenetic relationships of these bacteria remain largely unknown in the low- and middle-income countries. Therefore, we conducted whole-genome sequencing on 15 L. monocytogenes and 55 L. innocua isolates obtained from different levels of the dairy supply chains across three regions in Ethiopia. Genomes were assembled and used for MLST genotyping and single nucleotide polymorphism (SNP) analysis to infer phylogenetic relationships. We identified a total of 3 L. monocytogenes (i.e., 2, 145, and 18) and 12 L. innocua (i.e., 1489, 1619, 603, 537, 1010, 3186, 492, 3007, 1087, 474, 1008, and 637) MLST sequence types among the studied isolates. Some of these sequence types showed region-specific occurrence, while others were broadly distributed across regions. Through high-quality SNP analysis, we found that among 13 L. monocytogenes identified as ST 2, 11 of them were highly similar with low genetic variation, differing by only 1 to 10 SNPs, suggesting potential selection in the dairy food supply chain. The L. innocua isolates also exhibited low intra-ST genetic variation with only 0-10 SNP differences, except for the ST 1619, which displayed a greater diversity.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"12"},"PeriodicalIF":1.9,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10829315/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139652310","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}
引用次数: 0
BRCA 1/2 mutations and risk of uterine cancer: a systematic review and meta-analysis. BRCA 1/2突变与子宫癌风险:系统回顾与荟萃分析。
IF 1.9
BMC genomic data Pub Date : 2024-01-31 DOI: 10.1186/s12863-024-01189-y
Faezeh Zakerinasab, Qumars Behfar, Reza Parsaee, Reza Hossein Zadeh, Elaheh Foroughi, Amirhesam Amirbeik, Ghazalehsadat Ahmadi
{"title":"BRCA 1/2 mutations and risk of uterine cancer: a systematic review and meta-analysis.","authors":"Faezeh Zakerinasab, Qumars Behfar, Reza Parsaee, Reza Hossein Zadeh, Elaheh Foroughi, Amirhesam Amirbeik, Ghazalehsadat Ahmadi","doi":"10.1186/s12863-024-01189-y","DOIUrl":"10.1186/s12863-024-01189-y","url":null,"abstract":"<p><strong>Purpose: </strong>In this study, we aim to investigate the association between BRCA1/2 mutation and uterine cancer incidence.</p><p><strong>Material and method: </strong>We systematically searched three databases including PubMed, Scopus, and Google Scholar up to August 2023; and reviewed 23 cohorts and cross-sectional studies to explore the association between BRCA1/2 mutations and uterine cancer incidence.</p><p><strong>Results: </strong>This systematic review comprised a total of 21 cohort studies and 2 cross-sectional studies after the screening process. According to meta-analysis the prevalence of the BRCA1/2 gene in patients with uterine cancer was 0.02 (95%CI = [0.01,0.03], P < 0.01, I<sup>2</sup> = 94.82%) CONCLUSIONS: Our meta-analysis investigates a 2% prevalence of BRCA1/2 mutation in patients with uterine cancer. Patients with BRCA1/2 mutations might be more conscious of uterine malignancies.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"13"},"PeriodicalIF":1.9,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10829221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139652309","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}
引用次数: 0
Genomic insights into the endangered white-eared night heron (Gorsachius magnificus). 对濒危白耳夜鹭(Gorsachius magnificus)基因组的深入研究。
IF 1.9
BMC genomic data Pub Date : 2024-01-30 DOI: 10.1186/s12863-024-01194-1
Haoran Luo, Qingxian Lin, Wenzhen Fang, Xiaolin Chen, Xiaoping Zhou
{"title":"Genomic insights into the endangered white-eared night heron (Gorsachius magnificus).","authors":"Haoran Luo, Qingxian Lin, Wenzhen Fang, Xiaolin Chen, Xiaoping Zhou","doi":"10.1186/s12863-024-01194-1","DOIUrl":"10.1186/s12863-024-01194-1","url":null,"abstract":"<p><strong>Objectives: </strong>A genome sequence of a threatened species can provide valuable genetic information that is important for improving the conservation strategies. The white-eared night heron (Gorsachius magnificus) is an endangered and poorly known ardeid bird. In order to support future studies on conservation genetics and evolutionary adaptation of this species, we have reported a de novo assembled and annotated whole-genome sequence of the G. magnificus.</p><p><strong>Data description: </strong>The final draft genome assembly of the G. magnificus was 1.19 Gb in size, with a contig N50 of 187.69 kb and a scaffold N50 of 7,338.28 kb. According to BUSCO analysis, the genome assembly contained 97.49% of the 8,338 genes in the Aves (odb10) dataset. Approximately 10.52% of the genome assembly was composed of repetitive sequences. A total of 14,613 protein-coding genes were predicted in the genome assembly, with functional annotations available for 14,611 genes. The genome assembly exhibited a heterozygosity rate of 0.49 heterozygosity per kilobase pair. This draft genome of G. magnificus provides valuable genomic resources for future studies on conservation and evolution.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"11"},"PeriodicalIF":1.9,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10826008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139643510","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}
引用次数: 0
Comparative analysis and characterization of the chloroplast genome of Krascheninnikovia ceratoides (Amarathaceae): a xerophytic semi-shrub exhibiting drought resistance and high-quality traits. Krascheninnikovia ceratoides(Amarathaceae)叶绿体基因组的比较分析和特征描述:一种表现出抗旱性和高品质特征的旱生半灌木。
IF 1.9
BMC genomic data Pub Date : 2024-01-29 DOI: 10.1186/s12863-024-01197-y
Yuping Liu, Changyuan Zheng, Xu Su, Jinyuan Chen, Xiaoli Li, Chenglin Sun, Mir Muhammad Nizamani
{"title":"Comparative analysis and characterization of the chloroplast genome of Krascheninnikovia ceratoides (Amarathaceae): a xerophytic semi-shrub exhibiting drought resistance and high-quality traits.","authors":"Yuping Liu, Changyuan Zheng, Xu Su, Jinyuan Chen, Xiaoli Li, Chenglin Sun, Mir Muhammad Nizamani","doi":"10.1186/s12863-024-01197-y","DOIUrl":"10.1186/s12863-024-01197-y","url":null,"abstract":"<p><strong>Background: </strong>Krascheninnikovia ceratoides, a perennial halophytic semi-shrub belonging to the genus Krascheninnikovia (Amarathaceae), possesses noteworthy ecological, nutritional, and economic relevance. This species is primarily distributed across arid, semi-arid, and saline-alkaline regions of the Eurasian continent, encompassing Inner Mongolia, Xinjiang, Qinghai, Gansu, Ningxia, and Tibet.</p><p><strong>Results: </strong>We reported the comprehensive chloroplast (cp) genome of K. ceratoides, characterized by a circular conformation spanning 151,968 bp with a GC content of 36.60%. The cp genome encompassed a large single copy (LSC, 84,029 bp), a small single copy (SSC, 19,043 bp), and a pair of inverted repeats (IRs) regions (24,448 bp each). This genome harbored 128 genes and encompassed 150 simple sequence repeats (SSRs). Through comparative analyses involving cp genomes from other Cyclolobeae (Amarathaceae) taxa, we observed that the K. ceratoides cp genome exhibited high conservation, with minor divergence events in protein-coding genes (PCGs) accD, matK, ndhF, ndhK, ycf1, and ycf2. Phylogenetic reconstructions delineated K. ceratoides as the sister taxon to Atriplex, Chenopodium, Dysphania, and Suaeda, thus constituting a robust clade. Intriguingly, nucleotide substitution ratios (Ka/Ks) between K. ceratoides and Dysphania species for ycf1 and ycf2 genes surpassed 1.0, indicating the presence of positive selection pressure on these loci.</p><p><strong>Conclusions: </strong>The findings of this study augment the genomic repository for the Amarathaceae family and furnish crucial molecular instruments for subsequent investigations into the ecological adaptation mechanisms of K. ceratoides within desert ecosystems.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"10"},"PeriodicalIF":1.9,"publicationDate":"2024-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10826016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139576979","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}
引用次数: 0
Mapping phenotypic performance and novel SNPs for cold tolerance in tomato (Solanum lycopersicum) genotypes through GWAS and population genetics. 通过 GWAS 和群体遗传学绘制番茄(Solanum lycopersicum)基因型耐寒性的表型表现和新型 SNPs。
IF 1.9
BMC genomic data Pub Date : 2024-01-27 DOI: 10.1186/s12863-024-01190-5
Labiba Riyaz Shah, Nazeer Ahmed, Khursheed Hussain, Sheikh Mansoor, Tamana Khan, Imran Khan, Sumati Narayan, Baseerat Afroza, Imtiyaz Murtaza, Asif Bashir Shikari, Basharat Bhat, Khalid Z Masoodi
{"title":"Mapping phenotypic performance and novel SNPs for cold tolerance in tomato (Solanum lycopersicum) genotypes through GWAS and population genetics.","authors":"Labiba Riyaz Shah, Nazeer Ahmed, Khursheed Hussain, Sheikh Mansoor, Tamana Khan, Imran Khan, Sumati Narayan, Baseerat Afroza, Imtiyaz Murtaza, Asif Bashir Shikari, Basharat Bhat, Khalid Z Masoodi","doi":"10.1186/s12863-024-01190-5","DOIUrl":"10.1186/s12863-024-01190-5","url":null,"abstract":"<p><p>The cold stress susceptibility of tomato (Solanum lycopersicum) curtails its cultivation, with significant impact in temperate regions and on cropping seasons. To unravel genomic regions responsible for cold stress resilience, a diverse set of fifty genotypes encompassing cultivated, wild species, and landraces were genotyped using genotyping-by-sequencing. Over two years and six trials employing both early and late sowing, these lines were evaluated. Illumina-based next-generation sequencing produced up to 3 million reads per sample from individually sequenced library pools. The Tassel pipeline yielded 10,802 variants, subsequently filtered to 3,854 SNPs for genome-wide association analysis (GWAS). Employing clustering methods (population structure) via TASSEL, SNPhylo, and Kinship matrix, the fifty genotypes clustered into four distinct gene pools. The GWAS for cold tolerance in tomato integrated key traits including yield. Using six independent phenotypic datasets representing various environments, the study identified 4,517 significant marker-trait associations for cold tolerance traits. Notably, pivotal variations (> 10%) in cold stress tolerance, particularly proline content, were linked to marker-trait associations. Additionally, 5,727 significant marker-trait associations for yield and yield-related traits were unveiled, shedding light on fruit yield and directly associated attributes. The investigation pinpointed 685 candidate genes across all examined traits, including 60 genes associated with biological processes within these genomic regions. Remarkably, 7 out of the 60 genes were directly linked to abiotic stress tolerance, functioning as stress-responsive genes either directly or indirectly. The identified genes, particularly those associated with stress response, could hold the key to enhancing cold tolerance and overall crop productivity in tomato cultivation.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"9"},"PeriodicalIF":1.9,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10822167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139572400","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}
引用次数: 0
An improved and extended dual-index multiplexed 16S rRNA sequencing for the Illumina HiSeq and MiSeq platform. 用于 Illumina HiSeq 和 MiSeq 平台的改进型和扩展型双指数多重 16S rRNA 测序技术。
IF 1.9
BMC genomic data Pub Date : 2024-01-22 DOI: 10.1186/s12863-024-01192-3
A K Larin, K M Klimina, V A Veselovsky, E I Olekhnovich, M D Morozov, D I Boldyreva, R A Yunes, A I Manolov, D E Fedorov, A V Pavlenko, Y S Galeeva, E V Starikova, E N Ilina
{"title":"An improved and extended dual-index multiplexed 16S rRNA sequencing for the Illumina HiSeq and MiSeq platform.","authors":"A K Larin, K M Klimina, V A Veselovsky, E I Olekhnovich, M D Morozov, D I Boldyreva, R A Yunes, A I Manolov, D E Fedorov, A V Pavlenko, Y S Galeeva, E V Starikova, E N Ilina","doi":"10.1186/s12863-024-01192-3","DOIUrl":"10.1186/s12863-024-01192-3","url":null,"abstract":"<p><strong>Background: </strong>Recent advancements in next-generation sequencing (NGS) technology have ushered in significant improvements in sequencing speed and data throughput, thereby enabling the simultaneous analysis of a greater number of samples within a single sequencing run. This technology has proven particularly valuable in the context of microbial community profiling, offering a powerful tool for characterizing the microbial composition at the species level within a given sample. This profiling process typically involves the sequencing of 16S ribosomal RNA (rRNA) gene fragments. By scaling up the analysis to accommodate a substantial number of samples, sometimes as many as 2,000, it becomes possible to achieve cost-efficiency and minimize the introduction of potential batch effects. Our study was designed with the primary objective of devising an approach capable of facilitating the comprehensive analysis of 1,711 samples sourced from diverse origins, including oropharyngeal swabs, mouth cavity swabs, dental swabs, and human fecal samples. This analysis was based on data obtained from 16S rRNA metagenomic sequencing conducted on the Illumina MiSeq and HiSeq sequencing platforms.</p><p><strong>Results: </strong>We have designed a custom set of 10-base pair indices specifically tailored for the preparation of libraries from amplicons derived from the V3-V4 region of the 16S rRNA gene. These indices are instrumental in the analysis of the microbial composition in clinical samples through sequencing on the Illumina MiSeq and HiSeq platforms. The utilization of our custom index set enables the consolidation of a significant number of libraries, enabling the efficient sequencing of these libraries in a single run.</p><p><strong>Conclusions: </strong>The unique array of 10-base pair indices that we have developed, in conjunction with our sequencing methodology, will prove highly valuable to laboratories engaged in sequencing on Illumina platforms or utilizing Illumina-compatible kits.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"8"},"PeriodicalIF":1.9,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139522335","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}
引用次数: 0
Evaluation of biocontrol efficacy of rhizosphere dwelling bacteria for management of Fusarium wilt and Botrytis gray mold of chickpea. 评估根瘤菌对鹰嘴豆镰刀菌枯萎病和灰霉病的生物防治效果。
BMC genomic data Pub Date : 2024-01-15 DOI: 10.1186/s12863-023-01178-7
Gurreddi Bhargavi, Meenakshi Arya, Prashant Prakash Jambhulkar, Anshuman Singh, Ajaya Kumar Rout, Bijay Kumar Behera, Sushil Kumar Chaturvedi, Ashok Kumar Singh
{"title":"Evaluation of biocontrol efficacy of rhizosphere dwelling bacteria for management of Fusarium wilt and Botrytis gray mold of chickpea.","authors":"Gurreddi Bhargavi, Meenakshi Arya, Prashant Prakash Jambhulkar, Anshuman Singh, Ajaya Kumar Rout, Bijay Kumar Behera, Sushil Kumar Chaturvedi, Ashok Kumar Singh","doi":"10.1186/s12863-023-01178-7","DOIUrl":"10.1186/s12863-023-01178-7","url":null,"abstract":"<p><strong>Background: </strong>Chickpea (Cicer arietinum L.) production is affected by many biotic factors, among them Fusarium wilt caused by Fusarium oxysporum f. sp. ciceri and Botrytis gray mold caused by Botrytis cinerea led to severe losses. As fungicide application is not advisable, biological management is the best alternative for plant protection. The rhizosphere-dwelling antagonistic bacteria are one of the important successful alternative strategy to manage these diseases of chickpea. Rhizosphere dwelling bacteria serve as biocontrol agents by different mechanisms like producing antibiotics, different enzymes, siderophores against pathogens and thereby reducing the growth of pathogens.</p><p><strong>Results: </strong>The present study aimed to isolate rhizospheric bacteria from the soils of different chickpea fields to evaluate biocontrol efficacy of the isolated bacteria to manage Fusarium wilt and Botrytis gray mold in chickpea. A total of 67 bacteria were isolated from chickpea rhizosphere from Bundelkhand region of India. Study revealed the isolated bacteria could reduce the Fusarium oxysporum f. sp. ciceris and Botrytis cinerea infection in chickpea between 17.29 and 75.29%. After screening of all the bacteria for their biocontrol efficacy, 13 most promising bacterial isolates were considered for further study out of which, three bacterial isolates (15d, 9c and 14a) have shown the maximum in vitro antagonistic effects against Fusarium oxysporum f. sp. ciceri and Botrytis cinerea comparable to in vivo effects. However, Isolate (15d) showed highest 87.5% and 82.69% reduction in disease against Fusarium wilt and Botrytis gray mold respectively, under pot condition. Three most potential isolates were characterized at molecular level using 16S rRNA gene and found to be Priestia megaterium (9c and 14a) and Serratia marcescens (15d).</p><p><strong>Conclusion: </strong>This study identified two native biocontrol agents Priestia megaterium and Serratia marcescens from the rhizospheric soils of Bundelkhand region of India for control of Fusarium wilt, Botrytis gray mold. In future, efforts should be made to further validate the biocontrol agents in conjugation with nanomaterials for enhancing the synergistic effects in managing the fungal diseases in chickpea. This study will definitely enhance our understanding of these bioagents, and to increase their performance by developing effective formulations, application methods, and integrated strategies.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10790480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139473102","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}
引用次数: 0
Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina Hemerocallis citrina 线粒体基因组的密码子用法特征和系统发育分析
BMC genomic data Pub Date : 2024-01-13 DOI: 10.1186/s12863-024-01191-4
Kun Zhang, Yiheng Wang, Yue Zhang, Xiaofei Shan
{"title":"Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina","authors":"Kun Zhang, Yiheng Wang, Yue Zhang, Xiaofei Shan","doi":"10.1186/s12863-024-01191-4","DOIUrl":"https://doi.org/10.1186/s12863-024-01191-4","url":null,"abstract":"","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"18 4","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139437227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
rDNA and mtDNA analysis for the identification of genetic characters in the hybrid grouper derived from hybridization of Cromileptes altivelis (female) × Epinephelus lanceolatus (male). 利用 rDNA 和 mtDNA 分析鉴定 Cromileptes altivelis(雌性)× Epinephelus lanceolatus(雄性)杂交产生的杂交石斑鱼的遗传特征。
BMC genomic data Pub Date : 2024-01-12 DOI: 10.1186/s12863-023-01188-5
Liu Cao, Pan Chen, Xingrong Hou, Jun Ma, Ning Yang, Yan Lu, Hai Huang
{"title":"rDNA and mtDNA analysis for the identification of genetic characters in the hybrid grouper derived from hybridization of Cromileptes altivelis (female) × Epinephelus lanceolatus (male).","authors":"Liu Cao, Pan Chen, Xingrong Hou, Jun Ma, Ning Yang, Yan Lu, Hai Huang","doi":"10.1186/s12863-023-01188-5","DOIUrl":"10.1186/s12863-023-01188-5","url":null,"abstract":"<p><strong>Background: </strong>Hybridization is a useful strategy to produce offspring with more desirable phenotypic characteristics than those of parents. The hybrid grouper derived from the cross of Cromileptes altivelis (♀, 2n = 48) with Epinephelus lanceolatus (♂, 2n = 48) exhibits improved growth compared with its female parent, which makes it valuable to aquaculture. However, the genetic traits of the hybrid grouper are poorly understood.</p><p><strong>Results: </strong>The observations showed that the hybrid grouper was diploid (2n = 48) and displayed intermediate morphology with the parent's measurable characteristics. The ribosomal DNA (rDNA) and mitochondria DNA (mtDNA) were characterized at molecular and phylogenetic level. High similarity and low genetic distance of 5S rDNA and mtDNA sequences between the hybrid grouper and C. altivelis showed that the hybrid grouper had a closer genetic relationship with female parents. The reconstructed phylogenetic tree based on COI gene and D-loop region of mtDNA recovered that mtDNA was maternally inherited in the hybrid grouper. Additionally, the DNA methylation level of 5S rDNA intergenic spacers (IGS) sequence was tested in here. The results showed that the DNA methylation status of the hybrid grouper was significantly lower than that of C. altivelis.</p><p><strong>Conclusion: </strong>Results of this study provide important data on the genetic characteristics of the hybrid derived from the cross of C. altivelis and E. lanceolatus, and contribute the knowledge of both evolution and marine fish breeding.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10787421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139433222","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}
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