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Li X, Li Z, Shen Q, Pan Y, Dong X, Xu Z, Duan S, Li Y, Du Y, Chen S, Ma Z, Dong Y. HGFDB: a collective database of helmeted guinea fowl genomics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6070151. [PMID: 33417691 PMCID: PMC7792568 DOI: 10.1093/database/baaa116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/21/2020] [Accepted: 12/22/2020] [Indexed: 11/12/2022]
Abstract
As a vigorous and hardy and an almost disease-free game bird, the domestic helmeted guinea fowl (Numida meleagris, hereafter HGF) has attracted considerable attention in a large number of genetic study projects. However, none of the current/recent avian databases are related to this agriculturally and commercially important poultry species. To address this data gap, we developed Helmeted Guinea Fowl Database (HGFDB), which manages and shares HGF genomic and genetic data. By processing the data of genome assembly, sequencing reads and genetic variations, we organized them into eight modules, which correspond to ‘Home’, ‘Genome’, ‘Re-sequence’, ‘Gene’, ‘Variation’, ‘Download’, ‘Tools’ and ‘Help’, HGFDB provides the most comprehensive view of the HGF genome to date and will be relevant for future studies on HGF structural and functional genomics and genetic improvement. Database URL:http://hgfdb.ynau.edu.cn/
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Affiliation(s)
- Xuzhen Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China.,Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Zhi Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650093, China
| | - Quankuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi 999070, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yunbin Pan
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Xiao Dong
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Zetan Xu
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Shengchang Duan
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Yunfei Li
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Yuan Du
- Nowbio Biotechnology Company, No. 168 Yunjing Road, Kunming, Yunnan 650201, China
| | - Shanshan Chen
- College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan 650201, China
| | - Zhaocheng Ma
- Shanghai Yangjing-Juyuan Experimental School, No 333 Pucheng Road, Pudong, Shanghai 200120, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China.,College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan 650201, China
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Zhen Y. CardioTF, a database of deconstructing transcriptional circuits in the heart system. PeerJ 2016; 4:e2339. [PMID: 27635320 PMCID: PMC5012272 DOI: 10.7717/peerj.2339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 07/18/2016] [Indexed: 11/29/2022] Open
Abstract
Background: Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method. Methods: The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results. Results: Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype. Discussion: The CardioTF database can be used as a portal to construct transcriptional network of cardiac development. Availability and Implementation: Database URL: http://www.cardiosignal.org/database/cardiotf.html.
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An assessment of opportunities to dissect host genetic variation in resistance to infectious diseases in livestock. Animal 2012; 3:415-36. [PMID: 22444313 DOI: 10.1017/s1751731108003522] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
This paper reviews the evidence for host genetic variation in resistance to infectious diseases for a wide variety of diseases of economic importance in poultry, cattle, pig, sheep and Atlantic salmon. Further, it develops a method of ranking each disease in terms of its overall impact, and combines this ranking with published evidence for host genetic variation and information on the current state of genomic tools in each host species. The outcome is an overall ranking of the amenability of each disease to genomic studies that dissect host genetic variation in resistance. Six disease-based assessment criteria were defined: industry concern, economic impact, public concern, threat to food safety or zoonotic potential, impact on animal welfare and threat to international trade barriers. For each category, a subjective score was assigned to each disease according to the relative strength of evidence, impact, concern or threat posed by that particular disease, and the scores were summed across categories. Evidence for host genetic variation in resistance was determined from available published data, including breed comparison, heritability studies, quantitative trait loci (QTL) studies, evidence of candidate genes with significant effects, data on pathogen sequence and on host gene expression analyses. In total, 16 poultry diseases, 13 cattle diseases, nine pig diseases, 11 sheep diseases and three Atlantic salmon diseases were assessed. The top-ranking diseases or pathogens, i.e. those most amenable to studies dissecting host genetic variation, were Salmonella in poultry, bovine mastitis, Marek's disease and coccidiosis, both in poultry. The top-ranking diseases or pathogens in pigs, sheep and Atlantic salmon were Escherichia coli, mastitis and infectious pancreatic necrosis, respectively. These rankings summarise the current state of knowledge for each disease and broadly, although not entirely, reflect current international research efforts. They will alter as more information becomes available and as genome tools become more sophisticated for each species. It is suggested that this approach could be used to rank diseases from other perspectives as well, e.g. in terms of disease control strategies.
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Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 290] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
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Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
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Romanov MN, Tuttle EM, Houck ML, Modi WS, Chemnick LG, Korody ML, Mork EMS, Otten CA, Renner T, Jones KC, Dandekar S, Papp JC, Da Y, Green ED, Magrini V, Hickenbotham MT, Glasscock J, McGrath S, Mardis ER, Ryder OA. The value of avian genomics to the conservation of wildlife. BMC Genomics 2009; 10 Suppl 2:S10. [PMID: 19607652 PMCID: PMC2966331 DOI: 10.1186/1471-2164-10-s2-s10] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affecting genetic variation, adaptation and evolution. Developing genomic tools and resources including genomic libraries and a genetic map of the California condor is a prerequisite for identification of candidate loci for a heritable embryonic lethal condition. The white-throated sparrow exhibits a stable genetic polymorphism (i.e. chromosomal rearrangements) associated with variation in morphology, physiology, and behavior (e.g., aggression, social behavior, sexual behavior, parental care). In this paper we outline the utility of these species as well as report on recent advances in the study of their genomes. Results Genotyping of the condor resource population at 17 microsatellite loci provided a better assessment of the current population's genetic variation. Specific New World vulture repeats were found in the condor genome. Using condor BAC library and clones, chicken-condor comparative maps were generated. A condor fibroblast cell line transcriptome was characterized using the 454 sequencing technology. Our karyotypic analyses of the sparrow in combination with other studies indicate that the rearrangements in both chromosomes 2m and 3a are complex and likely involve multiple inversions, interchromosomal linkage, and pleiotropy. At least a portion of the rearrangement in chromosome 2m existed in the common ancestor of the four North American species of Zonotrichia, but not in the one South American species, and that the 2m form, originally thought to be the derived condition, might actually be the ancestral one. Conclusion Mining and characterization of candidate loci in the California condor using molecular genetic and genomic techniques as well as linkage and comparative genomic mapping will eventually enable the identification of carriers of the chondrodystrophy allele, resulting in improved genetic management of this disease. In the white-throated sparrow, genomic studies, combined with ecological data, will help elucidate the basis of genic selection in a natural population. Morphs of the sparrow provide us with a unique opportunity to study intraspecific genomic differences, which have resulted from two separate yet linked evolutionary trajectories. Such results can transform our understanding of evolutionary and conservation biology.
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Affiliation(s)
- Michael N Romanov
- Genetics Division, San Diego Zoo's Institute for Conservation Research, Zoological Society of San Diego, Arnold and Mabel Beckman Center for Conservation Research, 15600 San Pasqual Valley Rd., Escondido, CA 92027, USA.
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