GigaByte (Hong Kong, China)最新文献_第6页

Genome assembly and annotation of the king ratsnake, Elaphe carinata. 鼠王蛇（Elaphe carinata）的基因组组装和注释。

GigaByte (Hong Kong, China) Pub Date : 2023-12-07 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.101

Jiale Fan, Ruyi Huang, Diancheng Yang, Yanan Gong, Zhangbo Cui, Xinge Wang, Zicheng Su, Jing Yu, Yi Zhang, Tierui Zhang, Zhihao Jiang, Tianming Lan, He Wang, Song Huang

{"title":"Genome assembly and annotation of the king ratsnake, Elaphe carinata.","authors":"Jiale Fan, Ruyi Huang, Diancheng Yang, Yanan Gong, Zhangbo Cui, Xinge Wang, Zicheng Su, Jing Yu, Yi Zhang, Tierui Zhang, Zhihao Jiang, Tianming Lan, He Wang, Song Huang","doi":"10.46471/gigabyte.101","DOIUrl":"https://doi.org/10.46471/gigabyte.101","url":null,"abstract":"The king ratsnake (Elaphe carinata) of the genus Elaphe is a common large, non-venomous snake widely distributed in Southeast and East Asia. It is an economically important farmed species. As a non-venomous snake, the king ratsnake predates venomous snakes, such as cobras and pit vipers. However, the immune and digestive mechanisms of the king ratsnake remain unclear. Despite their economic and research importance, we lack genomic resources that would benefit toxicology, phylogeography, and immunogenetics studies. Here, we used single-tube long fragment read sequencing to generate the first contiguous genome of a king ratsnake from Huangshan City, Anhui province, China. The genome size is 1.56 GB with a scaffold N50 of 6.53M. The total length of the genome is approximately 621 Mb, while the repeat content is 42.26%. Additionally, we predicted 22,339 protein-coding genes, including 22,065 with functional annotations. Our genome is a potentially useful addition to those available for snakes.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte101"},"PeriodicalIF":0.0,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10719989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138814642","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

Sampling collections and metadata of planorbidae (Mollusca: Gastropoda) in Brazil: a comprehensive analysis of the Oswaldo Cruz Institute's Mollusk Collection from 1948 to 2023. 巴西刨腹目（软体动物门：腹足纲）的采样采集和元数据：1948-2023 年奥斯瓦尔多-克鲁斯研究所软体动物采集的综合分析。

GigaByte (Hong Kong, China) Pub Date : 2023-12-07 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.102

Silvana Carvalho Thiengo, Mariana Gomes Lima, Alexandre Bonfim Pinheiro da Silva, Raiany Thuler Nogueira, Flávia Cristina Dos Santos Rangel, Suzete Rodrigues Gomes

{"title":"Sampling collections and metadata of planorbidae (Mollusca: Gastropoda) in Brazil: a comprehensive analysis of the Oswaldo Cruz Institute's Mollusk Collection from 1948 to 2023.","authors":"Silvana Carvalho Thiengo, Mariana Gomes Lima, Alexandre Bonfim Pinheiro da Silva, Raiany Thuler Nogueira, Flávia Cristina Dos Santos Rangel, Suzete Rodrigues Gomes","doi":"10.46471/gigabyte.102","DOIUrl":"https://doi.org/10.46471/gigabyte.102","url":null,"abstract":"Planorbidae comprises approximately 40 genera of freshwater gastropods, including roughly 250 species. Among the Planorbidae subfamilies, the significance of Planorbinae is due to its genus Biomphalaria, whose species are intermediate hosts of the trematode Schistosoma mansoni Sambon, 1907, which causes schistosomiasis in humans and animals. Here, we present the analysis of the dataset of Planorbidae housed in the Collection of Mollusks of the Oswaldo Cruz Institute, with a special focus on Biomphalaria species. This dataset includes 7,267 lots originating from 55 countries, representing 20 genera and 75 species collected from 1948 to 2023. Collections were performed in all regions of Brazil, comprising specimens from 26 states and the Federal District, particularly from the Southeast and Northeast. Within the dataset, Biomphalaria includes 3,926 lots of 31 species from 42 countries. These records will help improve our comprehension of schistosomiasis transmission dynamics and the geographic distributions of these medically important species.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte102"},"PeriodicalIF":0.0,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10719988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138814644","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

A dataset of small-mammal detections in West Africa and their associated micro-organisms. 西非小型哺乳动物检测数据集及其相关微生物。

GigaByte (Hong Kong, China) Pub Date : 2023-12-04 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.100

David Simons, Lauren A Attfield, Kate E Jones, Deborah Watson-Jones, Richard Kock

{"title":"A dataset of small-mammal detections in West Africa and their associated micro-organisms.","authors":"David Simons, Lauren A Attfield, Kate E Jones, Deborah Watson-Jones, Richard Kock","doi":"10.46471/gigabyte.100","DOIUrl":"https://doi.org/10.46471/gigabyte.100","url":null,"abstract":"Rodents, a globally distributed and ecologically important mammalian order, serve as hosts for various zoonotic pathogens. However, sampling of rodents and their pathogens suffers from taxonomic and spatial biases. This affects consolidated databases, such as IUCN and GBIF, limiting inference regarding the spillover hazard of zoonotic pathogens into human populations. Here, we synthesised data from 127 rodent trapping studies conducted in 14 West African countries between 1964 and 2022. We combined occurrence data with pathogen screening results to produce a dataset containing detection/non-detection data for 65,628 individual small mammals identified to the species level from at least 1,611 trapping sites. We also included 32 microorganisms, identified to the species or genus levels, that are known or potential pathogens. The dataset is formatted to Darwin Core Standard with associated metadata. This dataset can mitigate spatial and taxonomic biases of current databases, improving understanding of rodent-associated zoonotic pathogen spillover across West Africa.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte100"},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10711198/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138814641","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

The genome assembly and annotation of the Chinese cobra, Naja atra. 中国眼镜蛇Naja atra的基因组组装与注释。

GigaByte (Hong Kong, China) Pub Date : 2023-11-20 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.99

Jiangang Wang, Yuxin Wu, Shiqing Wang, Weiwu Mu, Wenmei Zeng, Xi Chen, Kangfeng Jiang, Liangyu Yang, Guohai Hu, Fengping He

引用次数: 0

A reference assembly for the legume cover crop hairy vetch (Vicia villosa) 豆科覆盖作物毛豌豆(Vicia villosa)的参考组合

GigaByte (Hong Kong, China) Pub Date : 2023-11-13 DOI: 10.46471/gigabyte.98

Tyson Fuller, Derek M. Bickhart, Lisa M. Koch, Lisa Kissing Kucek, Shahjahan Ali, Haley Mangelson, Maria J. Monteros, Timothy Hernandez, Timothy P. L. Smith, Heathcliffe Riday, Michael L. Sullivan

引用次数: 1

Data from Entomological Collections of Aedes (Diptera: Culicidae) in a post-epidemic area of Chikungunya, City of Kinshasa, Democratic Republic of Congo 刚果民主共和国金沙萨市基孔肯雅流行后地区伊蚊(双翅目:库蚊科)昆虫学采集数据

GigaByte (Hong Kong, China) Pub Date : 2023-11-08 DOI: 10.46471/gigabyte.96

Victoire Nsabatien, Josue Zanga, Fiacre Agossa, Nono Mvuama, Maxwell Bamba, Osée Mansiangi, Leon Mbashi, Vanessa Mvudi, Glodie Diza, Dorcas Kantin, Narcisse Basosila, Hyacinthe Lukoki, Arsene Bokulu, Christelle Bosulu, Erick Bukaka, Jonas Nagahuedi, Jean Claude Palata, Emery Metelo

{"title":"Data from Entomological Collections of Aedes (Diptera: Culicidae) in a post-epidemic area of Chikungunya, City of Kinshasa, Democratic Republic of Congo","authors":"Victoire Nsabatien, Josue Zanga, Fiacre Agossa, Nono Mvuama, Maxwell Bamba, Osée Mansiangi, Leon Mbashi, Vanessa Mvudi, Glodie Diza, Dorcas Kantin, Narcisse Basosila, Hyacinthe Lukoki, Arsene Bokulu, Christelle Bosulu, Erick Bukaka, Jonas Nagahuedi, Jean Claude Palata, Emery Metelo","doi":"10.46471/gigabyte.96","DOIUrl":"https://doi.org/10.46471/gigabyte.96","url":null,"abstract":"Arbovirus epidemics (chikungunya, dengue, West Nile fever, yellow fever and zika) are a growing threat in African areas where Aedes (Stegomyia) aegypti (Linnaeus, 1762) and Aedes albopictus (Skuse, 1895) are present. The lack of comprehensive sampling of these two vectors limits our understanding of their propagation dynamics in areas at risk of arboviruses. Here, we collected 6,943 observations (both larval and human capture) of Ae. aegypti and Ae. albopictus between 2020 and 2022. The study was carried out in the Vallee de la Funa, a post-epidemic zone in the city of Kinshasa, Democratic Republic of Congo. Our results provide important information for future basic and advanced studies on the ecology and phenology of these vectors, as well as on vector dynamics after a post-epidemic period. The data from this study are published in the public domain as the Darwin Core Archive in the Global Biodiversity Information Facility.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"8 14","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135391259","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

Genome assembly and annotation of the Brown-Spotted Pit viper Protobothrops mucrosquamatus 棕斑蝮蛇(Protobothrops mucrosquamatus)基因组组装与注释

GigaByte (Hong Kong, China) Pub Date : 2023-11-07 DOI: 10.46471/gigabyte.97

Xiaotong Niu, Haorong Lu, Minhui Shi, Shiqing Wang, Yajie Zhou, Huan Liu

引用次数: 0

Spatial patterns associated with the distribution of immature stages of Aedes aegypti in three dengue high-risk municipalities of Southwestern Colombia. 哥伦比亚西南部三个登革热高危城市埃及伊蚊未成熟期分布的空间格局。

GigaByte (Hong Kong, China) Pub Date : 2023-10-27 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.95

Cristina Sánchez Gutierrez, Erika Santamaría, Carlos Andrés Morales, María Camila Lesmes, Horacio Cadena, Alvaro Avila-Diaz, Patricia Fuya, Catalina Marceló-Díaz

{"title":"Spatial patterns associated with the distribution of immature stages of Aedes aegypti in three dengue high-risk municipalities of Southwestern Colombia.","authors":"Cristina Sánchez Gutierrez, Erika Santamaría, Carlos Andrés Morales, María Camila Lesmes, Horacio Cadena, Alvaro Avila-Diaz, Patricia Fuya, Catalina Marceló-Díaz","doi":"10.46471/gigabyte.95","DOIUrl":"10.46471/gigabyte.95","url":null,"abstract":"Aedes aegypti mosquitoes are the main vector of human arbovirosis in tropical and subtropical areas. Their adaptation to urban and rural environments generates infestations inside households. Therefore, entomological surveillance associated with spatio-temporal analysis is an innovative approach for vector control and dengue management. Here, our main aim was to inspect immature pupal stages in households belonging to municipalities at high risk of dengue in Cauca, Colombia, by implementing entomological indices and relating how they influence adult mosquitos' density. We provide novel data for the geographical distribution of 3,806 immature pupal stages of Ae. aegypti. We also report entomological indices and spatial characterization. Our results suggest that, for Ae. aegypti species, pupal productivity generates high densities of adult mosquitos in neighbouring households, evidencing seasonal behaviour. Our dataset is essential as it provides an innovative strategy for mitigating vector-borne diseases using vector spatial patterns. It also delineates the association between these vector spatial patterns, entomological indicators, and breeding sites in high-risk neighbourhoods.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte95"},"PeriodicalIF":0.0,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10620433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71489644","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

Genome assembly of the bearded iris, Iris pallida Lam. 苍白鸢尾的基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2023-10-05 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.94

Robert E Bruccoleri, Edward J Oakeley, Ann Marie E Faust, Marc Altorfer, Sophie Dessus-Babus, David Burckhardt, Mevion Oertli, Ulrike Naumann, Frank Petersen, Joanne Wong

{"title":"Genome assembly of the bearded iris, Iris pallida Lam.","authors":"Robert E Bruccoleri, Edward J Oakeley, Ann Marie E Faust, Marc Altorfer, Sophie Dessus-Babus, David Burckhardt, Mevion Oertli, Ulrike Naumann, Frank Petersen, Joanne Wong","doi":"10.46471/gigabyte.94","DOIUrl":"10.46471/gigabyte.94","url":null,"abstract":"Irises are perennial plants, representing a large genus with hundreds of species. While cultivated extensively for their ornamental value, commercial interest in irises lies in the secondary metabolites present in their rhizomes. The Dalmatian Iris (Iris pallida Lam.) is an ornamental plant that also produces secondary metabolites with potential value to the fragrance and pharmaceutical industries. In addition to providing base notes for the fragrance industry, iris tissues and extracts possess antioxidant, anti-inflammatory and immunomodulatory effects. However, study of these secondary metabolites has been hampered by a lack of genomic information, requiring difficult extraction and analysis techniques. Here, we report the genome sequence of Iris pallida Lam., generated with Pacific Bioscience long-read sequencing, resulting in a 10.04-Gbp assembly with a scaffold N50 of 14.34 Mbp and 91.8% complete BUSCOs. This reference genome will allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte94"},"PeriodicalIF":0.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41222110","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

The genome assembly and annotation of the Oriental rat snake Ptyas mucosa. 东方大鼠蛇Ptyas粘膜的基因组组装与注释。

GigaByte (Hong Kong, China) Pub Date : 2023-09-20 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.92

Jiangang Wang, Shiqing Wang, Song Huang, Qing Wang, Tianming Lan, Ming Jiang, Haitao Wu, Yuxiang Yuan

引用次数: 0