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The genome of the mustard hill coral, Porites astreoides. 芥子山珊瑚(Porites astreoides)的基因组。
GigaByte (Hong Kong, China) Pub Date : 2022-07-29 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.65
Kevin H Wong, Hollie M Putnam
{"title":"The genome of the mustard hill coral, <i>Porites astreoides</i>.","authors":"Kevin H Wong, Hollie M Putnam","doi":"10.46471/gigabyte.65","DOIUrl":"10.46471/gigabyte.65","url":null,"abstract":"<p><p>Anthropogenic effects have contributed to substantial declines in coral reefs worldwide. However, some corals are more resilient to environmental changes and have increased in relative abundance, thus these species may shape future reef communities. Here, we provide the first draft reference genome for the mustard hill coral, <i>Porites astreoides</i>, collected in Bermuda. DNA was sequenced via Pacific Biosciences (PacBio) HiFi long-read technology. PacBio read assembly with FALCON UnZip resulted in a 678-Mbp assembly with 3051 contigs with an N50 of 412,256 and the BUSCO completeness analysis resulted in 90.9% of the metazoan gene set. An <i>ab initio</i> transcriptome was also produced with 64,636 gene models with a transcriptome BUSCO completeness analysis of 77.5% versus the metazoan gene set. Functional annotation was completed for 86.6% of proteins. These data are valuable resources for improving biological knowledge of <i>P. astreoides</i>, facilitating comparative genomics for corals, and supporting evidence-based restoration and human-assisted evolution of corals.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte65"},"PeriodicalIF":0.0,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9693771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10773250","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
Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes. 长读数 HiFi 测序正确组装出新飞蛾和笛蝇基因组中的重复重纤维蛋白丝基因。
GigaByte (Hong Kong, China) Pub Date : 2022-06-30 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.64
Akito Y Kawahara, Caroline G Storer, Amanda Markee, Jacqueline Heckenhauer, Ashlyn Powell, David Plotkin, Scott Hotaling, Timothy P Cleland, Rebecca B Dikow, Torsten Dikow, Ryoichi B Kuranishi, Rebeccah Messcher, Steffen U Pauls, Russell J Stewart, Koji Tojo, Paul B Frandsen
{"title":"Long-read HiFi sequencing correctly assembles repetitive <i>heavy fibroin</i> silk genes in new moth and caddisfly genomes.","authors":"Akito Y Kawahara, Caroline G Storer, Amanda Markee, Jacqueline Heckenhauer, Ashlyn Powell, David Plotkin, Scott Hotaling, Timothy P Cleland, Rebecca B Dikow, Torsten Dikow, Ryoichi B Kuranishi, Rebeccah Messcher, Steffen U Pauls, Russell J Stewart, Koji Tojo, Paul B Frandsen","doi":"10.46471/gigabyte.64","DOIUrl":"10.46471/gigabyte.64","url":null,"abstract":"<p><p>Insect silk is a versatile biomaterial. Lepidoptera and Trichoptera display some of the most diverse uses of silk, with varying strength, adhesive qualities, and elastic properties. Silk fibroin genes are long (>20 Kbp), with many repetitive motifs that make them challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (<i>Plodia interpunctella</i>) and genomic sequences for the caddisfly <i>Eubasilissa regina</i>. Both genomes were highly contiguous (N50  = 9.7 Mbp/32.4 Mbp, L50  = 13/11) and complete (BUSCO complete  = 99.3%/95.2%), with complete and contiguous recovery of silk <i>heavy fibroin</i> gene sequences. We show that HiFi long-read sequencing is helpful for understanding genes with long, repetitive regions.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte64"},"PeriodicalIF":0.0,"publicationDate":"2022-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9693786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9336291","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 chromosome-level genome assembly and annotation of the maize elite breeding line Dan340. 玉米优良育种品系 Dan340 的染色体级基因组组装和注释。
GigaByte (Hong Kong, China) Pub Date : 2022-06-14 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.63
Yikun Zhao, Yuancong Wang, De Ma, Guang Feng, Yongxue Huo, Zhihao Liu, Ling Zhou, Yunlong Zhang, Liwen Xu, Liang Wang, Han Zhao, Jiuran Zhao, Fengge Wang
{"title":"A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340.","authors":"Yikun Zhao, Yuancong Wang, De Ma, Guang Feng, Yongxue Huo, Zhihao Liu, Ling Zhou, Yunlong Zhang, Liwen Xu, Liang Wang, Han Zhao, Jiuran Zhao, Fengge Wang","doi":"10.46471/gigabyte.63","DOIUrl":"10.46471/gigabyte.63","url":null,"abstract":"<p><strong>Background: </strong>Maize is an important model organism for genetics and genomics research. Though reference genomes of maize are available, some genomes of important genetic germplasms for maize breeding are still lacking, for instance, the cultivar Dan340, which is a backbone inbred line of the LvDa Red Cob Group with several desirable characteristics. In this study, we constructed a high-quality chromosome-level reference genome for Dan340 by using long HiFi reads, short reads, and Hi-C. The final assembly of the Dan340 genome was 2348.72 Mb, which was anchored to 10 chromosomes. Repeat sequences accounted for 73.40% of the genome and 39,733 protein-coding genes were annotated. Comparative genomic analysis between Dan340 and other maize lines identified that 1806 genes from 359 gene families were specific to Dan340.</p><p><strong>Conclusions: </strong>Our genome assembly and annotation provide a valuable resource for improving maize breeding and further understanding the intraspecific genome diversity in maize.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte63"},"PeriodicalIF":0.0,"publicationDate":"2022-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9694154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9336292","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
Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes 长读HiFi测序正确组装重复重丝素基因在新的飞蛾和球蛾基因组
GigaByte (Hong Kong, China) Pub Date : 2022-06-03 DOI: 10.1101/2022.06.01.494423
A. Kawahara, Caroline G. Storer, A. Markee, J. Heckenhauer, A. Powell, David M. Plotkin, S. Hotaling, T. Cleland, Rebecca B. Dikow, Torsten Dikow, Ryoichi B. Kuranishi, Rebeccah L. Messcher, S. Pauls, R. Stewart, K. Tojo, P. Frandsen
{"title":"Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes","authors":"A. Kawahara, Caroline G. Storer, A. Markee, J. Heckenhauer, A. Powell, David M. Plotkin, S. Hotaling, T. Cleland, Rebecca B. Dikow, Torsten Dikow, Ryoichi B. Kuranishi, Rebeccah L. Messcher, S. Pauls, R. Stewart, K. Tojo, P. Frandsen","doi":"10.1101/2022.06.01.494423","DOIUrl":"https://doi.org/10.1101/2022.06.01.494423","url":null,"abstract":"Insect silk is an incredibly versatile biomaterial. Lepidoptera and their sister lineage, Trichoptera, display some of the most diverse uses of silk with varying strength, adhesive qualities and elastic properties. It is well known that silk fibroin genes are long (> 20 kb) and have many repetitive motifs. These features make these genes challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (Plodia interpunctella) and genomic sequences for the caddisfly, Eubasilissa regina. Both genomes were highly contiguous (N50 = 9.7 Mbp/32.4 Mbp, L50 = 13/11) and complete (BUSCO Complete = 99.3%/95.2%), with complete and contiguous recovery of silk heavy fibroin gene sequences. This study demonstrates that HiFi long-read sequencing can significantly help our understanding of genes with highly contiguous, repetitive regions.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47676720","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: 11
AIMSurv: First pan-European harmonized surveillance of Aedes invasive mosquito species of relevance for human vector-borne diseases. AIMSurv:首次对与人类病媒传播疾病有关的伊蚊入侵物种进行泛欧统一监测。
GigaByte (Hong Kong, China) Pub Date : 2022-05-31 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.57
Miguel Ángel Miranda, Carlos Barceló, Daniele Arnoldi, Xenia Augsten, Karin Bakran-Lebl, George Balatsos, Mikel Bengoa, Philippe Bindler, Kristina Boršová, Maria Bourquia, Daniel Bravo-Barriga, Viktória Čabanová, Beniamino Caputo, Maria Christou, Sarah Delacour, Roger Eritja, Ouafaa Fassi-Fihri, Martina Ferraguti, Eleonora Flacio, Eva Frontera, Hans-Peter Fuehrer, Ana L García-Pérez, Pantelis Georgiades, Sandra Gewehr, Fátima Goiri, Mikel Alexander González, Martin Gschwind, Rafael Gutiérrez-López, Cintia Horváth, Adolfo Ibáñez-Justicia, Viola Jani, Përparim Kadriaj, Katja Kalan, Mihaela Kavran, Ana Klobucar, Kornélia Kurucz, Javier Lucientes, Renke Lühken, Sergio Magallanes, Giovanni Marini, Angeliki F Martinou, Alice Michelutti, Andrei Daniel Mihalca, Tomás Montalvo, Fabrizio Montarsi, Spiros Mourelatos, Nesade Muja-Bajraktari, Pie Müller, Gregoris Notarides, Hugo Costa Osório, José A Oteo, Kerem Oter, Igor Pajović, John R B Palmer, Suncica Petrinic, Cristian Răileanu, Christian Ries, Elton Rogozi, Ignacio Ruiz-Arrondo, Isis Sanpera-Calbet, Nebojša Sekulić, Kivanc Sevim, Kurtesh Sherifi, Cornelia Silaghi, Manuel Silva, Nikolina Sokolovska, Zoltán Soltész, Tatiana Sulesco, Jana Šušnjar, Steffanie Teekema, Andrea Valsecchi, Marlen Ines Vasquez, Enkelejda Velo, Antonios Michaelakis, William Wint, Dušan Petrić, Francis Schaffner, Alessandra Della Torre
{"title":"AIMSurv: First pan-European harmonized surveillance of <i>Aedes</i> invasive mosquito species of relevance for human vector-borne diseases.","authors":"Miguel Ángel Miranda, Carlos Barceló, Daniele Arnoldi, Xenia Augsten, Karin Bakran-Lebl, George Balatsos, Mikel Bengoa, Philippe Bindler, Kristina Boršová, Maria Bourquia, Daniel Bravo-Barriga, Viktória Čabanová, Beniamino Caputo, Maria Christou, Sarah Delacour, Roger Eritja, Ouafaa Fassi-Fihri, Martina Ferraguti, Eleonora Flacio, Eva Frontera, Hans-Peter Fuehrer, Ana L García-Pérez, Pantelis Georgiades, Sandra Gewehr, Fátima Goiri, Mikel Alexander González, Martin Gschwind, Rafael Gutiérrez-López, Cintia Horváth, Adolfo Ibáñez-Justicia, Viola Jani, Përparim Kadriaj, Katja Kalan, Mihaela Kavran, Ana Klobucar, Kornélia Kurucz, Javier Lucientes, Renke Lühken, Sergio Magallanes, Giovanni Marini, Angeliki F Martinou, Alice Michelutti, Andrei Daniel Mihalca, Tomás Montalvo, Fabrizio Montarsi, Spiros Mourelatos, Nesade Muja-Bajraktari, Pie Müller, Gregoris Notarides, Hugo Costa Osório, José A Oteo, Kerem Oter, Igor Pajović, John R B Palmer, Suncica Petrinic, Cristian Răileanu, Christian Ries, Elton Rogozi, Ignacio Ruiz-Arrondo, Isis Sanpera-Calbet, Nebojša Sekulić, Kivanc Sevim, Kurtesh Sherifi, Cornelia Silaghi, Manuel Silva, Nikolina Sokolovska, Zoltán Soltész, Tatiana Sulesco, Jana Šušnjar, Steffanie Teekema, Andrea Valsecchi, Marlen Ines Vasquez, Enkelejda Velo, Antonios Michaelakis, William Wint, Dušan Petrić, Francis Schaffner, Alessandra Della Torre","doi":"10.46471/gigabyte.57","DOIUrl":"10.46471/gigabyte.57","url":null,"abstract":"<p><p>Human and animal vector-borne diseases, particularly mosquito-borne diseases, are emerging or re-emerging worldwide. Six <i>Aedes</i> invasive mosquito (AIM) species were introduced to Europe since the 1970s: <i>Aedes aegypti</i>, <i>Ae. albopictus</i>, <i>Ae. japonicus</i>, <i>Ae. koreicus</i>, <i>Ae. atropalpus</i> and <i>Ae. triseriatus</i>. Here, we report the results of AIMSurv2020, the first pan-European surveillance effort for AIMs. Implemented by 42 volunteer teams from 24 countries. And presented in the form of a dataset named \"AIMSurv Aedes Invasive Mosquito species harmonized surveillance in Europe. AIM-COST Action. Project ID: CA17108\". AIMSurv2020 harmonizes field surveillance methodologies for sampling different AIMs life stages, frequency and minimum length of sampling period, and data reporting. Data include minimum requirements for sample types and recommended requirements for those teams with more resources. Data are published as a Darwin Core archive in the Global Biodiversity Information Facility- Spain, comprising a core file with 19,130 records (EventID) and an occurrences file with 19,743 records (OccurrenceID). AIM species recorded in AIMSurv2020 were <i>Ae. albopictus</i>, <i>Ae. japonicus</i> and <i>Ae. koreicus</i>, as well as native mosquito species.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte57"},"PeriodicalIF":0.0,"publicationDate":"2022-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9321529","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
Mosquito alert: leveraging citizen science to create a GBIF mosquito occurrence dataset. 蚊子警报:利用公民科学创建 GBIF 蚊子发生数据集。
GigaByte (Hong Kong, China) Pub Date : 2022-05-30 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.54
Živko Južnič-Zonta, Isis Sanpera-Calbet, Roger Eritja, John R B Palmer, Agustí Escobar, Joan Garriga, Aitana Oltra, Alex Richter-Boix, Francis Schaffner, Alessandra Della Torre, Miguel Ángel Miranda, Marion Koopmans, Luisa Barzon, Frederic Bartumeus Ferre
{"title":"Mosquito alert: leveraging citizen science to create a GBIF mosquito occurrence dataset.","authors":"Živko Južnič-Zonta, Isis Sanpera-Calbet, Roger Eritja, John R B Palmer, Agustí Escobar, Joan Garriga, Aitana Oltra, Alex Richter-Boix, Francis Schaffner, Alessandra Della Torre, Miguel Ángel Miranda, Marion Koopmans, Luisa Barzon, Frederic Bartumeus Ferre","doi":"10.46471/gigabyte.54","DOIUrl":"10.46471/gigabyte.54","url":null,"abstract":"<p><p>The Mosquito Alert dataset includes occurrence records of adult mosquitoes collected worldwide in 2014-2020 through Mosquito Alert, a citizen science system for investigating and managing disease-carrying mosquitoes. Records are linked to citizen science-submitted photographs and validated by entomologists to determine the presence of five targeted European mosquito vectors: <i>Aedes albopictus</i>, <i>Ae. aegypti</i>, <i>Ae. japonicus</i>, <i>Ae. koreicus</i>, and <i>Culex pipiens</i>. Most records are from Spain, reflecting Spanish national and regional funding, but since autumn 2020 substantial records from other European countries are included, thanks to volunteer entomologists coordinated by the AIM-COST Action, and to technological developments to increase scalability. Among other applications, the Mosquito Alert dataset will help develop citizen science-based early warning systems for mosquito-borne disease risk. It can also be reused for modelling vector exposure risk, or to train machine-learning detection and classification routines on the linked images, to assist with data validation and establishing automated alert systems.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte54"},"PeriodicalIF":0.0,"publicationDate":"2022-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10773249","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
Sand fly (Diptera: Psychodidae: Phlebotominae) records in Acre, Brazil: a dataset. 巴西阿克里的沙蝇(双翅目:食蚜蝇科:食蚜蝇属)记录:数据集。
GigaByte (Hong Kong, China) Pub Date : 2022-05-27 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.60
Rodrigo Espindola Godoy, Andrey José de Andrade, Paloma Helena Fernandes Shimabukuro, Andreia Fernandes Brilhante
{"title":"Sand fly (Diptera: Psychodidae: Phlebotominae) records in Acre, Brazil: a dataset.","authors":"Rodrigo Espindola Godoy, Andrey José de Andrade, Paloma Helena Fernandes Shimabukuro, Andreia Fernandes Brilhante","doi":"10.46471/gigabyte.60","DOIUrl":"10.46471/gigabyte.60","url":null,"abstract":"<p><p>Amazonian phlebotomine sand fly fauna is one of the most diverse in the world. The Amazon region is also the most prevalent for leishmaniasis in Brazil and South America. The state of Acre, in this region, also stands out in terms of the diversity of sand fly fauna, as well as the occurrence of American tegumentary leishmaniasis. In this context, the present dataset comprises a bibliographic review of sand fly species recorded in Acre state, Brazil. A total of 1,094 observations from material citations and two of preserved specimens are presented using 33 variables according to Darwin Core terms. The bibliographic review was performed in PubMed, Google Scholar, SciELO, Biblioteca Virtual em Saúde, and references cited in related scientific articles. Thus, this report will be valuable for further studies on sand flies in Acre and other Amazon states.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte60"},"PeriodicalIF":0.0,"publicationDate":"2022-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10831319","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
MEMO: Monitoring of exotic mosquitoes in Belgium. 备忘录:监测比利时的外来蚊子。
GigaByte (Hong Kong, China) Pub Date : 2022-05-26 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.59
Isra Deblauwe, Dimitri Brosens, Katrien De Wolf, Nathalie Smitz, Adwine Vanslembrouck, Anna Schneider, Jacobus De Witte, Ingrid Verlé, Wouter Dekoninck, Marc De Meyer, Thierry Backeljau, Sophie Gombeer, Kenny Meganck, Ann Vanderheyden, Ruth Müller, Wim Van Bortel
{"title":"MEMO: Monitoring of exotic mosquitoes in Belgium.","authors":"Isra Deblauwe, Dimitri Brosens, Katrien De Wolf, Nathalie Smitz, Adwine Vanslembrouck, Anna Schneider, Jacobus De Witte, Ingrid Verlé, Wouter Dekoninck, Marc De Meyer, Thierry Backeljau, Sophie Gombeer, Kenny Meganck, Ann Vanderheyden, Ruth Müller, Wim Van Bortel","doi":"10.46471/gigabyte.59","DOIUrl":"10.46471/gigabyte.59","url":null,"abstract":"<p><strong>'memo: </strong>Monitoring of Exotic MOsquitoes in Belgium' is a sampling event dataset published by the Institute of Tropical Medicine (ITM) in Antwerp, Belgium. It forms part of the early detection of exotic mosquito species (EMS) along high-risk introduction routes in Belgium, where data are collected at defined points of entry (PoEs) using a standardised protocol. The MEMO dataset contains mosquito sampling counts performed between 2017 and 2020. MEMO+2020, an extension of the MEMO dataset, contains only <i>Aedes albopictus</i> mosquito trap counts performed in 2020. Here, we present these data published as a standardised Darwin Core archive, which includes, for each sampling event, an eventID, date, location and sampling protocol (in the event core); and an occurrenceID for each occurrence (tube), the number of collected individuals per tube, species status (present/absent), information on the identification and scientific name (in the occurrence extension).</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte59"},"PeriodicalIF":0.0,"publicationDate":"2022-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10773248","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 chromosome-level genome assembly and annotation of a maize elite breeding line Dan340 玉米优良选育系Dan340染色体水平基因组的组装与注释
GigaByte (Hong Kong, China) Pub Date : 2022-05-20 DOI: 10.1101/2021.04.26.441299
Yikun Zhao, Yuancong Wang, De Ma, Guang Feng, Yongxue Huo, Zhihao Liu, Ling Zhou, Yunlong Zhang, Liwen Xu, Liang Wang, Han Zhao, Jiuran Zhao, Fengge Wang
{"title":"A chromosome-level genome assembly and annotation of a maize elite breeding line Dan340","authors":"Yikun Zhao, Yuancong Wang, De Ma, Guang Feng, Yongxue Huo, Zhihao Liu, Ling Zhou, Yunlong Zhang, Liwen Xu, Liang Wang, Han Zhao, Jiuran Zhao, Fengge Wang","doi":"10.1101/2021.04.26.441299","DOIUrl":"https://doi.org/10.1101/2021.04.26.441299","url":null,"abstract":"Background Maize is not only one of the most important crops grown worldwide for food, forage, and biofuel, but also an important model organism for fundamental research in genetics and genomics. Owing to its importance in crop science, genetics and genomics, several reference genomes of common maize inbred line (genetic material) have been released, but some genomes of important genetic germplasm resources in maize breeding research are still lacking. The maize cultivar Dan340 is an excellent backbone inbred line of the Luda Red Cob Group with several desirable characteristics, such as disease resistance, lodging resistance, high combining ability, and wide adaptability. Findings In this study, we constructed a high-quality chromosome-level reference genome for Dan340 by combining PacBio long HiFi sequencing reads, Illumina short reads and chromosomal conformational capture (Hi-C) sequencing reads. The final assembly of the Dan340 genome was 2,348.72 Mb, including 2,738 contigs and 2,315 scaffolds with N50 of 41.49 Mb and 215.35 Mb, respectively. Repeat sequences accounted for 73.40% of the genome size and 39,733 protein-coding genes were annotated. Analysis of genes in the Dan340 genome, together with those from B73, Mo17 and SK, were clustered into 27,654 gene families. There were 1,806 genes from 359 gene families that were specific to Dan340, of which many had functional gene ontology annotations relating to “porphyrin-containing compound metabolic process”, “tetrapyrrole biosynthetic process”, and “tetrapyrrole metabolic process”. Conclusions The completeness and continuity of the genome were comparable to those of other important maize inbred lines. The assembly and annotation of this genome not only facilitates our understanding about of intraspecific genome diversity in maize, but also provides a novel resource for maize breeding improvement. Research Areas Genetics and Genomics; Agriculture, Plant Genetics Data Description","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"62327921","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: 1
Arbovirus vectors in municipalities with a high risk of dengue in Cauca, Southwestern Colombia. 哥伦比亚西南部考卡地区登革热高风险城市中的虫媒病毒载体。
GigaByte (Hong Kong, China) Pub Date : 2022-05-16 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.53
Catalina Marceló-Díaz, Carlos Andres Morales, Maria Camila Lesmes, Patricia Fuya, Sergio Andres Mendez, Horacio Cadena, Alvaro Ávila-Díaz, Erika Santamaria
{"title":"Arbovirus vectors in municipalities with a high risk of dengue in Cauca, Southwestern Colombia.","authors":"Catalina Marceló-Díaz,&nbsp;Carlos Andres Morales,&nbsp;Maria Camila Lesmes,&nbsp;Patricia Fuya,&nbsp;Sergio Andres Mendez,&nbsp;Horacio Cadena,&nbsp;Alvaro Ávila-Díaz,&nbsp;Erika Santamaria","doi":"10.46471/gigabyte.53","DOIUrl":"10.46471/gigabyte.53","url":null,"abstract":"<p><p>The Culicidae family has two of the most important disease vector genus: <i>Aedes</i> spp. and <i>Culex</i> spp. Both of these are involved in the transmission of arboviruses. Here, we provide novel data for the geographical distribution of 2,383 specimens in the Culicidae family. We also report the percentage of houses infested with these vectors, and Shannon and Simpson diversity indices in three municipalities located in Cauca, Colombia. This dataset is relevant for research on vector-borne diseases because <i>Aedes</i> spp. can transmit arboviruses such as dengue, Zika and chikungunya, and <i>Culex</i> spp. is a well-known vector of West Nile virus and Venezuelan equine encephalitis.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte53"},"PeriodicalIF":0.0,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10774023","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: 2
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