GigaByte (Hong Kong, China)最新文献_第10页

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":"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: Aedes albopictus, Ae. aegypti, Ae. japonicus, Ae. koreicus, and Culex pipiens. 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.","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

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":"'memo: 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 Aedes albopictus 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).","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

引用次数: 2

LT1, an ONT long-read-based assembly scaffolded with Hi-C data and polished with short reads. LT1是一个基于ONT长读数的装配，使用Hi-C数据搭建脚手架，并用短读数进行打磨。

GigaByte (Hong Kong, China) Pub Date : 2022-05-04 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.51

Hui-Su Kim, Asta Blazyte, Sungwon Jeon, Changhan Yoon, Yeonkyung Kim, Changjae Kim, Dan Bolser, Ji-Hye Ahn, Jeremy S Edwards, Jong Bhak

{"title":"LT1, an ONT long-read-based assembly scaffolded with Hi-C data and polished with short reads.","authors":"Hui-Su Kim, Asta Blazyte, Sungwon Jeon, Changhan Yoon, Yeonkyung Kim, Changjae Kim, Dan Bolser, Ji-Hye Ahn, Jeremy S Edwards, Jong Bhak","doi":"10.46471/gigabyte.51","DOIUrl":"10.46471/gigabyte.51","url":null,"abstract":"We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly, constructed using 57× nanopore long reads and polished using 47× short paired-end reads. We utilized 72 GB of Hi-C chromosomal mapping data for scaffolding, to maximize assembly contiguity and accuracy. The contig assembly of LT1 was 2.73 Gbp in length, comprising 4490 contigs with an NG50 value of 12.0 Mbp. After scaffolding with Hi-C data and manual curation, the final assembly has an NG50 value of 137 Mbp and 4699 scaffolds. Assessment of gene prediction quality using Benchmarking Universal Single-Copy Orthologs (BUSCO) identified 89.3% of the single-copy orthologous genes included in the benchmark. Detailed characterization of LT1 suggests it has 73,744 predicted transcripts, 4.2 million autosomal SNPs, 974,616 short indels, and 12,079 large structural variants. These data may be used as a benchmark for further in-depth genomic analyses of Baltic populations.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte51"},"PeriodicalIF":0.0,"publicationDate":"2022-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9650228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9321530","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

1D and 2D NMR spectra of coffee from 27 countries. 27 个国家咖啡的一维和二维 NMR 光谱。

GigaByte (Hong Kong, China) Pub Date : 2022-04-21 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.50

Javier Osorio, Victoria A Arana, Jessica M Medina, Rodrigo Alarcon, Edgar Moreno, Julien Wist

引用次数: 0

Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, Diaphorina citri, reveals novel features. 对亚洲柑橘木虱 Hox 簇和 Hox 辅助因子基因的注释揭示了新的特征。

GigaByte (Hong Kong, China) Pub Date : 2022-04-08 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.49

Teresa D Shippy, Prashant S Hosmani, Mirella Flores-Gonzalez, Lukas A Mueller, Wayne B Hunter, Susan J Brown, Tom D'Elia, Surya Saha

{"title":"Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, Diaphorina citri, reveals novel features.","authors":"Teresa D Shippy, Prashant S Hosmani, Mirella Flores-Gonzalez, Lukas A Mueller, Wayne B Hunter, Susan J Brown, Tom D'Elia, Surya Saha","doi":"10.46471/gigabyte.49","DOIUrl":"10.46471/gigabyte.49","url":null,"abstract":"Hox genes and their cofactors are essential developmental genes specifying regional identity in animals. Hox genes have a conserved arrangement in clusters in the same order in which they specify identity along the anterior-posterior axis. A few insect species have breaks in the cluster, but these are exceptions. We annotated the 10 Hox genes of the Asian citrus psyllid Diaphorina citri, and found a split in its Hox cluster between the Deformed and Sex combs reduced genes - the first time a break at this position has been observed in an insect Hox cluster. We also annotated D. citri orthologs of the Hox cofactor genes homothorax, PKNOX and extradenticle and found an additional copy of extradenticle in D. citri that appears to be a retrogene. Expression data and sequence conservation suggest that the extradenticle retrogene may have retained the original extradenticle function and allowed divergence of the parental extradenticle gene.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte49"},"PeriodicalIF":0.0,"publicationDate":"2022-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9933525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9321525","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

Annotation of putative circadian rhythm-associated genes in Diaphorina citri (Hemiptera: Liviidae). Diaphorina citri（半翅目：Liviidae）昼夜节律相关基因的标注。

GigaByte (Hong Kong, China) Pub Date : 2022-04-01 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.48

Max Reynolds, Lucas de Oliveira, Chad Vosburg, Thomson Paris, Crissy Massimino, Jordan Norus, Yasmin Ortiz, Michelle Espino, Nina Davis, Ron Masse, Alan Neiman, Rachel Holcomb, Kylie Gervais, Melissa Kemp, Maria Hoang, Teresa D Shippy, Prashant S Hosmani, Mirella Flores-Gonzalez, Kirsten Pelz-Stelinski, Jawwad A Qureshi, Lukas A Mueller, Wayne B Hunter, Joshua B Benoit, Susan J Brown, Tom D'Elia, Surya Saha

{"title":"Annotation of putative circadian rhythm-associated genes in Diaphorina citri (Hemiptera: Liviidae).","authors":"Max Reynolds, Lucas de Oliveira, Chad Vosburg, Thomson Paris, Crissy Massimino, Jordan Norus, Yasmin Ortiz, Michelle Espino, Nina Davis, Ron Masse, Alan Neiman, Rachel Holcomb, Kylie Gervais, Melissa Kemp, Maria Hoang, Teresa D Shippy, Prashant S Hosmani, Mirella Flores-Gonzalez, Kirsten Pelz-Stelinski, Jawwad A Qureshi, Lukas A Mueller, Wayne B Hunter, Joshua B Benoit, Susan J Brown, Tom D'Elia, Surya Saha","doi":"10.46471/gigabyte.48","DOIUrl":"10.46471/gigabyte.48","url":null,"abstract":"The circadian rhythm involves multiple genes that generate an internal molecular clock, allowing organisms to anticipate environmental conditions produced by the Earth's rotation on its axis. Here, we present the results of the manual curation of 27 genes that are associated with circadian rhythm in the genome of Diaphorina citri, the Asian citrus psyllid. This insect is the vector for the bacterial pathogen Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening disease (Huanglongbing). This disease severely affects citrus industries and has drastically decreased crop yields worldwide. Based on cry1 and cry2 identified in the psyllid genome, D. citri likely possesses a circadian model similar to the lepidopteran butterfly, Danaus plexippus. Manual annotation will improve the quality of circadian rhythm gene models, allowing the future development of molecular therapeutics, such as RNA interference or antisense technologies, to target these genes to disrupt the psyllid biology.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte48"},"PeriodicalIF":0.0,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9662589/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10778796","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

Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, Diaphorina citri. 亚洲柑橘木虱几丁质酶家族基因的手工整理和系统发育分析。

GigaByte (Hong Kong, China) Pub Date : 2022-03-17 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.46

Teresa D Shippy, Sherry Miller, Blessy Tamayo, Prashant S Hosmani, Mirella Flores-Gonzalez, Lukas A Mueller, Wayne B Hunter, Susan J Brown, Tom D'Elia, Surya Saha

{"title":"Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, Diaphorina citri.","authors":"Teresa D Shippy, Sherry Miller, Blessy Tamayo, Prashant S Hosmani, Mirella Flores-Gonzalez, Lukas A Mueller, Wayne B Hunter, Susan J Brown, Tom D'Elia, Surya Saha","doi":"10.46471/gigabyte.46","DOIUrl":"10.46471/gigabyte.46","url":null,"abstract":"Chitinases are enzymes that digest the polysaccharide polymer chitin. During insect development, breakdown of chitin is an essential step in molting of the exoskeleton. Knockdown of chitinases required for molting is lethal to insects, making chitinase genes an interesting target for RNAi-based pest control methods. The Asian citrus psyllid, Diaphorina citri, carries the bacterium causing Huanglongbing, or citrus greening disease, a devastating citrus disease. We identified and annotated 12 chitinase family genes from D. citri as part of a community effort to create high-quality gene models to aid the design of interdictory molecules for pest control. We categorized the D. citri chitinases according to an established classification scheme and re-evaluated the classification of chitinases in other hemipterans. In addition to chitinases from known groups, we identified a novel class of chitinases present in D. citri and several related hemipterans that appears to be the result of horizontal gene transfer.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte46"},"PeriodicalIF":0.0,"publicationDate":"2022-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9933517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10831318","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