Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21224.1
Denise C. Wawman
We present a genome assembly from an individual male Pasiphila rectangulata (the Green Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 582.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.74 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,153 protein coding genes.
{"title":"The genome sequence of the Green Pug moth, Pasiphila rectangulata (Linnaeus, 1758)","authors":"Denise C. Wawman","doi":"10.12688/wellcomeopenres.21224.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21224.1","url":null,"abstract":"We present a genome assembly from an individual male Pasiphila rectangulata (the Green Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 582.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.74 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,153 protein coding genes.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"62 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140972090","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}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21585.1
R. Mitchell, Duncan Sivell, G. Broad
We present a genome assembly from an individual male Amblyjoppa fuscipennis (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 278.5 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 35.62 kilobases in length.
{"title":"The genome sequence of an ichneumonid wasp, Amblyjoppa fuscipennis (Wesmael, 1844)","authors":"R. Mitchell, Duncan Sivell, G. Broad","doi":"10.12688/wellcomeopenres.21585.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21585.1","url":null,"abstract":"We present a genome assembly from an individual male Amblyjoppa fuscipennis (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 278.5 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 35.62 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"44 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140974310","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}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21623.1
Inez Januszczak, David C. Lees
We present a genome assembly from an individual male Xanthia icteritia (the Sallow moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 664.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,792 protein coding genes.
{"title":"The genome sequence of the Sallow moth, Xanthia icteritia (Hufnagel, 1766)","authors":"Inez Januszczak, David C. Lees","doi":"10.12688/wellcomeopenres.21623.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21623.1","url":null,"abstract":"We present a genome assembly from an individual male Xanthia icteritia (the Sallow moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 664.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,792 protein coding genes.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"56 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140973229","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}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21586.1
Simon H. Martin, K. Lohse, Sam Ebdon, A. Mackintosh
We present a genome assembly from an individual male Boloria euphrosyne (the Pearl-bordered Fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 400.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.17 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,138 protein coding genes.
{"title":"The genome sequence of the Pearl-bordered Fritillary, Boloria euphrosyne (Linnaeus, 1758)","authors":"Simon H. Martin, K. Lohse, Sam Ebdon, A. Mackintosh","doi":"10.12688/wellcomeopenres.21586.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21586.1","url":null,"abstract":"We present a genome assembly from an individual male Boloria euphrosyne (the Pearl-bordered Fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 400.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.17 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,138 protein coding genes.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"56 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140974515","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}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21626.1
G. Broad, C. Fletcher, Inez Januszczak
We present a genome assembly from an individual female Diplazon laetatorius (ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 251.0 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 29.27 kilobases in length.
{"title":"The genome sequence of an ichneumonid wasp, Diplazon laetatorius (Fabricius, 1781)","authors":"G. Broad, C. Fletcher, Inez Januszczak","doi":"10.12688/wellcomeopenres.21626.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21626.1","url":null,"abstract":"We present a genome assembly from an individual female Diplazon laetatorius (ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 251.0 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 29.27 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"50 25","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140975367","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}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21552.1
Sahr Mian, M. Christenhusz, I. Leitch, Andrew R Leitch
We present a genome assembly from an individual Salicornia ramosissima (purple glasswort; Tracheophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence is 529.1 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 328.55 kilobases and 153.3 kilobases in length, respectively.
{"title":"The genome sequence of purple glasswort, Salicornia ramosissima Woods (Amaranthaceae)","authors":"Sahr Mian, M. Christenhusz, I. Leitch, Andrew R Leitch","doi":"10.12688/wellcomeopenres.21552.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21552.1","url":null,"abstract":"We present a genome assembly from an individual Salicornia ramosissima (purple glasswort; Tracheophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence is 529.1 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 328.55 kilobases and 153.3 kilobases in length, respectively.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"130 31","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140976899","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}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21567.1
D. Boyes, G. Broad, P. Holland
We present a genome assembly from an individual male Nycteola revayana (the Oak Nycteoline moth; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 621.0 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,235 protein-coding genes.
{"title":"The genome sequence of the Oak Nycteoline moth, Nycteola revayana (Scopoli, 1772)","authors":"D. Boyes, G. Broad, P. Holland","doi":"10.12688/wellcomeopenres.21567.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21567.1","url":null,"abstract":"We present a genome assembly from an individual male Nycteola revayana (the Oak Nycteoline moth; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 621.0 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,235 protein-coding genes.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"13 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140974278","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}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21568.1
D. Boyes, Liam M. Crowley, Lucy M. Morley
We present a genome assembly from a female Tortrix viridana (the Green Oak Leaf Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 456.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length.
我们展示了雌性卷叶蛾（Tortrix viridana，绿橡树卷叶蛾；节肢动物门；昆虫纲；鳞翅目；卷蛾科）的基因组序列。基因组序列跨度为 456.6 兆字节。大部分基因组组装成 31 个染色体假分子支架，包括 Z 和 W 性染色体。线粒体基因组也已组装完成，长度为 16.43 千碱基。
{"title":"The genome sequence of the Green Oak Leaf Roller, Tortrix viridana (Linnaeus, 1758)","authors":"D. Boyes, Liam M. Crowley, Lucy M. Morley","doi":"10.12688/wellcomeopenres.21568.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21568.1","url":null,"abstract":"We present a genome assembly from a female Tortrix viridana (the Green Oak Leaf Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 456.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140976234","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}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21571.1
David C. Lees
We present a genome assembly from an individual male Udea ferrugalis (the Rusty-dot Pearl moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 495.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,035 protein coding genes.
{"title":"The genome sequence of the Rusty-dot Pearl moth, Udea ferrugalis (Hübner, 1796)","authors":"David C. Lees","doi":"10.12688/wellcomeopenres.21571.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21571.1","url":null,"abstract":"We present a genome assembly from an individual male Udea ferrugalis (the Rusty-dot Pearl moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 495.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,035 protein coding genes.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"15 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140974921","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}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.20998.1
Sanjay C. Nagi, Faisal Ashraf, Alistair Miles, M. J. Donnelly
The major malaria mosquitoes, Anopheles gambiae s.l and Anopheles funestus, are some of the most studied organisms in medical research and also some of the most genetically diverse. When designing polymerase chain reaction (PCR) or hybridisation-based molecular assays, reliable primer and probe design is crucial. However, single nucleotide polymorphisms (SNPs) in primer binding sites can prevent primer binding, leading to null alleles, or bind suboptimally, leading to preferential amplification of specific alleles. Given the extreme genetic diversity of Anopheles mosquitoes, researchers need to consider this genetic variation when designing primers and probes to avoid amplification problems. In this note, we present a Python package, AnoPrimer, which exploits the Ag1000G and Af1000 datasets and allows users to rapidly design primers in An. gambiae or An. funestus, whilst summarising genetic variation in the primer binding sites and visualising the position of primer pairs. AnoPrimer allows the design of both genomic DNA and cDNA primers and hybridisation probes. By coupling this Python package with Google Colaboratory, AnoPrimer is an open and accessible platform for primer and probe design, hosted in the cloud for free. AnoPrimer is available here https://github.com/sanjaynagi/AnoPrimer and we hope it will be a useful resource for the community to design probe and primer sets that can be reliably deployed across the An. gambiae and funestus species ranges.
{"title":"AnoPrimer: Primer Design in malaria vectors informed by range-wide genomic variation","authors":"Sanjay C. Nagi, Faisal Ashraf, Alistair Miles, M. J. Donnelly","doi":"10.12688/wellcomeopenres.20998.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.20998.1","url":null,"abstract":"The major malaria mosquitoes, Anopheles gambiae s.l and Anopheles funestus, are some of the most studied organisms in medical research and also some of the most genetically diverse. When designing polymerase chain reaction (PCR) or hybridisation-based molecular assays, reliable primer and probe design is crucial. However, single nucleotide polymorphisms (SNPs) in primer binding sites can prevent primer binding, leading to null alleles, or bind suboptimally, leading to preferential amplification of specific alleles. Given the extreme genetic diversity of Anopheles mosquitoes, researchers need to consider this genetic variation when designing primers and probes to avoid amplification problems. In this note, we present a Python package, AnoPrimer, which exploits the Ag1000G and Af1000 datasets and allows users to rapidly design primers in An. gambiae or An. funestus, whilst summarising genetic variation in the primer binding sites and visualising the position of primer pairs. AnoPrimer allows the design of both genomic DNA and cDNA primers and hybridisation probes. By coupling this Python package with Google Colaboratory, AnoPrimer is an open and accessible platform for primer and probe design, hosted in the cloud for free. AnoPrimer is available here https://github.com/sanjaynagi/AnoPrimer and we hope it will be a useful resource for the community to design probe and primer sets that can be reliably deployed across the An. gambiae and funestus species ranges.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"8 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140971904","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}
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