Pub Date : 2024-07-22DOI: 10.12688/wellcomeopenres.22703.1
Will J. Nash, R. Mitchell
We present a genome assembly from an individual female Megamerina dolium (the Bearded Fool; Arthropoda; Insecta; Diptera; Megamerinidae). The genome sequence is 500.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.67 kilobases in length.
{"title":"The genome sequence of the Bearded Fool fly, Megamerina dolium (Fabricus, 1805)","authors":"Will J. Nash, R. Mitchell","doi":"10.12688/wellcomeopenres.22703.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22703.1","url":null,"abstract":"We present a genome assembly from an individual female Megamerina dolium (the Bearded Fool; Arthropoda; Insecta; Diptera; Megamerinidae). The genome sequence is 500.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.67 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"80 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141817772","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 : 2024-07-22DOI: 10.12688/wellcomeopenres.22693.1
Olga Sivell, R. Mitchell, Judy Webb, Gavin R. Broad
We present a genome assembly from an individual female Chalcis sispes (chalcid wasp; Arthropoda; Insecta; Hymenoptera; Chalcididae). The genome sequence is 412.4 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.9 kilobases in length.
{"title":"The genome sequence of the chalcid wasp, Chalcis sispes Linnaeus, 1761","authors":"Olga Sivell, R. Mitchell, Judy Webb, Gavin R. Broad","doi":"10.12688/wellcomeopenres.22693.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22693.1","url":null,"abstract":"We present a genome assembly from an individual female Chalcis sispes (chalcid wasp; Arthropoda; Insecta; Hymenoptera; Chalcididae). The genome sequence is 412.4 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.9 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"31 14","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141815550","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 : 2024-07-22DOI: 10.12688/wellcomeopenres.22744.1
Gavin R. Broad, Stephanie Holt, Laura Sivess
We present a genome assembly from an individual male Oligia fasciuncula (the Middle-barred Minor moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence spans 617.70 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,994 protein-coding genes.
{"title":"The genome sequence of the Middle-barred Minor moth, Oligia fasciuncula (Haworth, 1809)","authors":"Gavin R. Broad, Stephanie Holt, Laura Sivess","doi":"10.12688/wellcomeopenres.22744.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22744.1","url":null,"abstract":"We present a genome assembly from an individual male Oligia fasciuncula (the Middle-barred Minor moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence spans 617.70 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,994 protein-coding genes.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141815997","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 : 2024-07-22DOI: 10.12688/wellcomeopenres.22739.1
Gavin R. Broad, Ian Barnes
We present a genome assembly from an individual female Bombus muscorum (the moss carder bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence spans 317.70 megabases. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,668 protein-coding genes.
{"title":"The genome sequence of the moss carder bee, Bombus muscorum (Linnaeus, 1758)","authors":"Gavin R. Broad, Ian Barnes","doi":"10.12688/wellcomeopenres.22739.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22739.1","url":null,"abstract":"We present a genome assembly from an individual female Bombus muscorum (the moss carder bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence spans 317.70 megabases. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,668 protein-coding genes.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"83 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141817300","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 : 2024-07-22DOI: 10.12688/wellcomeopenres.22705.1
Patrick Adkins, Robert J. Mrowicki, Vengamanaidu Modepalli
We present a genome assembly from an individual Candelabrum cocksii (hydroid; Cnidaria; Hydrozoa; Anthoathecata; Candelabridae). The genome sequence is 232.9 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.55 kilobases in length.
{"title":"The genome sequence of a hydroid, Candelabrum cocksii (Cocks, 1854)","authors":"Patrick Adkins, Robert J. Mrowicki, Vengamanaidu Modepalli","doi":"10.12688/wellcomeopenres.22705.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22705.1","url":null,"abstract":"We present a genome assembly from an individual Candelabrum cocksii (hydroid; Cnidaria; Hydrozoa; Anthoathecata; Candelabridae). The genome sequence is 232.9 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.55 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"14 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141815731","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 : 2024-07-19DOI: 10.12688/wellcomeopenres.22697.1
M. Koko, Laurie Fabian, Iaroslav Popov, Ruth Y. Eberhardt, Gennadii Zakharov, Qin Qin Huang, Emma E. Wade, R. Azad, Petr Danecek, Karen Ho, Amy Hough, Wei Huang, Sarah J. Lindsay, Daniel S. Malawsky, Davide Bonfanti, D. Mason, Deborah Plowman, Michael A. Quail, Susan M. Ring, Gemma Shireby, S. Widaa, E. Fitzsimons, Vivek Iyer, D. Bann, Nicolas Timpson, John Wright, M. Hurles, Hilary C. Martin
Birth cohort studies involve repeated surveys of large numbers of individuals from birth and throughout their lives. They collect information useful for a wide range of life course research domains, and biological samples which can be used to derive data from an increasing collection of omic technologies. This rich source of longitudinal data, when combined with genomic data, offers the scientific community valuable insights ranging from population genetics to applications across the social sciences. Here we present quality-controlled whole exome sequencing data from three UK birth cohorts: the Avon Longitudinal Study of Parents and Children (8,436 children and 3,215 parents), the Millenium Cohort Study (7,667 children and 6,925 parents) and Born in Bradford (8,784 children and 2,875 parents). The overall objective of this coordinated effort is to make the resulting high-quality data widely accessible to the global research community in a timely manner. We describe how the datasets were generated and subjected to quality control at the sample, variant and genotype level. We then present some preliminary analyses to illustrate the quality of the datasets and probe potential sources of bias. We introduce measures of ultra-rare variant burden to the variables available for researchers working on these cohorts, and show that the exome-wide burden of deleterious protein-truncating variants, S het burden, is associated with educational attainment and cognitive test scores. The whole exome sequence data from these birth cohorts (CRAM & VCF files) are available through the European Genome-Phenome Archive, and here provide guidance for their use.
{"title":"Exome sequencing of UK birth cohorts","authors":"M. Koko, Laurie Fabian, Iaroslav Popov, Ruth Y. Eberhardt, Gennadii Zakharov, Qin Qin Huang, Emma E. Wade, R. Azad, Petr Danecek, Karen Ho, Amy Hough, Wei Huang, Sarah J. Lindsay, Daniel S. Malawsky, Davide Bonfanti, D. Mason, Deborah Plowman, Michael A. Quail, Susan M. Ring, Gemma Shireby, S. Widaa, E. Fitzsimons, Vivek Iyer, D. Bann, Nicolas Timpson, John Wright, M. Hurles, Hilary C. Martin","doi":"10.12688/wellcomeopenres.22697.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22697.1","url":null,"abstract":"Birth cohort studies involve repeated surveys of large numbers of individuals from birth and throughout their lives. They collect information useful for a wide range of life course research domains, and biological samples which can be used to derive data from an increasing collection of omic technologies. This rich source of longitudinal data, when combined with genomic data, offers the scientific community valuable insights ranging from population genetics to applications across the social sciences. Here we present quality-controlled whole exome sequencing data from three UK birth cohorts: the Avon Longitudinal Study of Parents and Children (8,436 children and 3,215 parents), the Millenium Cohort Study (7,667 children and 6,925 parents) and Born in Bradford (8,784 children and 2,875 parents). The overall objective of this coordinated effort is to make the resulting high-quality data widely accessible to the global research community in a timely manner. We describe how the datasets were generated and subjected to quality control at the sample, variant and genotype level. We then present some preliminary analyses to illustrate the quality of the datasets and probe potential sources of bias. We introduce measures of ultra-rare variant burden to the variables available for researchers working on these cohorts, and show that the exome-wide burden of deleterious protein-truncating variants, S het burden, is associated with educational attainment and cognitive test scores. The whole exome sequence data from these birth cohorts (CRAM & VCF files) are available through the European Genome-Phenome Archive, and here provide guidance for their use.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":" 1124","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141823166","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 : 2024-07-18DOI: 10.12688/wellcomeopenres.22609.1
David C. Lees, I. Sims
We present a genome assembly from an individual male Scotopteryx bipunctaria (the Chalk Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 326.4 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 16.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,083 protein coding genes.
{"title":"The genome sequence of the Chalk Carpet moth, Scotopteryx bipunctaria ([Denis & Schiffermüller], 1775)","authors":"David C. Lees, I. Sims","doi":"10.12688/wellcomeopenres.22609.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22609.1","url":null,"abstract":"We present a genome assembly from an individual male Scotopteryx bipunctaria (the Chalk Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 326.4 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 16.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,083 protein coding genes.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":" 32","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141827960","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 : 2024-07-18DOI: 10.12688/wellcomeopenres.22622.1
S. Falk, Ruth Y. Akinmusola
We present a genome assembly from an individual female Metopia argyrocephala (the silver-fronted satellite fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 626.9 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.21 kilobases in length.
{"title":"The genome sequence of the silver-fronted satellite fly, Metopia argyrocephala (Meigen, 1824)","authors":"S. Falk, Ruth Y. Akinmusola","doi":"10.12688/wellcomeopenres.22622.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22622.1","url":null,"abstract":"We present a genome assembly from an individual female Metopia argyrocephala (the silver-fronted satellite fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 626.9 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.21 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":" 77","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141827152","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 : 2024-07-18DOI: 10.12688/wellcomeopenres.22612.1
Liam M. Crowley, Andrew Green
We present a genome assembly from an individual male Macrophya annulata (sawfly; Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence is 236.8 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 31.23 kilobases in length.
{"title":"The genome sequence of a sawfly Macrophya annulata (Geoffroy, 1785)","authors":"Liam M. Crowley, Andrew Green","doi":"10.12688/wellcomeopenres.22612.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22612.1","url":null,"abstract":"We present a genome assembly from an individual male Macrophya annulata (sawfly; Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence is 236.8 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 31.23 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":" 23","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141826414","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 : 2024-07-18DOI: 10.12688/wellcomeopenres.22611.1
R. Mitchell, Riccardo Poloni
We present a genome assembly from an individual female Leptura quadrifasciata (the four-banded longhorn beetle; Arthropoda; Insecta; Coleoptera; Cerambycidae). The genome sequence is 1,403.9 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.45 kilobases in length.
{"title":"The genome sequence of the four-banded longhorn beetle, Leptura quadrifasciata Linnaeus, 1758","authors":"R. Mitchell, Riccardo Poloni","doi":"10.12688/wellcomeopenres.22611.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22611.1","url":null,"abstract":"We present a genome assembly from an individual female Leptura quadrifasciata (the four-banded longhorn beetle; Arthropoda; Insecta; Coleoptera; Cerambycidae). The genome sequence is 1,403.9 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.45 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":" 41","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141824613","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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