Wellcome Open Research最新文献

{"title":"The genome sequence of <i>Inga leiocalycina</i> Benth.","authors":"Rowan J Schley, R Toby Pennington, Alex D Twyford, Kyle G Dexter, Catherine Kidner, Todd P Michael","doi":"10.12688/wellcomeopenres.23131.1","DOIUrl":"10.12688/wellcomeopenres.23131.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual of <i>Inga leiocalycina</i> (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 948.00 megabases. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The assembled mitochondrial genome sequences have lengths of 1,019.42 and 98.74 kilobases, and the plastid genome assembly is 175.51 kb long. Gene annotation of the nuclear genome assembly on Ensembl identified 33,457 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"606"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11531642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569743","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}

{"title":"The genome sequence of black elder, <i>Sambucus nigra</i> Linnaeus, 1753 (Adoxaceae).","authors":"Maarten J M Christenhusz, Ilia J Leitch","doi":"10.12688/wellcomeopenres.23147.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23147.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual <i>Sambucus nigra</i> (the European elder; Streptophyta; Magnoliopsida; Dipsacales; Adoxaceae). The genome sequence has a total length of 11,813.70 megabases. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 724.11 kilobases and 158.06 kilobases, respectively.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"609"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11555357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142628835","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}

{"title":"The genome sequence of the willow leaf beetle, <i>Lochmaea capreae</i> Linnaeus, 1758.","authors":"Maxwell V L Barclay, Danaë Vassiliades, Will Bayfield-Farrell, Joana Cristóvão, Keita Matsumoto, Michael Geiser","doi":"10.12688/wellcomeopenres.22424.2","DOIUrl":"10.12688/wellcomeopenres.22424.2","url":null,"abstract":"<p><p>We present a genome assembly from an individual female <i>Lochmaea capreae</i> (the willow leaf beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence is 534.7 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.85 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,254 protein coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"304"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503005/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509147","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}

{"title":"The genome sequence of the common awl robberfly, <i>Neoitamus cyanurus</i> (Loew, 1849).","authors":"Liam M Crowley, Ruth Y Akinmusola","doi":"10.12688/wellcomeopenres.22253.2","DOIUrl":"10.12688/wellcomeopenres.22253.2","url":null,"abstract":"<p><p>We present a genome assembly from an individual female <i>Neoitamus cyanurus</i> (the common awl robberfly; Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a total length of 365.5 megabases. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,046 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"289"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11494275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509143","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}

{"title":"The genome sequence of the Atlantic mackerel, <i>Scomber scombrus</i> Linnaeus, 1758.","authors":"Mitchell Brennan, Kimberly Bird, Birthe Zancker, Vengamanaidu Modepali, Patrick Adkins","doi":"10.12688/wellcomeopenres.23186.1","DOIUrl":"10.12688/wellcomeopenres.23186.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual <i>Scomber scombrus</i> (the Atlantic mackerel; Chordata; Actinopteri; Scombriformes; Scombridae). The genome sequence has a total length of 764.10 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.56 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"610"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11558169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142628743","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}

{"title":"The genome sequence of <i>Inga</i> <i>oerstediana</i> Benth.","authors":"Rowan J Schley, R Toby Pennington, Alex D Twyford, Kyle G Dexter, Catherine Kidner, Todd P Michael","doi":"10.12688/wellcomeopenres.23146.1","DOIUrl":"10.12688/wellcomeopenres.23146.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual of <i>Inga oerstediana</i> (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 970.60 megabases. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 1,166.81 and 175.18 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 33,334 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"607"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11599804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740544","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}

{"title":"The genome sequence of the acorn piercer, <i>Pammene fasciana</i> (Linnaeus, 1761).","authors":"Douglas Boyes, Thomas Lewin","doi":"10.12688/wellcomeopenres.18114.2","DOIUrl":"10.12688/wellcomeopenres.18114.2","url":null,"abstract":"<p><p>We present a genome assembly from an individual male <i>Pammene fasciana</i> (acorn piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 564 megabases in span. Most of the assembly (99.94%) is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,224 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"7 ","pages":"258"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11512137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509136","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}

{"title":"Improved gene editing and fluorescent-protein tagging in <i>Aspergillus nidulans</i> using a Golden Gate-based CRISPR-Cas9 plasmid system.","authors":"Domenico Modaffari, Aimée Finlayson, Yuyang Miao, Edward W J Wallace, Kenneth E Sawin","doi":"10.12688/wellcomeopenres.23086.1","DOIUrl":"10.12688/wellcomeopenres.23086.1","url":null,"abstract":"<p><p>CRISPR-Cas9 systems can be used for precise genome editing in filamentous fungi, including <i>Aspergillus nidulans</i>. However, current CRISPR-Cas9 systems for <i>A. nidulans</i> rely on relatively complex or multi-step cloning methods to build a plasmid expressing both Cas9 and an sgRNA targeting a genomic locus. In this study we improve on existing plasmid-based CRISPR-Cas9 systems for <i>Aspergilli</i> by creating an extremely simple-to-use CRISPR-Cas9 system for <i>A. nidulans</i> genome editing. In our system, a plasmid containing both Cas9 and an sgRNA is assembled in a one-step Golden Gate reaction. We demonstrate precise, scarless genome editing with nucleotide-level DNA substitutions, and we demonstrate markerless gene tagging by fusing fluorescent-protein coding sequences to the endogenous coding sequences of several <i>A. nidulans</i> genes. We also describe <i>A. nidulans</i> codon-adjusted versions of multiple recent-generation fluorescent proteins, which will be useful to the wider <i>Aspergillus</i> community.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"602"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11617824/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787203","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}

{"title":"The genome sequence of the planthopper, <i>Conomelus anceps</i> (Germar, 1821).","authors":"Stephen Moran, Andy Griffiths, Liam M Crowley","doi":"10.12688/wellcomeopenres.23104.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23104.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual male <i>Conomelus anceps</i> (planthopper; Arthropoda; Insecta; Hemiptera; Delphacidae). The genome sequence has a total length of 957.80 megabases. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.98 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"605"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11555367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142628877","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}

{"title":"A nationwide longitudinal investigation on the role of prenatal exposure to infectious diseases on the onset of chronic conditions in children and adolescents in Brazil.","authors":"Enny S Paixao, Thiago Cerqueira-Silva, Pilar T V Florentino, Orlagh Carroll, Nuria Sanchez Clemente, Deborah A Lawlor, Rita de Cássia Ribeiro Silva, Laura Cunha Rodrigues, Liam Smeeth, Mauricio L Barreto","doi":"10.12688/wellcomeopenres.22430.2","DOIUrl":"10.12688/wellcomeopenres.22430.2","url":null,"abstract":"<p><strong>Background: </strong>In utero exposure to infections might set the stage for a chain of events leading to a wide spectrum of long-term health outcomes observed in children and adolescents. This proposal aims to investigate whether syphilis, zika, dengue and chikungunya during pregnancy can increase the risk of the offspring developing a non-infectious chronic condition during childhood and adolescence.</p><p><strong>Objectives: </strong>1) Estimate the risk of non-infectious chronic conditions associated to syphilis, zika, dengue and chikungunya during pregnancy and when appropriate, explore if the risk varies by timing during pregnancy when the infection is acquired (first, second or third trimester) and severity (such as severe or mild dengue); 2) Investigate whether in uterus exposure to maternal infection affects the growth pattern of children and adolescents; 3) Examine the extent to which the relationship between maternal infection and non-infectious chronic outcomes are mediated by intrauterine growth restriction and preterm birth.</p><p><strong>Methods: </strong>We will compare health outcomes and growth trajectories of children and adolescents born to mothers with and without specific infections during pregnancy using conventional multivariable regression in the whole study population, in a within sibship design, using the subgroup of offspring with at least one sibling who is not exposed to the infection, and negative control outcome. Then we will decompose the direct and mediated effects (by preterm birth and small for gestational age) of maternal infection on chronic disorders.</p><p><strong>Results and conclusions: </strong>The results from this study will advance our understanding of the relationship between infections during pregnancy and chronic disorders, with widespread implications enabling targeting of critical points along the path from in utero exposure to outcomes to avoid or mitigate illness and disability over the life course.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"320"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11489840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476095","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}