Breanna B Raymond, Pierre Guenzi-Tiberi, Eric Maréchal, Lynne M Quarmby
{"title":"通过全新基因组组装和注释揭示的雪藻 Sanguina aurantia。","authors":"Breanna B Raymond, Pierre Guenzi-Tiberi, Eric Maréchal, Lynne M Quarmby","doi":"10.1093/g3journal/jkae181","DOIUrl":null,"url":null,"abstract":"<p><p>To thrive on melting alpine and polar snow, some Chlorophytes produce an abundance of astaxanthin, causing red blooms, often dominated by genus Sanguina. The red cells have not been cultured, but we recently grew a green biciliate conspecific with Sanguina aurantia from a sample of watermelon snow. This culture provided source material for Oxford Nanopore Technology and Illumina sequencing. Our assembly pipeline exemplifies the value of a hybrid long- and short-read approach for the complexities of working with a culture grown from a field sample. Using bioinformatic tools, we separated assembled contigs into 2 genomic pools based on a difference in GC content (57.5 and 55.1%). We present the data as 2 assemblies of S. aurantia variants but explore other possibilities. High-throughput chromatin conformation capture analysis (Hi-C sequencing) was used to scaffold the assemblies into a 96-Mb genome designated as \"A\" and a 102-Mb genome designated as \"B.\" Both assemblies are highly contiguous: genome A consists of 38 scaffolds with an N50 of 5.4 Mb, while genome B has 50 scaffolds with an N50 of 6.4 Mb. RNA sequencing was used to improve gene annotation.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1000,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457085/pdf/","citationCount":"0","resultStr":"{\"title\":\"Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation.\",\"authors\":\"Breanna B Raymond, Pierre Guenzi-Tiberi, Eric Maréchal, Lynne M Quarmby\",\"doi\":\"10.1093/g3journal/jkae181\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>To thrive on melting alpine and polar snow, some Chlorophytes produce an abundance of astaxanthin, causing red blooms, often dominated by genus Sanguina. The red cells have not been cultured, but we recently grew a green biciliate conspecific with Sanguina aurantia from a sample of watermelon snow. This culture provided source material for Oxford Nanopore Technology and Illumina sequencing. Our assembly pipeline exemplifies the value of a hybrid long- and short-read approach for the complexities of working with a culture grown from a field sample. Using bioinformatic tools, we separated assembled contigs into 2 genomic pools based on a difference in GC content (57.5 and 55.1%). We present the data as 2 assemblies of S. aurantia variants but explore other possibilities. High-throughput chromatin conformation capture analysis (Hi-C sequencing) was used to scaffold the assemblies into a 96-Mb genome designated as \\\"A\\\" and a 102-Mb genome designated as \\\"B.\\\" Both assemblies are highly contiguous: genome A consists of 38 scaffolds with an N50 of 5.4 Mb, while genome B has 50 scaffolds with an N50 of 6.4 Mb. RNA sequencing was used to improve gene annotation.</p>\",\"PeriodicalId\":12468,\"journal\":{\"name\":\"G3: Genes|Genomes|Genetics\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":2.1000,\"publicationDate\":\"2024-10-07\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457085/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"G3: Genes|Genomes|Genetics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/g3journal/jkae181\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"G3: Genes|Genomes|Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/g3journal/jkae181","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
摘要
为了在融化的高山和极地积雪上茁壮成长,一些叶绿藻会产生大量的虾青素,从而形成红色的花朵,通常以桑吉纳属为主。红细胞尚未培养出来,但我们最近从西瓜雪样本中培养出了一种与 Sanguina aurantia 同种的绿色双生叶植物。这种培养物为牛津纳米孔技术和 Illumina 测序提供了源材料。我们的组装流水线体现了长短线程混合方法的价值,可用于处理从野外样本中培育出的复杂培养物。利用生物信息学工具,我们根据 GC 含量的差异(57.5% 和 55.1%)将组装的等位基因分成了两个基因组池。我们将这些数据作为 S. aurantia 变异体的两个集合,但也探讨了其他可能性。我们利用高通量染色质构象捕获分析(Hi-C 测序)将两个基因组组装成一个 96 MB 的基因组 "A "和一个 102 MB 的基因组 "B"。这两个组装体高度连续:基因组 A 由 38 个支架组成,N50 为 5.4 Mb,而基因组 B 有 50 个支架,N50 为 6.4 Mb。RNA 测序用于改进基因注释。
Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation.
To thrive on melting alpine and polar snow, some Chlorophytes produce an abundance of astaxanthin, causing red blooms, often dominated by genus Sanguina. The red cells have not been cultured, but we recently grew a green biciliate conspecific with Sanguina aurantia from a sample of watermelon snow. This culture provided source material for Oxford Nanopore Technology and Illumina sequencing. Our assembly pipeline exemplifies the value of a hybrid long- and short-read approach for the complexities of working with a culture grown from a field sample. Using bioinformatic tools, we separated assembled contigs into 2 genomic pools based on a difference in GC content (57.5 and 55.1%). We present the data as 2 assemblies of S. aurantia variants but explore other possibilities. High-throughput chromatin conformation capture analysis (Hi-C sequencing) was used to scaffold the assemblies into a 96-Mb genome designated as "A" and a 102-Mb genome designated as "B." Both assemblies are highly contiguous: genome A consists of 38 scaffolds with an N50 of 5.4 Mb, while genome B has 50 scaffolds with an N50 of 6.4 Mb. RNA sequencing was used to improve gene annotation.
期刊介绍:
G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights.
G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.