Giacomo Bernardi , Geraldine D. Kavembe , Harold L. Bergman , Giuseppe Bucciarelli , Chris M. Wood
{"title":"马加迪湖罗非鱼(Oreochromis Alcolapia grahami)基因组的组织结构--罗非鱼是慈鲷中的一种极端嗜食鱼类","authors":"Giacomo Bernardi , Geraldine D. Kavembe , Harold L. Bergman , Giuseppe Bucciarelli , Chris M. Wood","doi":"10.1016/j.jglr.2024.102326","DOIUrl":null,"url":null,"abstract":"<div><p>The genome of vertebrates is made of a mosaic of long stretches of DNA, called isochores, which are compositionally uniform, and belong to a few families of GC-poor (L1 and L2) and GC-rich (H1, H2, and H3) components. Poikilotherms tend to have GC-poor genomes, while endotherms comprise both GC-poor and GC-rich isochores. The thermal theory claimed that temperature and natural selection played an active role in favoring GC-rich genomic regions, yet empirical evidence was difficult to obtain. Early work based on cesium chloride ultracentrifugation gradients showed that the Lake Magadi tilapia, a hot-water adapted fish species, displayed GC-rich regions that were absent from a close relative that lives in colder water. The goal of this study was to revisit the original study using full genome sequencing. We found that the original GC-rich regions are indeed present, that they are interspersed in the genome. Indeed, when comparing Lake Magadi tilapia with the temperate Nile tilapia, we found that 59.3 % of the genome of Lake Magadi tilapia had a base composition higher than 40 %GC, as opposed to 55.3 % of the genome of the Nile tilapia having a base composition higher than 40 % GC. We also found that their genomes comprised similar amounts of repetitive elements (20 % and 19.5 %, respectively) indicating that the shifts in base composition might not be due to repetitive elements. Further work on repetitive element analyses, protein coding genes and additional hot-water adapted fishes will provide clues as to the origin of GC-rich isochores in Lake Magadi tilapia.</p></div>","PeriodicalId":54818,"journal":{"name":"Journal of Great Lakes Research","volume":"50 3","pages":"Article 102326"},"PeriodicalIF":2.4000,"publicationDate":"2024-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"The genome organization of the Lake Magadi tilapia, Oreochromis Alcolapia grahami, a cichlid extremophile\",\"authors\":\"Giacomo Bernardi , Geraldine D. Kavembe , Harold L. Bergman , Giuseppe Bucciarelli , Chris M. Wood\",\"doi\":\"10.1016/j.jglr.2024.102326\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>The genome of vertebrates is made of a mosaic of long stretches of DNA, called isochores, which are compositionally uniform, and belong to a few families of GC-poor (L1 and L2) and GC-rich (H1, H2, and H3) components. Poikilotherms tend to have GC-poor genomes, while endotherms comprise both GC-poor and GC-rich isochores. The thermal theory claimed that temperature and natural selection played an active role in favoring GC-rich genomic regions, yet empirical evidence was difficult to obtain. Early work based on cesium chloride ultracentrifugation gradients showed that the Lake Magadi tilapia, a hot-water adapted fish species, displayed GC-rich regions that were absent from a close relative that lives in colder water. The goal of this study was to revisit the original study using full genome sequencing. We found that the original GC-rich regions are indeed present, that they are interspersed in the genome. Indeed, when comparing Lake Magadi tilapia with the temperate Nile tilapia, we found that 59.3 % of the genome of Lake Magadi tilapia had a base composition higher than 40 %GC, as opposed to 55.3 % of the genome of the Nile tilapia having a base composition higher than 40 % GC. We also found that their genomes comprised similar amounts of repetitive elements (20 % and 19.5 %, respectively) indicating that the shifts in base composition might not be due to repetitive elements. Further work on repetitive element analyses, protein coding genes and additional hot-water adapted fishes will provide clues as to the origin of GC-rich isochores in Lake Magadi tilapia.</p></div>\",\"PeriodicalId\":54818,\"journal\":{\"name\":\"Journal of Great Lakes Research\",\"volume\":\"50 3\",\"pages\":\"Article 102326\"},\"PeriodicalIF\":2.4000,\"publicationDate\":\"2024-03-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Great Lakes Research\",\"FirstCategoryId\":\"93\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0380133024000583\",\"RegionNum\":3,\"RegionCategory\":\"环境科学与生态学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"ENVIRONMENTAL SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Great Lakes Research","FirstCategoryId":"93","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0380133024000583","RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"ENVIRONMENTAL SCIENCES","Score":null,"Total":0}
The genome organization of the Lake Magadi tilapia, Oreochromis Alcolapia grahami, a cichlid extremophile
The genome of vertebrates is made of a mosaic of long stretches of DNA, called isochores, which are compositionally uniform, and belong to a few families of GC-poor (L1 and L2) and GC-rich (H1, H2, and H3) components. Poikilotherms tend to have GC-poor genomes, while endotherms comprise both GC-poor and GC-rich isochores. The thermal theory claimed that temperature and natural selection played an active role in favoring GC-rich genomic regions, yet empirical evidence was difficult to obtain. Early work based on cesium chloride ultracentrifugation gradients showed that the Lake Magadi tilapia, a hot-water adapted fish species, displayed GC-rich regions that were absent from a close relative that lives in colder water. The goal of this study was to revisit the original study using full genome sequencing. We found that the original GC-rich regions are indeed present, that they are interspersed in the genome. Indeed, when comparing Lake Magadi tilapia with the temperate Nile tilapia, we found that 59.3 % of the genome of Lake Magadi tilapia had a base composition higher than 40 %GC, as opposed to 55.3 % of the genome of the Nile tilapia having a base composition higher than 40 % GC. We also found that their genomes comprised similar amounts of repetitive elements (20 % and 19.5 %, respectively) indicating that the shifts in base composition might not be due to repetitive elements. Further work on repetitive element analyses, protein coding genes and additional hot-water adapted fishes will provide clues as to the origin of GC-rich isochores in Lake Magadi tilapia.
期刊介绍:
Published six times per year, the Journal of Great Lakes Research is multidisciplinary in its coverage, publishing manuscripts on a wide range of theoretical and applied topics in the natural science fields of biology, chemistry, physics, geology, as well as social sciences of the large lakes of the world and their watersheds. Large lakes generally are considered as those lakes which have a mean surface area of >500 km2 (see Herdendorf, C.E. 1982. Large lakes of the world. J. Great Lakes Res. 8:379-412, for examples), although smaller lakes may be considered, especially if they are very deep. We also welcome contributions on saline lakes and research on estuarine waters where the results have application to large lakes.