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

IF 2.4 3区 环境科学与生态学 Q3 ENVIRONMENTAL SCIENCES Journal of Great Lakes Research Pub Date : 2024-03-10 DOI:10.1016/j.jglr.2024.102326
Giacomo Bernardi , Geraldine D. Kavembe , Harold L. Bergman , Giuseppe Bucciarelli , Chris M. Wood
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引用次数: 0

摘要

脊椎动物的基因组是由长长的 DNA 片段(称为等位基因)拼接而成的,这些 DNA 片段在成分上是一致的,分属于 GC 贫乏(L1 和 L2)和 GC 丰富(H1、H2 和 H3)的几个家族。Poikilotherms 的基因组往往是 GC 贫乏的,而 endotherms 则由 GC 贫乏和 GC 丰富的等位基因组成。热理论认为,温度和自然选择在偏好富含 GC 的基因组区域方面发挥了积极作用,但很难获得经验证据。早期基于氯化铯超速离心梯度的研究表明,马加迪湖罗非鱼(一种适应热水的鱼类)显示出富含 GC 的区域,而生活在冷水中的近亲却不存在。本研究的目的是利用全基因组测序重新审视最初的研究。我们发现,原来的富含 GC 的区域确实存在,它们在基因组中交错分布。事实上,在比较马加迪湖罗非鱼和温带尼罗罗非鱼时,我们发现马加迪湖罗非鱼基因组中 59.3% 的碱基组成高于 40%GC,而尼罗罗非鱼基因组中 55.3% 的碱基组成高于 40%GC。我们还发现,它们的基因组中重复元素的数量相似(分别为 20% 和 19.5%),这表明碱基组成的变化可能不是重复元素造成的。有关重复元素分析、蛋白质编码基因和其他适应热水的鱼类的进一步工作将为马加迪湖罗非鱼富含 GC 的等位基因的起源提供线索。
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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.

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来源期刊
Journal of Great Lakes Research
Journal of Great Lakes Research 生物-海洋与淡水生物学
CiteScore
5.10
自引率
13.60%
发文量
178
审稿时长
6 months
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.
期刊最新文献
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