Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species.
Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species.
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DOI：
10.1371/journal.pbio.2004830
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发表时间：
2018-04
期刊：
影响因子：
9.8
通讯作者：
Barraclough TG
中科院分区：
文献类型：
--
作者：
Nowell RW;Almeida P;Wilson CG;Smith TP;Fontaneto D;Crisp A;Micklem G;Tunnacliffe A;Boschetti C;Barraclough TG
蛭形轮虫是一类微小的无脊椎动物，已经存在了数百万年，显然没有性或减数分裂。它们栖息在全球各种临时和永久的淡水栖息地，许多物种对干燥具有显著的耐受性。蛭形轮虫提供了一个更好地了解性别和重组进化的机会，但以前的工作强调干燥是这个群体中几个不寻常的基因组特征的原因。在这里，我们提出了高质量的全基因组序列的3蛭类物种：大斑轮藻和R。magnacalcarata和Adineta ricciae，这两种植物都是不耐干燥的，而Adineta ricciae是耐干燥的。结合已发表的A. vaga也具有脱水耐受性，我们应用比较基因组学方法来评估脱水耐受性和无性性对蛭形生物基因组进化的潜在影响。我们发现，祖先的四倍体是保守的所有4蛭类物种，但同源分歧专性水生Rotaria基因组出乎意料的低。这一发现与目前关于干燥在塑造蛭形生物基因组中的作用的模型相反。此外，我们还发现A. ricciae大部分是共线的，并且不形成回文重复，如在公开的A.瓦加大会。因此，解释为长期无减数分裂进化的基因组证据的几个功能并不普遍的所有蛭形动物物种，即使在同一属。最后，我们证实了以前的研究结果，高水平的水平转移nonmetazoan基因在干燥和nondesircating蛭形虫物种，并表明这种不寻常的功能是不共享的其他动物门，即使是那些具有耐干燥的代表。这些比较提出了问题，在介导水平遗传转移的脱水作用。蛭形轮虫是生活在世界各地淡水栖息地的微小动物。两个生活史特征将这些普通的无脊椎动物区分为非凡的。首先，它们已经存在了数百万年，显然没有性别：雄性没有报道，雌性通过单性生殖产生基因相同的女儿。其次，大多数蛭形生物对干燥有很强的适应力，可以在没有水的情况下存活很长一段时间（这一过程被称为脱水共生）。这两个属性已经被预测在蛭形虫基因组中留下签名。在这里，我们提出了新的草案基因组3蛭类物种，并采用比较基因组学探索蛭类的基因组结构和内容的不寻常的生活方式的潜在影响。我们发现，许多提出的无性和干燥耐受性的基因组后果并不适用于所有物种。蛭形动物的基因组可能比以前认为的更类似于其他动物，尽管一个显著的例外是从非后生动物类群水平获得的基因比例很高。我们的研究结果需要重新评估无性和干燥对蛭形轮虫基因组进化的影响。
Bdelloid rotifers are a class of microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasised desiccation as the cause of several unusual genomic features in this group. Here, we present high-quality whole-genome sequences of 3 bdelloid species: Rotaria macrura and R. magnacalcarata, which are both desiccation intolerant, and Adineta ricciae, which is desiccation tolerant. In combination with the published assembly of A. vaga, which is also desiccation tolerant, we apply a comparative genomics approach to evaluate the potential effects of desiccation tolerance and asexuality on genome evolution in bdelloids. We find that ancestral tetraploidy is conserved among all 4 bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is unexpectedly low. This finding is contrary to current models regarding the role of desiccation in shaping bdelloid genomes. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. Consequently, several features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred nonmetazoan genes in both desiccating and nondesiccating bdelloid species and show that this unusual feature is not shared by other animal phyla, even those with desiccation-tolerant representatives. These comparisons call into question the proposed role of desiccation in mediating horizontal genetic transfer. Bdelloid rotifers are microscopic animals that live in freshwater habitats throughout the world. Two life history characteristics distinguish these common invertebrates as extraordinary. First, they have existed for millions of years apparently without sex: males have not been reported, and females produce genetically identical daughters via parthenogenesis. Second, most bdelloid species are highly resilient to desiccation and can survive without water for extended periods of time (a process known as anhydrobiosis). These 2 attributes have been predicted to leave signatures in bdelloid genomes. Here, we present new draft genomes for 3 bdelloid species and employ comparative genomics to explore the potential impacts of bdelloids’ unusual lifestyle on genome structure and content. We find that many proposed genomic consequences of asexuality and desiccation tolerance do not hold true for all species. The genomes of bdelloids may be more similar to those of other animals than previously thought, though a remarkable exception is the high proportion of genes acquired horizontally from nonmetazoan taxa. Our findings necessitate a reevaluation of the effects of asexuality and desiccation on genome evolution in bdelloid rotifers.
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影响因子：
16.6
作者：
Adema CM;Hillier LW;Jones CS;Loker ES;Knight M;Minx P;Oliveira G;Raghavan N;Shedlock A;do Amaral LR;Arican-Goktas HD;Assis JG;Baba EH;Baron OL;Bayne CJ;Bickham-Wright U;Biggar KK;Blouin M;Bonning BC;Botka C;Bridger JM;Buckley KM;Buddenborg SK;Lima Caldeira R;Carleton J;Carvalho OS;Castillo MG;Chalmers IW;Christensens M;Clifton S;Cosseau C;Coustau C;Cripps RM;Cuesta-Astroz Y;Cummins SF;di Stephano L;Dinguirard N;Duval D;Emrich S;Feschotte C;Feyereisen R;FitzGerald P;Fronick C;Fulton L;Galinier R;Gava SG;Geusz M;Geyer KK;Giraldo-Calderón GI;de Souza Gomes M;Gordy MA;Gourbal B;Grunau C;Hanington PC;Hoffmann KF;Hughes D;Humphries J;Jackson DJ;Jannotti-Passos LK;de Jesus Jeremias W;Jobling S;Kamel B;Kapusta A;Kaur S;Koene JM;Kohn AB;Lawson D;Lawton SP;Liang D;Limpanont Y;Liu S;Lockyer AE;Lovato TL;Ludolf F;Magrini V;McManus DP;Medina M;Misra M;Mitta G;Mkoji GM;Montague MJ;Montelongo C;Moroz LL;Munoz-Torres MC;Niazi U;Noble LR;Oliveira FS;Pais FS;Papenfuss AT;Peace R;Pena JJ;Pila EA;Quelais T;Raney BJ;Rast JP;Rollinson D;Rosse IC;Rotgans B;Routledge EJ;Ryan KM;Scholte LLS;Storey KB;Swain M;Tennessen JA;Tomlinson C;Trujillo DL;Volpi EV;Walker AJ;Wang T;Wannaporn I;Warren WC;Wu XJ;Yoshino TP;Yusuf M;Zhang SM;Zhao M;Wilson RK
通讯作者：
Wilson RK
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
4.9
作者：
Ament-Velasquez, S. L.;Figuet, E.;Galtier, N.
通讯作者：
Galtier, N.
DOI：
10.1073/pnas.97.26.14473
发表时间：
2000-12-19
影响因子：
11.1
作者：
Arkhipova, I;Meselson, M
通讯作者：
Meselson, M
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.