Evolution of Dosage Compensation - An Empirical Test using Turtles with Independently Evolved XX/XY and ZZ/ZW Chromosomes

本项目将通过将甲鱼种类与XX/XY、ZZ/ZW和温度相关(TSD)性别决定进行对比来说明剂量补偿(DC)的演变。在像人类这样的物种中，XX/XY雌性在X染色体上有两个拷贝的基因，雄性有一个，因为雌性携带两个X，雄性携带一个X和一个Y。基因剂量的不平衡，例如由性别之间X或Z染色体数量的差异引起的不平衡，可能会降低适应性，甚至导致死亡，没有重新建立平衡的机制。剂量补偿机制(DCM)使位于X或Z(X连锁或Z连锁)染色体之间以及雄性和雌性之间的基因的活性相等。DC对正常发育很重要，并对基因组和物种形成的进化产生影响。然而，DCM的多样性和进化仍然不清楚。由于甲鱼的XX/XY和ZZ/ZW染色体多次独立进化，且海龟基因组资源日益丰富，因此是研究海龟DCM进化的理想材料。为了解决这一难题，人们正在将海龟的基因表达与性别决定的相反机制进行比较。这些结果将通过阐明DCM是否存在跨生物体的一般规则，或者是否在每个谱系中独立地进化出独特的解决方案，来促进我们对DMC的多样性和进化的理解。该项目通过招收生物学本科生，涉及本科生基于发现的学习，并扩大了未被充分代表的群体在生物学领域的参与。本科生将接受各种生物学领域的培训，参加反思会议，并在科学会议上展示他们的成果。结果将通过演示文稿、出版物和双语网站传播。当XX/XY或ZZ/ZW染色体在二倍体物种中进化时，Y或W染色体上的基因会丢失(或失去功能)，因为它们会随着时间的推移而退化，因为它们的重组程度较低。这种缺失意味着XY-雄性携带X基因的一个功能拷贝，而XX-雌性携带两个拷贝(同样，ZW雌性携带一个Z-基因拷贝，ZZ-雄性携带两个拷贝)。由于X和Z连锁基因是遗传网络的一部分，基因拷贝数的不平等会导致转录的不平衡，这可能会产生次优或致命的表型，除非存在重新建立平衡的机制。在缺乏这种机制的情况下，转录将不同(A)这些染色体上的基因和XY男性(或ZW女性)的常染色体上的基因，以及(B)X基因(或Z基因)的男性和女性之间的差异。剂量补偿(DC)是一种平衡X或Z连锁基因活性的系统，以抵消差异基因拷贝数的有害影响。DC重新建立了这些基因和常染色体基因之间的平衡(“染色体到常染色体”补偿)，以及性别之间的平衡(“男性到女性”补偿)。机制可能平衡整个染色体(全局补偿)，其他只是一些基因(局部补偿)。这个项目测试了这样的假设，即全局DC(即整个染色体)并不必然随着染色体的进化而进化，相反，当存在DC时(即只影响某些基因)，DC往往是局部的，并且与染色体的大小、进化年龄和基因含量无关。因此，该项目正在对显微切割的甲鱼染色体进行测序，并通过arrayCGH进行检测，并通过转录组学来评估这些基因的表达。

This project will illuminate the evolution of dosage compensation (DC) by contrasting turtle species with XX/XY, ZZ/ZW and temperature-dependent (TSD) gender determination. In species like humans, XX/XY females have two copies of genes in the X chromosome and males one because females carry two Xs and males one X and one Y. An imbalance in gene dosage, such the one caused by the difference in the number of X or Z chromosomes between genders, may reduce fitness or even cause death, without a mechanism to re-establish a balance. Dosage compensation mechanisms (DCM) equalize the activity of genes located in the X or Z (X-linked or Z-linked) between chromosomes, and between males and females. DC is important for normal development, and has consequences for the evolution of genomes and speciation. Yet, DCM diversity and evolution remain unclear. Turtles are ideal to study DCM evolution because XX/XY and ZZ/ZW chromosomes have evolved independently multiple times, and there are increasing turtle genomic resources. To address this puzzle, gene expression is being compared in turtles with contrasting mechanisms of gender determination. The results will advance our understanding of the diversity and evolution of DMC by illuminating whether there are general rules to DCM across organisms or whether unique solutions evolved independently in each lineage. This project involves undergraduate discovery-based learning by recruiting biology undergraduates, and broadens the participation of underrepresented groups in biology. Undergraduates will be trained in a variety of biological fields, participate in reflection sessions and present their results at scientific meetings. Results will be disseminated via presentations, publications, and a bilingual web-site. When XX/XY or ZZ/ZW chromosomes evolve in diploid species, genes are lost from the Y or W (or lose their function) as they degenerate over time due to their lower recombination. This loss means that XY-males carry a single functional copy of X-genes while XX-females carry two copies (likewise, ZW females have one copy of Z-genes and ZZ-males have two copies). Because X- and Z-linked genes are part of genetic networks, the inequality of gene copy number causes an imbalance in transcription which may produce sub-optimal or lethal phenotypes, unless a mechanism existed to re-establish a balance. In the absence of such mechanism, transcription will differ (a) between genes in these chromosomes and autosomes in XY males (or ZW females), and (b) between males and females for X-genes (or Z-genes). Dosage compensation (DC) is a system to equalize the activity of X- or Z-linked genes to counterbalance the deleterious effects of differential gene copy number. DC re-establishes a balance between these genes and autosomal genes ("chromosome-to-autosome" compensation), and between the genders ("male-to-female" compensation). Mechanisms may balance entire chromosomes (global compensation), other some genes only (local compensation). This project tests the hypothesis that global DC (i.e. chromosome-wide) does not evolve inevitably with the evolution of chromosomes, but instead that DC tends to be local when present (i.e. affecting some genes only), and independent of the size, evolutionary age, and gene content of the chromosomes. Accordingly, this project it is sequencing microdissected turtle chromosomes, and examining them by arrayCGH, and assessing the expression of these genes via transcriptomics.