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

本项目将通过对比海龟种类XX/XY、ZZ/ZW和温度依赖（TSD）性别决定来阐明剂量补偿（DC）的演变。在像人类这样的物种中，XX/XY的女性在X染色体上有两个基因拷贝，男性有一个基因拷贝，因为女性携带两个X，男性携带一个X和一个y。基因剂量的不平衡，如性别之间X或Z染色体数量的差异造成的基因剂量的不平衡，可能会降低适应性，甚至导致死亡，而没有一种机制来重新建立平衡。剂量补偿机制（DCM）平衡了染色体之间、雄性和雌性之间位于X或Z （X连锁或Z连锁）的基因的活性。DC对正常发育非常重要，并对基因组和物种形成的进化产生影响。然而，DCM的多样性及其演化仍不清楚。海龟是研究DCM进化的理想对象，因为XX/XY和ZZ/ZW染色体多次独立进化，而且海龟基因组资源不断增加。为了解决这个难题，研究人员将海龟的基因表达与不同的性别决定机制进行了比较。这些结果将通过阐明是否存在跨生物DCM的一般规则或是否在每个谱系中独立进化的独特解决方案来推进我们对DMC多样性和进化的理解。该项目通过招收生物学本科生，涉及以发现为基础的本科学习，并扩大生物学中代表性不足的群体的参与。本科生将接受各种生物领域的培训，参加反思会议，并在科学会议上展示他们的成果。研究结果将通过演讲、出版物和双语网站传播。在二倍体物种中，当XX/XY或ZZ/ZW染色体进化时，随着时间的推移，由于其较低的重组，基因从Y或W中丢失（或失去其功能）。这种缺失意味着xy -雄性携带一个x基因的功能拷贝，而xx -雌性携带两个拷贝（同样，ZW雌性有一个z基因拷贝，zz -雄性有两个拷贝）。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导致转录不平衡，可能产生次优或致死表型，除非存在重新建立平衡的机制。在缺乏这种机制的情况下，这些染色体和常染色体中的基因在XY雄性（或ZW雌性）之间的转录将会不同，以及(b) x基因（或z基因）在雄性和雌性之间的转录将会不同。剂量补偿（DC）是一种平衡X-或z -连锁基因活性的系统，以抵消基因拷贝数差异的有害影响。DC重新建立了这些基因和常染色体基因（“染色体对常染色体”补偿）以及性别之间（“男性对女性”补偿）的平衡。机制可能平衡整个染色体（全局补偿），也可能仅平衡某些基因（局部补偿）。这个项目检验了这样一个假设，即全局DC（即染色体范围）并不随着染色体的进化而不可避免地进化，相反，DC在存在时往往是局部的（即只影响某些基因），并且与染色体的大小、进化年龄和基因含量无关。因此，这个项目是测序微解剖的海龟染色体，并通过arrayCGH检查它们，并通过转录组学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.