School of Biosciences, University of Kent, Canterbury, UK.
Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK.
Genome Biol. 2018 Oct 24;19(1):171. doi: 10.1186/s13059-018-1550-x.
The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions.
We used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest.
The tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects.
从头基因组序列组装的数量呈指数级增长；然而，相对较少的组装包含每个染色体的一个支架/连续体。这种组装对于研究基因型-表型关联、基因组的总体进化和物种形成至关重要。种间差异可能源于进化过程中固定的染色体变化，我们之前假设，负选择的元素比例较高有助于鸟类特有的表型和鸟类基因组组织稳定性。本研究的目的是生成三个先前报道的染色体重排的鸟类物种（游隼、虎皮鹦鹉和鸵鸟）的染色体水平组装体，与大多数鸟类相比，这些物种的染色体发生了重排。我们还测试了保守非编码元件的密度与进化断点区域位置相关的假设。
我们使用参考辅助染色体组装、PCR 和基于实验室的分子方法，生成了三个物种的染色体水平组装体。我们从鸟类祖先的角度绘制了染色体间和染色体内的变化，发现鸵鸟基因组中没有染色体间重排，尽管它以前被描述为染色体重排。我们发现进化断点区域中保守非编码元件的平均密度显著降低。断裂进化断点区域的保守非编码元件密度最低，而染色体内进化断点区域的密度最高。
这里使用的工具可以生成廉价、高效的染色体水平组装体，>80%的组装体被分配到染色体上，这与使用高密度物理或遗传图谱组装的基因组相当。此外，保守的非编码元件是在进化过程中确定重排（尤其是染色体间重排）的重要因素，而不会产生有害影响。
