Andreyushkova Daria A, Makunin Alexey I, Beklemisheva Violetta R, Romanenko Svetlana A, Druzhkova Anna S, Biltueva Larisa B, Serdyukova Natalya A, Graphodatsky Alexander S, Trifonov Vladimir A
Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
Synthetic Biological Unit, Novosibirsk State University, 630090 Novosibirsk, Russia.
Genes (Basel). 2017 Nov 10;8(11):318. doi: 10.3390/genes8110318.
Several whole genome duplication (WGD) events followed by rediploidization took place in the evolutionary history of vertebrates. Acipenserids represent a convenient model group for investigation of the consequences of WGD as their representatives underwent additional WGD events in different lineages resulting in ploidy level variation between species, and these processes are still ongoing. Earlier, we obtained a set of sterlet (Acipenser ruthenus) chromosome-specific libraries by microdissection and revealed that they painted two or four pairs of whole sterlet chromosomes, as well as additional chromosomal regions, depending on rediploidization status and chromosomal rearrangements after genome duplication. In this study, we employed next generation sequencing to estimate the content of libraries derived from different paralogous chromosomes of sterlet. For this purpose, we aligned the obtained reads to the spotted gar (Lepisosteus oculatus) reference genome to reveal syntenic regions between these two species having diverged 360 Mya. We also showed that the approach is effective for synteny prediction at various evolutionary distances and allows one to clearly distinguish paralogous chromosomes in polyploid genomes. We postulated that after the acipenserid-specific WGD sterlet karyotype underwent multiple interchromosomal rearrangements, but different chromosomes were involved in this process unequally.
在脊椎动物的进化史上发生了几次全基因组复制（WGD）事件，随后是再二倍体化。鲟形目鱼类是研究WGD后果的一个便利模型群体，因为它们的代表在不同谱系中经历了额外的WGD事件，导致物种间倍性水平的变化，而且这些过程仍在进行中。此前，我们通过显微切割获得了一组小体鲟（Acipenser ruthenus）染色体特异性文库，并发现根据再二倍体化状态和基因组复制后的染色体重排情况，它们可标记出两对或四对小体鲟的整条染色体以及其他染色体区域。在本研究中，我们采用新一代测序技术来估计从小体鲟不同同源染色体衍生的文库内容。为此，我们将获得的读数与雀鳝（Lepisosteus oculatus）参考基因组进行比对，以揭示这两个在3.6亿年前就已分化的物种之间的同线性区域。我们还表明，该方法在各种进化距离下对同线性预测都是有效的，并且能够在多倍体基因组中清晰地区分同源染色体。我们推测，在鲟形目特异性WGD之后，小体鲟核型经历了多次染色体间重排，但不同染色体在这一过程中的参与程度并不相同。
