Species-specific abundant retrotransposons elucidate the genomic composition of modern sugarcane cultivars.

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Chromosoma Pub Date : 2020-03-01 Epub Date: 2019-12-17 DOI:10.1007/s00412-019-00729-1

Yongji Huang, Hong Chen, Jinlei Han, Ya Zhang, Shulin Ma, Guangrun Yu, Zonghua Wang, Kai Wang

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引用次数: 10

Abstract

Modern sugarcane cultivars are highly polyploid and derived from the hybridization of Saccharum officinarum and S. spontaneum, thus leading to singularly complex genomes. The complex genome has hindered the study of genomic structures. Here, we adopted a computational strategy to isolate highly repetitive and abundant sequences in either S. officinarum or S. spontaneum and isolated four S. spontaneum-enriched retrotransposons. Fluorescence in situ hybridization (FISH) assays with these repetitive DNA sequences generated whole-genome painting signals for S. spontaneum but not for S. officinarum. We demonstrated that these repetitive sequence-based probes distinguish the parental S. spontaneum genome in hybrids derived from crosses between it and S. officinarum. A cytological analysis of 14 modern sugarcane cultivars revealed that the percentages of chromosomes with introgressive S. spontaneum fragments ranged from 11.9 to 40.9% and substantially exceeded those determined for previously investigated cultivars (5-13%). The comparatively higher percentages of introgressive S. spontaneum fragments detected in the aforementioned cultivars indicate frequent recombination between parental genomes. Here, we present the application of our strategy to isolate species-specific cytological markers. This information may help to elucidate complex plant genomic structures and trace their evolutionary histories.

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物种特异的大量反转录转座子阐明了现代甘蔗品种的基因组组成。

现代甘蔗品种是高度多倍体的，是由Saccharum officinarum和S. spontanum杂交而来，从而导致了非常复杂的基因组。复杂的基因组阻碍了基因组结构的研究。在这里，我们采用计算策略分离出S. officinarum和S. spontanum中高度重复和丰富的序列，并分离出4个S. spontanum富集的反转录转座子。利用这些重复的DNA序列进行荧光原位杂交(FISH)分析，可以为S. spontanum产生全基因组绘制信号，但对S. officinarum则没有。我们证明了这些基于重复序列的探针在其与S. officinarum杂交衍生的杂种中区分亲本S. spontanum基因组。对14个现代甘蔗品种的细胞学分析表明，具有渐渗性天然甘蔗片段的染色体比例在11.9% ~ 40.9%之间，大大超过了先前研究的品种(5 ~ 13%)。在上述品种中检测到的相对较高百分比的渐渗性自发葡萄片段表明亲本基因组之间经常发生重组。在这里，我们提出了应用我们的策略来分离物种特异性细胞学标记。这些信息可能有助于阐明复杂的植物基因组结构和追踪它们的进化历史。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Chromosoma 生物-生化与分子生物学

CiteScore

3.30

自引率

6.20%

发文量

审稿时长

1 months

期刊介绍： Chromosoma publishes research and review articles on the functional organization of the eukaryotic cell nucleus, with a particular emphasis on the structure and dynamics of chromatin and chromosomes; the expression and replication of genomes; genome organization and evolution; the segregation of genomes during meiosis and mitosis; the function and dynamics of subnuclear compartments; the nuclear envelope and nucleocytoplasmic interactions, and more. The scope of Chromosoma encompasses genetic, biophysical, molecular and cell biological studies. Average time from receipt of contributions to first decision: 22 days Publishes research and review articles on the functional organization of the eukaryotic cell nucleus Topics include structure and dynamics of chromatin and chromosomes; the expression and replication of genomes; genome organization and evolution; the segregation of genomes during meiosis and mitosis and more Encompasses genetic, biophysical, molecular and cell biological studies.