Characterization, Genomic Organization, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons in Erianthus arundinaceus.
Characterization, Genomic Organization, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons in Erianthus arundinaceus.
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花茅 Ty1-copia 反转录转座子的特征、基因组组织、丰度和染色体分布
DOI：
10.3389/fpls.2017.00924
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发表时间：
2017
影响因子：
5.6
通讯作者：
Zhang M
中科院分区：
文献类型：
--
作者：
Huang Y;Luo L;Hu X;Yu F;Yang Y;Deng Z;Wu J;Chen R;Zhang M
毛花茅是甘蔗属的重要野生物种，具有许多有价值的性状。然而，其基因组的组成和结构很大程度上未知，这阻碍了其在甘蔗育种和进化研究中的应用。逆转录转座子构成了植物基因组的重要部分，并且可能在基因组的进化和序列组织中发挥了重要作用。在本研究中，我们首次研究了Ty1-copia反转录转座子的系统发育多样性和基因组丰度，并检查了它们在青竹中的染色体分布模式。总共获得了 70 个具有显着异质性的 Ty1-copia 逆转录酶 (RT) 序列。系统发育分析显示这些 Ty1-copia 逆转录转座子被分为四个不同的进化谱系（Tork/TAR、Tork/Angela、Retrofit/Ale 和 Sire/Maximus）。斑点印迹分析显示，估计青竹基因组中 Ty1-copia 反转录转座子的总拷贝数约为 4.5 × 103，表明它们是一个重要组成部分。荧光原位杂交显示，来自四个谱系的 Ty1-copia 反转录转座子具有惊人相似的染色体富集模式，仅富集于大多数青竹染色体的亚末端异染色质区域。这是青竹亚末端异染色质中存在 Ty1-copia 逆转录转座子的第一个明确证据。总而言之，这些结果促进了对 Ty1-copia 反转录转座子多样化的理解，并揭示了它们在青竹中的染色体分布模式。
Erianthus arundinaceus is an important wild species of the genus Saccharum with many valuable traits. However, the composition and structure of its genome are largely unknown, which have hindered its utilization in sugarcane breeding and evolutionary research. Retrotransposons constitute an appreciable fraction of plant genomes and may have played a significant role in the evolution and sequence organization of genomes. In the current study, we investigate the phylogenetic diversity and genomic abundance of Ty1-copia retrotransposons for the first time and inspect their chromosomal distribution patterns in E. arundinaceus. In total, 70 Ty1-copia reverse transcriptase (RT) sequences with significant levels of heterogeneity were obtained. The phylogenetic analysis revealed these Ty1-copia retrotransposons were classified into four distinct evolutionary lineages (Tork/TAR, Tork/Angela, Retrofit/Ale, and Sire/Maximus). Dot-blot analysis showed estimated the total copy number of Ty1-copia retrotransposons to be about 4.5 × 103 in the E. arundinaceus genome, indicating they were a significant component. Fluorescence in situ hybridization revealed that Ty1-copia retrotransposons from the four lineages had strikingly similar patterns of chromosomal enrichment, being exclusively enriched in the subterminal heterochromatic regions of most E. arundinaceus chromosomes. This is the first clear evidence of the presence of Ty1-copia retrotransposons in the subterminal heterochromatin of E. arundinaceus. Altogether, these results promote the understanding of the diversification of Ty1-copia retrotransposons and shed light on their chromosomal distribution patterns in E. arundinaceus.