单分子测序（single-molecule real-time sequencing, SMRT）技术由于具有通量高、Contig读长长、拼接容易、仪器和试剂成本低、操作简单等优势而比第二代测序技术有更广阔的应用空间。虽然，很多作物有个自己的基因组序列，但是由于受到技术的限制，很多区域还没有组装完整。SMRT测序技术将可以解决这一问题。
最近，冷泉港实验室利用SMRT技术和高分辨率光学作图技术对玉米的一个参考基因组序列进行了重新的组装和注释。相对于以前的基因组参考序列，本次得到的Contig长度增加了52倍，基因间和端粒区的组装效果明显得到了改善。基因重复区的深入分析揭示了130,000多个转座元件。111,000个全长转录本的SMRT测序使得基因组的注释得到更新。此外，两个玉米自交系的高分辨率光学图谱分析显示出一段共同的缺失区域。完整准确的参考基因组将为玉米功能基因组研究、新基因挖掘、基因组遗传操作带来更大的便利。
Nature, 12 June 2017
Improved maize reference genome with single-molecule technologies
Author
Yinping Jiao, Paul Peluso, Jinghua Shi……Alex Hastie, David R. Rank & Doreen Ware
Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
USDA-ARS, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, USA
Abstract
Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.
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