Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
Genomics Proteomics Bioinformatics. 2023 Jun;21(3):427-439. doi: 10.1016/j.gpb.2023.04.004. Epub 2023 Apr 25.
Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity, highly repetitive sequences, or high ploidy characteristics of complex genomes. Herein, we summarize the challenges of and advances in complex plant genome assembly, including feasible experimental strategies, upgrades to sequencing technology, existing assembly methods, and different phasing algorithms. Moreover, we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes. Finally, we expect that the accurate, gapless, telomere-to-telomere, and fully phased assembly of complex plant genomes could soon become routine.
在过去的 20 年中，测序技术和计算算法的巨大进步推动了植物基因组研究进入了一个繁荣的时代，已经有数百个基因组被破译，范围从非维管束植物到开花植物。然而，复杂植物基因组的组装仍然具有挑战性，由于复杂基因组的高度杂合性、高度重复序列或高倍性特征，传统的测序和组装方法仍然难以完全解决。在此，我们总结了复杂植物基因组组装的挑战和进展，包括可行的实验策略、测序技术的升级、现有的组装方法和不同的相位算法。此外，我们列出了复杂基因组项目的实际案例，供读者参考，以解决未来与复杂基因组相关的问题。最后，我们期望复杂植物基因组的准确、无间隙、端粒到端粒和完全相位组装能够很快成为常规。
