Sharma Priyanka, Al-Dossary Othman, Alsubaie Bader, Al-Mssallem Ibrahim, Nath Onkar, Mitter Neena, Rodrigues Alves Margarido Gabriel, Topp Bruce, Murigneux Valentine, Kharabian Masouleh Ardashir, Furtado Agnelo, Henry Robert J
Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia.
College of Agriculture and Food Sciences, King Faisal University, Al Hofuf, Saudi Arabia.
GigaByte. 2021 Jun 10;2021:gigabyte24. doi: 10.46471/gigabyte.24. eCollection 2021.
Advances in DNA sequencing have made it easier to sequence and assemble plant genomes. Here, we extend an earlier study, and compare recent methods for long read sequencing and assembly. Updated Oxford Nanopore Technology software improved assemblies. Using more accurate sequences produced by repeated sequencing of the same molecule (Pacific Biosciences HiFi) resulted in less fragmented assembly of sequencing reads. Using data for increased genome coverage resulted in longer contigs, but reduced total assembly length and improved genome completeness. The original model species, , was also compared with three other species, as well as avocado () and jojoba (). In these angiosperms, increasing sequence data volumes caused a linear increase in contig size, decreased assembly length and further improved already high completeness. Differences in genome size and sequence complexity influenced the success of assembly. Advances in long read sequencing technology continue to improve plant genome sequencing and assembly. However, results were improved by greater genome coverage, with the amount needed to achieve a particular level of assembly being species dependent.
DNA测序技术的进步使得植物基因组的测序和组装变得更加容易。在此，我们扩展了一项早期研究，并比较了近期长读长测序和组装的方法。更新后的牛津纳米孔技术软件改进了组装效果。使用通过对同一分子进行重复测序（太平洋生物科学公司的HiFi技术）产生的更准确序列，使得测序 reads 的组装片段化程度降低。使用增加基因组覆盖度的数据导致重叠群更长，但总组装长度减少且基因组完整性提高。原始模式物种 也与其他三个物种以及鳄梨（ ）和霍霍巴（ ）进行了比较。在这些被子植物中，增加序列数据量导致重叠群大小呈线性增加，组装长度减少，并进一步提高了原本就很高的完整性。基因组大小和序列复杂性的差异影响了组装的成功率。长读长测序技术的进步继续改进植物基因组测序和组装。然而，通过更高的基因组覆盖度可改善结果，实现特定组装水平所需的覆盖度因物种而异。
