Improvements in the Sequencing and Assembly of Plant Genomes
Priyanka Sharma, Othman Al-dossary, Bader Alsubaie, Ibrahim Al-mssallem, Onkar Nath, Neena Mitter, Gabriel Rodrigues Alves Margarido, Bruce Topp, Valentine Murigneux, Ardashir Kharabian Masouleh, Agnelo Furtado, Robert J. Henry, Improvements in the sequencing and assembly of plant genomes, Gigabyte, 1, 2021 https://doi.org/10.46471/gigabyte.24
Abstract
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, Macadamia jansenii, was also compared with three other Macadamia species, as well as avocado (Persea americana) and jojoba (Simmondsia chinensis). 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.
https://doi.org/10.46471/gigabyte.24
GIH contribution
As a follow on from the GIH funded project "Assembly of complex genome (Macadamia) using single molecule sequencing", Dual GIH and QCIF team member Valentine Murigneux contributed to this publication through her involvement in the conceptualization, data curation, funding aquisition and drafting of the manuscript.
This article is the first update article pulished by the journal GigByte. The original article produced through the GIH collaborative project is published in GigaScience:
Valentine Murigneux, Subash Kumar Rai, Agnelo Furtado, Timothy J C Bruxner, Wei Tian, Ivon Harliwong, Hanmin Wei, Bicheng Yang, Qianyu Ye, Ellis Anderson, Qing Mao, Radoje Drmanac, Ou Wang, Brock A Peters, Mengyang Xu, Pei Wu, Bruce Topp, Lachlan J M Coin, Robert J Henry, Comparison of long-read methods for sequencing and assembly of a plant genome, GigaScience, Volume 9, Issue 12, December 2020, giaa146, https://doi.org/10.1093/gigascience/giaa146
