Improvements in the sequencing and assembly of plant genomes

Sharma, Priyanka; Al-Dossary, Othman; Alsubaie, Bader; Al-Mssallem, Ibrahim S.; Nath, Onkar; Mitter, Neena; Margarido, Gabriel Rodrigues Alves; Topp, Bruce; Murigneux, Valentine; Masouleh, Ardashir Kharabian; Furtado, Agnelo; Henry, Robert J.

doi:10.46471/gigabyte.24

Cited by 25 publications

(21 citation statements)

References 31 publications

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“…Short-read (Illumina) sequencing data were from Murigneux et al (2020) and long read data (PacBio HiFi) were from Sharma et al (2021a).…”

Section: Sequencing Datamentioning

confidence: 99%

“…Recent advances in long read sequencing technology have allowed a single molecule to be sequenced multiple times to produce long high fidelity reads (HiFi; PacBio) with a base level accuracy of 99.9% (Wenger et al., 2019 ). We have used Macadamia jansenii to compare methods for the sequencing and assembly of plant genomes (Murigneux et al., 2020 ; Sharma et al., 2021a ). This genome has a size (approximately 800 Mb) typical of many plant genomes but with a relatively low heterozygosity (Sharma et al., 2021b ).…”

Section: Introductionmentioning

confidence: 99%

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De novo chromosome level assembly of a plant genome from long read sequence data

et al. 2021

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Recent advances in the sequencing and assembly of plant genomes have allowed the generation of genomes with increasing contiguity and sequence accuracy. Chromosome level genome assemblies using sequence contigs generated from long read sequencing have involved the use of proximity analysis (Hi-C) or traditional genetic maps to guide the placement of sequence contigs within chromosomes. The development of highly accurate long reads by repeated sequencing of circularized DNA (HiFi; PacBio) has greatly increased the size of contigs. We now report the use of HiFiasm to assemble the genome of Macadamia jansenii, a genome that has been used as a model to test sequencing and assembly. This achieved almost complete chromosome level assembly from the sequence data alone without the need for higher level chromosome map information. Eight of the 14 chromosomes were represented by a single large contig (six with telomere repeats at both ends) and the other six assembled from two to four main contigs. The small number of chromosome breaks appears to be the result of highly repetitive regions including ribosomal genes that cannot be assembled by these approaches. De novo assembly of near complete chromosome level plant genomes now appears possible using these sequencing and assembly tools. Further targeted strategies might allow these remaining gaps to be closed.

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“…Short-read (Illumina) sequencing data were from Murigneux et al (2020) and long read data (PacBio HiFi) were from Sharma et al (2021a).…”

Section: Sequencing Datamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

De novo chromosome level assembly of a plant genome from long read sequence data

et al. 2021

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“…Genome sequencing and assembly requires an adequate depth of sequencing. The size of contigs that can be assembled as long read sequence data has been shown to increase in an almost linear way [8]. The size of the assembled genomes reduces slightly with more contiguous assemblies, probably due to the joining of homologous contig ends, as does the completeness [8].…”

Section: Advancesmentioning

confidence: 99%

“…The size of contigs that can be assembled as long read sequence data has been shown to increase in an almost linear way [8]. The size of the assembled genomes reduces slightly with more contiguous assemblies, probably due to the joining of homologous contig ends, as does the completeness [8]. Improved software has also enabled improvements in the assembly of long read sequences [35].…”

Section: Advancesmentioning

confidence: 99%

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Progress in Plant Genome Sequencing

Henry

2022

Applied Biosciences

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The genome sequence of any organism is key to understanding the biology and utility of that organism. Plants have diverse, complex and sometimes very large nuclear genomes, mitochondrial genomes and much smaller and more highly conserved chloroplast genomes. Plant genome sequences underpin our understanding of plant biology and serve as a key platform for the genetic selection and improvement of crop plants to achieve food security. The development of technology that can capture large volumes of sequence data at low costs and with high accuracy has driven the acceleration of plant genome sequencing advancements. More recently, the development of long read sequencing technology has been a key advance for supporting the accurate sequencing and assembly of chromosome-level plant genomes. This review explored the progress in the sequencing and assembly of plant genomes and the outcomes of plant genome sequencing to date. The outcomes support the conservation of biodiversity, adaptations to climate change and improvements in the sustainability of agriculture, which support food and nutritional security.

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Genomics in neglected and underutilized fruit crops: A chromosome‐scale genome sequence of cherimoya (Annona cherimola)

Talavera

Fernandez-Pozo

Matas-Arroyo

et al. 2023

Plants People Planet

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Societal Impact Statement Cherimoya has been an important food source since Pre‐Columbian times in the Americas. Although it is currently considered an underutilized fruit crop, it is still important at the local level in several regions of Central and South America, and has a clear niche for expansion in regions with subtropical climates. However, the availability of genomic resources to facilitate breeding programs and improve the understanding of Annonaceae genetic diversity is limited. In this work, we provide an important resource to fill this knowledge gap, with the hope that it will ultimately increase this crop's resilience under different climate change scenarios, which will increase food security in regions with subtropical climates. Summary Cherimoya (Annona cherimola Mill.) is a perennial fruit tree crop native to the Neotropics valued since pre‐Columbian times by different native American civilizations. It belongs to the Annonaceae, the largest family of the Magnoliid clade, sister to the eudicot and monocot clades of angiosperms. Despite its excellent organoleptic and nutritive qualities, this crop remains underutilized, although it has a clear niche for expansion in regions with subtropical climates. To date, no previous significant genomic information is available for this species, which would be a key tool to optimize breeding programs and advance in the study and conservation of its extant genetic diversity. A combination of different sequencing technologies (Illumina, Pacific Biosciences) has been implemented in order to assemble a chromosome‐level reference genome of A. cherimola. The final reference genome resulted in an assembly of 1.13 Gb and N50 of 170.86 Mb, anchored into seven pseudomolecules and with a completeness of 95.6%. A total of 41,413 protein‐coding genes were identified, many of which were related to secondary metabolism, defense mechanisms, stress response, and development. The results of this study provide novel significant genomic resources not only for cherimoya and other species of the Annonaceae but also for understanding the evolution of the earlier divergent angiosperms.

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Improvements in the sequencing and assembly of plant genomes

Cited by 25 publications

References 31 publications

De novo chromosome level assembly of a plant genome from long read sequence data

De novo chromosome level assembly of a plant genome from long read sequence data

Progress in Plant Genome Sequencing

Genomics in neglected and underutilized fruit crops: A chromosome‐scale genome sequence of cherimoya (Annona cherimola)

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