Genome assembly and annotation of<i>Macadamia tetraphylla</i>

Niu, Ying-Feng; Li, Guohua; Ni, Shu-Bang; He, Xu; Zheng, Cheng; Liu, Ziyan; Gong, Li-Dan; GuangHong, Kong; Liu, Jin

doi:10.1101/2020.03.11.987057

Cited by 8 publications

(10 citation statements)

References 58 publications

(37 reference statements)

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“…The macadamia genus contains 4 species: Macadamia integrifolia, Macadamia tetraphylla, Macadamia ternifolia , and Macadamia jansenii . Macadamia cultivars are diploid (2n = 28), with k -mer–based genome size estimates ranging from 758 Mb for M. tetraphylla [ 7 ] to 896 Mb for M. integrifolia [ 8 ]. The first draft genome assembly of the widely grown M. integrifolia cultivar HAES 741 was constructed from short-read Illumina sequence data and was highly fragmented (518 Mb, 193,493 scaffolds, N50 = 4,745 bp) [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

“…An improved HAES 741 assembly was generated using a combination of long-read Pacific Biosciences (PacBio) and paired-end Illumina sequence data (745 Mb, 4,094 scaffolds, N50 = 413 kb) [ 8 ]. The genome assembly of M. tetraphylla was also recently produced using a combination of long-read Oxford Nanopore Technologies (ONT) and short-read Illumina sequence data (751 Mb, 4,335 contigs, N50 = 1.18 Mb) [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

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Comparison of long-read methods for sequencing and assembly of a plant genome

et al. 2020

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Background Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample. Results Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements. Conclusions The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparison of long-read methods for sequencing and assembly of a plant genome

et al. 2020

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“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted January 22, 2021. ; https://doi.org/10.1101/2021.01.22.427724 doi: bioRxiv preprint N50 of contigs is plotted against the genome coverage. Genome sizes used to calculate coverage were; M.integrifolia, 895Mb [12]; M janseni, 780Mb [2]; M. tetraphylla, 758Mb [23] and M. ternifolia, 758Mb (not known but assumed the same as M. tetraphylla due to similar assembly size). Figure 2 Influence of data volume on assembly for diverse species.…”

Section: Figure Legendsmentioning

confidence: 99%

“…Influence of data volume on assembly for Macadamia species N50 of contigs is plotted against the genome coverage. Genome sizes used to calculate coverage were; M.integrifolia, 895Mb[12]; M janseni, 780Mb[2]; M. tetraphylla, 758Mb[23] and M. ternifolia, 758Mb (not known but assumed the same as M. tetraphylla due to similar assembly size). Influence of data volume on assembly for diverse species.…”

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confidence: 99%

Improvements in the Sequencing and Assembly of Plant Genomes

Sharma

Al-Dossary

Alsubaie

et al. 2021

Preprint

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BackgroundAdvances in DNA sequencing have reduced the difficulty of sequencing and assembling plant genomes. A range of methods for long read sequencing and assembly have been recently compared and we now extend the earlier study and report a comparison with more recent methods.ResultsUpdated Oxford Nanopore Technology software supported improved assemblies. The use of more accurate sequences produced by repeated sequencing of the same molecule (PacBio HiFi) resulted in much less fragmented assembly of sequencing reads. The use of more data to give increased genome coverage resulted in longer contigs (higher N50) but reduced the total length of the assemblies and improved genome completeness (BUSCO). The original model species, Macadamia jansenii, a basal eudicot, was also compared with the 3 other Macadamia species and with avocado (Persea americana), a magnoliid, and jojoba (Simmondsia chinensis) a core eudicot. In these phylogenetically diverse angiosperms, increasing sequence data volumes also caused a highly linear increase in contig size, decreased assembly length and further improved already high completeness. Differences in genome size and sequence complexity apparently influenced the success of assembly from these different species.ConclusionsAdvances in long read sequencing technology have continued to significantly improve the results of sequencing and assembly of plant genomes. However, results were consistently improved by greater genome coverage (using an increased number of reads) with the amount needed to achieve a particular level of assembly being species dependant.

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“…This genome, of cultivar HAES 741, has supported initial efforts at genome based breeding (O'Connor et al, 2018) and has recently been upgraded to chromosome level with a contig N50 of 413 Kb. The other species that has been a contributor to domesticated germplasm, M. tetraphylla, has been sequenced with an N50 of 1.18 Mb (Niu et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

The genome of the endangeredMacadamia janseniidisplays little diversity but represents an important genetic resource for plant breeding

Sharma

Murigneux

Haimovitz

et al. 2021

Preprint

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Macadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the diverse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii, being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 58 Mb and a total 758 Mb genome assembly size of which 56% is repetitive. Completeness assessment revealed that the assembly covered 96.9% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low diversity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies.

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Genome assembly and annotation ofMacadamia tetraphylla

Cited by 8 publications

References 58 publications

Comparison of long-read methods for sequencing and assembly of a plant genome

Comparison of long-read methods for sequencing and assembly of a plant genome

Improvements in the Sequencing and Assembly of Plant Genomes

The genome of the endangeredMacadamia janseniidisplays little diversity but represents an important genetic resource for plant breeding

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