ArticleThe Plant journal : for cell and molecular biology2022
De novo chromosome level assembly of a plant genome from long read sequence data.
Article in The Plant journal : for cell and molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A highly contiguous chromosome-level genome assembly of the Chilean jack mackerel Trachurus murphyi.Scientific data · 2026Article
- A chromosome-level genome assembly of Solanum brevicaule (PI 473011) Y1-5, a wild potato relative with robust resistance to potato cyst nematodes.The plant genome · 2026Article
- De novo assembly, gene annotation and marker development using illumina paired-end transcriptome sequences in nutmeg (3 Biotech · 2025Article
- De novo, high-quality assembly and annotation of the halophyte grass Aeluropus littoralis draft genome and identification of A20/AN1 zinc finger protein family.BMC plant biology · 2025Article
- A de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes.G3 (Bethesda, Md.) · 2024Article
- A chromosome-level genome of mango exclusively from long-read sequence data.The plant genome · 2024Article
- Genome assembly of Medicago truncatula accession SA27063 provides insight into spring black stem and leaf spot disease resistance.BMC genomics · 2024Article
- Reproducibility of next-generation-sequencing-based analysis of a CRISPR/Cas9 genome edited oil seed rape.Food chemistry. Molecular sciences · 2023Article
- Improving the Completeness of Chromosome-Level Assembly by Recalling Sequences from Lost Contigs.Genes · 2023Article
- A gap-free reference genome reveals structural variations associated with flowering time in rapeseed (Horticulture research · 2023Article
- Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.bioRxiv : the preprint server for biology · 2023Article
- A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes.Frontiers in plant science · 2023Article
- A de novo genome assembly of Solanum verrucosum Schlechtendal, a Mexican diploid species geographically isolated from other diploid A-genome species of potato relatives.G3 (Bethesda, Md.) · 2022Article
- Macadamia germplasm and genomic database (MacadamiaGGD): A comprehensive platform for germplasm innovation and functional genomics inFrontiers in plant science · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.