ArticleThe Plant journal : for cell and molecular biology2021
Large structural variations in the haplotype-resolved African cassava genome.
Article in The Plant journal : for cell and molecular biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 37 citations in OpenAlex.
- Universal orthologs infer deep phylogenies and improve genome quality assessments.BMC biology · 2025Article
- A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava.Genome biology · 2025Article
- The haplotype-resolved assembly of COL40 a cassava (Manihot esculenta) line with broad-spectrum resistance against viruses causing Cassava brown streak disease unveils a region of highly repeated elements on chromosome 12.G3 (Bethesda, Md.) · 2025Article
- Article
- Chromosome-scale and haplotype-resolved genome assembly ofHorticulture research · 2025Article
- Haplotype-resolved genome assembly of Ficus carica L. reveals allele-specific expression in the fruit.The Plant journal : for cell and molecular biology · 2025Article
- Article
- A data-driven genome annotation approach for cassava.The Plant journal : for cell and molecular biology · 2024Article
- CRISPR/Cas9-generated mutations in a sugar transporter gene reduce cassava susceptibility to bacterial blight.Plant physiology · 2024Article
- Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta).Scientific data · 2023Article
- Decoupling subgenomes within hybrid lavandin provide new insights into speciation and monoterpenoid diversification of Lavandula.Plant biotechnology journal · 2023Article
- Recent Advances in Assembly of Complex Plant Genomes.Genomics, proteomics & bioinformatics · 2023Review
- Fully sequencing the cassava full-length cDNA library reveals unannotated transcript structures and alternative splicing events in regions with a high density of single nucleotide variations, insertions-deletions, and heterozygous sequences.Plant molecular biology · 2023Article
- Haplotype-resolved DNA methylome of African cassava genome.Plant biotechnology journal · 2023Article
- Improving cassava bacterial blight resistance by editing the epigenome.Nature communications · 2023Article
- Core circadian clock and light signaling genes brought into genetic linkage across the green lineage.Plant physiology · 2022Article
- Assembly of complete diploid-phased chromosomes from draft genome sequences.G3 (Bethesda, Md.) · 2022Article
- Mutations in DNA polymerase δ subunit 1 co-segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses.Nature communications · 2022Article
- Maximizing value of genetic sequence data requires an enabling environment and urgency.Global food security · 2022Article
- Dissection of leucine-rich repeat receptor-like protein kinases: insight into resistance toPeerJ · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cassava (Manihot esculenta Crantz, 2n = 36) is a global food security crop. It has a highly heterozygous genome, high genetic load, and genotype-dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi-C to resolve each haplotype of the genome of a farmer-preferred cassava line, TME7 (Oko-iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON-Phase and Hi-C read data. The ultralong-range information from Hi-C sequencing was also used for scaffolding. Comparison of the two phases revealed >5000 large haplotype-specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele-specific expression was further explored. RNA-sequencing data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy-to-use web-based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype-specific structural variation, gene hemizygosity, and allele-specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.