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The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

Qi, Weihong; Lim, Yi-Wen; Patrignani, Andrea; Schläpfer, Pascal; Bratus-Neuenschwander, Anna; Grüter, Simon; Chanez, Christelle; Rodde, Nathalie; Prat, Elisa; Vautrin, Sonia; Fustier, Margaux-Alison; Pratas, Diogo; Schlapbach, Ralph; Gruissem, Wilhelm (2022). The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features. GigaScience, 11:giac028.

Abstract

Background: Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult-to-assemble genome.
Findings: Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present 2 chromosome-scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy >QV46, contig N50 >18 Mb, BUSCO completeness of 99%, and 35k phased gene loci, it is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly so far. Ab initio gene prediction with RNA-seq data and Iso-Seq transcripts identified abundant novel gene loci, with enriched functionality related to chromatin organization, meristem development, and cell responses. During tissue development, differentially expressed transcripts of different haplotype origins were enriched for different functionality. In each tissue, 20-30% of transcripts showed allele-specific expression (ASE) differences. ASE bias was often tissue specific and inconsistent across different tissues. Direction-shifting was observed in <2% of the ASE transcripts. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome rearrangements and abundant intra-genomic and inter-genomic divergent sequences, with large structural variations mostly related to LTR retrotransposons. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding.
Conclusions: The phased and annotated chromosome pairs allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness, and haplotype resolution. They will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy, and continuity.

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Functional Genomics Center Zurich
04 Faculty of Medicine > University Children's Hospital Zurich > Medical Clinic
04 Faculty of Medicine > Institute of Laboratory Animal Science
05 Vetsuisse Faculty > Veterinärwissenschaftliches Institut > Institute of Laboratory Animal Science
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
610 Medicine & health
Scopus Subject Areas:Health Sciences > Health Informatics
Physical Sciences > Computer Science Applications
Uncontrolled Keywords:Computer Science Applications, Health Informatics
Language:English
Date:24 March 2022
Deposited On:05 Aug 2022 17:27
Last Modified:27 Oct 2024 02:41
Publisher:Oxford University Press
ISSN:2047-217X
OA Status:Gold
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/gigascience/giac028
PubMed ID:35333302
Project Information:
  • Funder: Fundação para a Ciência e a Tecnologia
  • Grant ID:
  • Project Title:
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  • Language: English
  • Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)

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