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

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Qi , W , Lim , Y-W , Patrignani , A , Schlaepfer , P , Bratus-Neuenschwander , A , Gruter , S , Chanez , C , Rodde , N , Prat , E , Vautrin , S , Fustier , M-A , Pratas , D , Schlapbach , R & Gruissem , W 2022 , ' The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features ' , GigaScience , vol. 11 , 028 . https://doi.org/10.1093/gigascience/giac028

Title: The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features
Author: Qi, Weihong; Lim, Yi-Wen; Patrignani, Andrea; Schlaepfer, Pascal; Bratus-Neuenschwander, Anna; Gruter, Simon; Chanez, Christelle; Rodde, Nathalie; Prat, Elisa; Vautrin, Sonia; Fustier, Margaux-Alison; Pratas, Diogo; Schlapbach, Ralph; Gruissem, Wilhelm
Contributor organization: Medicum
Department of Virology
University of Helsinki
Date: 2022-03-24
Language: eng
Number of pages: 21
Belongs to series: GigaScience
ISSN: 2047-217X
DOI: https://doi.org/10.1093/gigascience/giac028
URI: http://hdl.handle.net/10138/346336
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
Subject: phased chromosome pairs
haplotype heterozygosity
pan-genome
allele-specific expression
POPULATION-GENETICS
VARIANTS
QUALITY
TOOL
IDENTIFICATION
ASSEMBLIES
FAMILIES
PROGRAM
3111 Biomedicine
11832 Microbiology and virology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


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