The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features
| Autor: | 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 |
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| Přispěvatelé: | University of Zurich, Qi, Weihong, Gruissem, Wilhelm, Medicum, Department of Virology, University of Helsinki, Virus infections and immunity |
| Rok vydání: | 2022 |
| Předmět: |
11832 Microbiology and virology
IDENTIFICATION ASSEMBLIES food and beverages 610 Medicine & health 10071 Functional Genomics Center Zurich Health Informatics allele-specific expression VARIANTS FAMILIES Computer Science Applications 10036 Medical Clinic haplotype heterozygosity PROGRAM 1706 Computer Science Applications QUALITY TOOL 570 Life sciences biology 590 Animals (Zoology) 10239 Institute of Laboratory Animal Science pan-genome POPULATION-GENETICS 3111 Biomedicine phased chromosome pairs 2718 Health Informatics |
| Zdroj: | GigaScience, 11 |
| ISSN: | 2047-217X |
| DOI: | 10.5167/uzh-219577 |
| Popis: | 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 GigaScience, 11 ISSN:2047-217X |
| Databáze: | OpenAIRE |
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