FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4221003137> ?p ?o ?g. }

• W4221003137 abstract "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.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.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." @default.
• W4221003137 created "2022-04-03" @default.
• W4221003137 creator A5006955632 @default.
• W4221003137 creator A5011479934 @default.
• W4221003137 creator A5028555979 @default.
• W4221003137 creator A5033629219 @default.
• W4221003137 creator A5034585384 @default.
• W4221003137 creator A5037036136 @default.
• W4221003137 creator A5039856975 @default.
• W4221003137 creator A5051149759 @default.
• W4221003137 creator A5051693451 @default.
• W4221003137 creator A5056584449 @default.
• W4221003137 creator A5063536926 @default.
• W4221003137 creator A5067055554 @default.
• W4221003137 creator A5075174734 @default.
• W4221003137 creator A5089938252 @default.
• W4221003137 date "2022-01-01" @default.
• W4221003137 modified "2023-10-09" @default.
• W4221003137 title "The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features" @default.
• W4221003137 cites W1598134722 @default.
• W4221003137 cites W1600438564 @default.
• W4221003137 cites W1983403167 @default.
• W4221003137 cites W2010361633 @default.
• W4221003137 cites W2020134788 @default.
• W4221003137 cites W2023275563 @default.
• W4221003137 cites W2035628732 @default.
• W4221003137 cites W2050534163 @default.
• W4221003137 cites W2051916497 @default.
• W4221003137 cites W2063368594 @default.
• W4221003137 cites W2067020018 @default.
• W4221003137 cites W2070342831 @default.
• W4221003137 cites W2084301655 @default.
• W4221003137 cites W2102843862 @default.
• W4221003137 cites W2107772251 @default.
• W4221003137 cites W2112814753 @default.
• W4221003137 cites W2115501618 @default.
• W4221003137 cites W2122138951 @default.
• W4221003137 cites W2124205617 @default.
• W4221003137 cites W2134907628 @default.
• W4221003137 cites W2135361281 @default.
• W4221003137 cites W2136145671 @default.
• W4221003137 cites W2136267660 @default.
• W4221003137 cites W2141292707 @default.
• W4221003137 cites W2151899848 @default.
• W4221003137 cites W2153218781 @default.
• W4221003137 cites W2155340974 @default.
• W4221003137 cites W2160378127 @default.
• W4221003137 cites W2168546919 @default.
• W4221003137 cites W2170747616 @default.
• W4221003137 cites W2179438025 @default.
• W4221003137 cites W2323326409 @default.
• W4221003137 cites W2340858006 @default.
• W4221003137 cites W2422772473 @default.
• W4221003137 cites W2538143681 @default.
• W4221003137 cites W2547365070 @default.
• W4221003137 cites W2581859137 @default.
• W4221003137 cites W2582800429 @default.
• W4221003137 cites W2583377988 @default.
• W4221003137 cites W2772231999 @default.
• W4221003137 cites W2784788330 @default.
• W4221003137 cites W2789843538 @default.
• W4221003137 cites W2809646241 @default.
• W4221003137 cites W2897774129 @default.
• W4221003137 cites W2901620691 @default.
• W4221003137 cites W2916627756 @default.
• W4221003137 cites W2941072767 @default.
• W4221003137 cites W2952615074 @default.
• W4221003137 cites W2962807110 @default.
• W4221003137 cites W2968499116 @default.
• W4221003137 cites W2969330652 @default.
• W4221003137 cites W2970442701 @default.
• W4221003137 cites W2972606315 @default.
• W4221003137 cites W2973833463 @default.
• W4221003137 cites W2977428858 @default.
• W4221003137 cites W2977727682 @default.
• W4221003137 cites W2985175171 @default.
• W4221003137 cites W3002583775 @default.
• W4221003137 cites W3017049640 @default.
• W4221003137 cites W3027273802 @default.
• W4221003137 cites W3042732083 @default.
• W4221003137 cites W3042744518 @default.
• W4221003137 cites W3049406222 @default.
• W4221003137 cites W3085758516 @default.
• W4221003137 cites W3090734171 @default.
• W4221003137 cites W3092652421 @default.
• W4221003137 cites W3096101680 @default.
• W4221003137 cites W3113006061 @default.
• W4221003137 cites W3113162057 @default.
• W4221003137 cites W3120801906 @default.
• W4221003137 cites W3128198169 @default.
• W4221003137 cites W3152736521 @default.
• W4221003137 cites W3156911762 @default.
• W4221003137 cites W3159728495 @default.
• W4221003137 cites W3180961869 @default.
• W4221003137 cites W3189835550 @default.
• W4221003137 cites W4221003137 @default.
• W4221003137 cites W4238708183 @default.
• W4221003137 cites W4247163635 @default.
• W4221003137 doi "https://doi.org/10.1093/gigascience/giac028" @default.
• W4221003137 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/35333302" @default.

• next