Gene expression analysis provides insight into the physiology of the important staple food crop cassava

Mutka, Andrew M.; Hummel, Aaron W.; Berry, Jeffrey C.; Chauhan, Raj Deepika; Vijayaraghavan, Anupama; Voytas, Daniel F.; Chitwood, Daniel H.; Bart, Rebecca

doi:10.1101/073213

Cited by 2 publications

(3 citation statements)

References 26 publications

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“…Wilson et al . used the Plant Total RNA 88 Kit (Sigma) for RNA extraction from non‐meristematic cassava tissues and the Arcturus PicoPure 89 RNA Isolation Kit for total RNA extraction from the shoot and root apical meristematic (SAM and RAM, respectively) cassava tissues. However, these kits are expensive and suitable only for analyzing a small amount of RNA from SAM and RAM, which reduces their applicability for RNA‐Seq library construction and qRT‐PCR, which require a large amount of RNA.…”

Section: Resultsmentioning

confidence: 99%

An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)

et al. 2019

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We developed and modified a precise, rapid, and reproducible protocol isolating high‐quality RNA from tissues of multiple varieties of cassava plants (Manihot esculenta Crantz). The resulting method is suitable for use in mini, midi, and maxi preparations and rapidly achieves high total RNA yields (170–600 μg·g−1) using low‐cost chemicals and consumables and with minimal contamination from polysaccharides, polyphenols, proteins, and other secondary metabolites. In particular, A260 : A280 ratios were > 2.0 for RNA from various tissues, and all of the present RNA samples yielded ribosomal integrity number values of greater than six. The resulting high purity and quality of isolated RNA will facilitate downstream applications (quantitative reverse transcriptase‐polymerase chain reaction or RNA sequencing) in cassava molecular breeding.

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Section: Resultsmentioning

confidence: 99%

An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)

et al. 2019

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“…In such cases, analyzing RNA-seq data using one haploid set of genes/transcripts as the reference could potentially miss haplotype-specific, novel expression patterns. Therefore we re-analyzed the previously published [31] RNA-seq data (Supplementary table 10) generated from two different tissues (TME204 leaf vs. stem) using our reference transcriptome of 119,805 unique transcripts, including both haplotype-specific isoforms and allelic pairs of common isoforms. In TME204 leaf and stem, 64,992 (54%) of transcripts were expressed, 6,696 (6%) transcripts showed significant difference in expression (Fold change above 4, adjusted p-value < 0.001).…”

Section: Tissue Specific Differentially Expressed Transcriptsmentioning

confidence: 99%

“…Unique transcripts were quality-controlled, filtered and classified using SQANTI3 (v4.1) [81] to identify novel transcripts and gene models. In detail, previously published Illumina RNA-seq data (Supplementary table 10) from TME204 [82] were used to check PacBio transcript coverage. Transcripts in which junction sites had low Illumina RNA-seq read support (<4) were filtered out.…”

Section: Repeat Modeling Genome Masking and Annotationmentioning

confidence: 99%

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

Lim

Patrignani

et al. 2021

Preprint

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BackgroundCassava (Manihot esculenta) is an important clonally propagated food crop in tropical and sub-tropical regions worldwide. Genetic gain by molecular breeding is limited because cassava has a highly heterozygous, repetitive and difficult to assemble genome.FindingsHere 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 two chromosome scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. Genome comparisons revealed extensive chromosome re-arrangements and abundant intra-genomic and inter-genomic divergent sequences despite high gene synteny, with most large structural variations being LTR-retrotransposon related. Allele-specific expression analysis of different tissues based on the haplotype-resolved transcriptome identified both stable and inconsistent alleles with imbalanced expression patterns, while most alleles expressed coordinately. Among tissue-specific differentially expressed transcripts, coordinately and biasedly regulated transcripts were functionally enriched for different biological processes. 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.ConclusionsThe haplotype-resolved genome allows the first systematic view of the heterozygous diploid genome organization in cassava. The completely phased and annotated chromosome pairs 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.

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Gene expression analysis provides insight into the physiology of the important staple food crop cassava

Cited by 2 publications

References 26 publications

An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)

An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

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