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

2021 ◽  
Author(s):  
Weihong Qi ◽  
Yi-Wen Lim ◽  
Andrea Patrignani ◽  
Pascal Schlaepfer ◽  
Anna Bratus-Neuenschwander ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Cost Effective ◽  
Structural Variations ◽  
Specific Expression ◽  
Tropical Regions ◽  
Reference Quality ◽  
Allele Specific ◽  
High Gene ◽  
Genome Assemblies ◽  
Genome Comparisons

Background: Cassava (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. 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 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. Conclusions: The 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.

scholarly journals Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Joel-E. Kuon ◽  
Weihong Qi ◽  
Pascal Schläpfer ◽  
Matthias Hirsch-Hoffmann ◽  
Philipp Rogalla von Bieberstein ◽  
...  
Keyword(s):  
De Novo ◽  
Haplotype Diversity ◽  
Mosaic Disease ◽  
Cassava Mosaic Disease ◽  
Specific Expression ◽  
Tropical Regions ◽  
Genome Maps ◽  
Gene Sets ◽  
Allele Specific ◽  
Genome Assemblies

Abstract Background Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Cassava breeders often use a single locus, CMD2, for introducing CMD resistance into susceptible cultivars. The CMD2 locus has been genetically mapped to a 10-Mbp region, but its organization and genes as well as their functions are unknown. Results We report haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava cultivar TME (tropical Manihot esculenta), which is the origin of CMD2, and the CMD-susceptible cultivar 60444. The assemblies provide phased haplotype information for over 80% of the genomes. Haplotype comparison identified novel features previously hidden in collapsed and fragmented cassava genomes, including thousands of allelic variants, inter-haplotype diversity in coding regions, and patterns of diversification through allele-specific expression. Reconstruction of the CMD2 locus revealed a highly complex region with nearly identical gene sets but limited microsynteny between the two cultivars. Conclusions The genome maps of the CMD2 locus in both 60444 and TME3, together with the newly annotated genes, will help the identification of the causal genetic basis of CMD2 resistance to geminiviruses. Our de novo cassava genome assemblies will also facilitate genetic mapping approaches to narrow the large CMD2 region to a few candidate genes for better informed strategies to develop robust geminivirus resistance in susceptible cassava cultivars.

scholarly journals Genome-Wide Analysis of Allele-Specific Expression Patterns in Seventeen Tissues of Korean Cattle (Hanwoo)

Animals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 727
Author(s):  
Kyu-Sang Lim ◽  
Sun-Sik Chang ◽  
Bong-Hwan Choi ◽  
Seung-Hwan Lee ◽  
Kyung-Tai Lee ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Expression Patterns ◽  
Monoallelic Expression ◽  
Specific Expression ◽  
Adult Cattle ◽  
Korean Cattle ◽  
Family Trio ◽  
Epigenetic Effects ◽  
Genome Wide ◽  
Allele Specific

The functional hemizygosity could be caused by the MAE of a given gene and it can be one of the sources to affect the phenotypic variation in cattle. We aimed to identify MAE genes across the transcriptome in Korean cattle (Hanwoo). For three Hanwoo family trios, the transcriptome data of 17 tissues were generated in three offspring. Sixty-two MAE genes had a monoallelic expression in at least one tissue. Comparing genotypes among each family trio, the preferred alleles of 18 genes were identified (maternal expression, n = 9; paternal expression, n = 9). The MAE genes are involved in gene regulation, metabolic processes, and immune responses, and in particular, six genes encode transcription factors (FOXD2, FOXM1, HTATSF1, SCRT1, NKX6-2, and UBN1) with tissue-specific expression. In this study, we report genome-wide MAE genes in seventeen tissues of adult cattle. These results could help to elucidate epigenetic effects on phenotypic variation in Hanwoo.

scholarly journals Large structural variations in the haplotype-resolved African cassava genome.

2021 ◽  
Author(s):  
Ben N Mansfeld ◽  
Adam Boyher ◽  
Jeffrey C Berry ◽  
Mark Wilson ◽  
Shujun Ou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Load ◽  
Specific Gene ◽  
Stem Cuttings ◽  
Structural Variations ◽  
Manihot Esculenta Crantz ◽  
Specific Expression ◽  
Global Food Security ◽  
Allele Specific ◽  
Two Phases

Cassava (Manihot esculenta Crantz, 2n=36) is a global food security crop. Cassava has a highly heterozygous genome, high genetic load, and genotype-dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi-C to resolve each haplotype of the genome of a farmer-preferred cassava line, TME7 (Oko-iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON-Phase and Hi-C read data. The ultra-long-range information from Hi-C sequencing was also used for scaffolding. Comparison of the two phases revealed more than 5,000 large haplotype-specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele specific expression was further explored. RNA-seq data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy-to-use web-based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype-specific structural variation, gene hemizygosity, and allele specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava.

scholarly journals Recent Applications of RNA Sequencing in Food and Agriculture

2021 ◽  
Author(s):  
Venkateswara R. Sripathi ◽  
Varsha C. Anche ◽  
Zachary B. Gossett ◽  
Lloyd T. Walker
Keyword(s):  
Rna Sequencing ◽  
Alternative Polyadenylation ◽  
Cost Effective ◽  
Circular Rnas ◽  
Rna Seq ◽  
Complete Collection ◽  
Specific Expression ◽  
Food And Agriculture ◽  
Allele Specific ◽  
Next Generation Sequencing Ngs

RNA sequencing (RNA-Seq) is the leading, routine, high-throughput, and cost-effective next-generation sequencing (NGS) approach for mapping and quantifying transcriptomes, and determining the transcriptional structure. The transcriptome is a complete collection of transcripts found in a cell or tissue or organism at a given time point or specific developmental or environmental or physiological condition. The emergence and evolution of RNA-Seq chemistries have changed the landscape and the pace of transcriptome research in life sciences over a decade. This chapter introduces RNA-Seq and surveys its recent food and agriculture applications, ranging from differential gene expression, variants calling and detection, allele-specific expression, alternative splicing, alternative polyadenylation site usage, microRNA profiling, circular RNAs, single-cell RNA-Seq, metatranscriptomics, and systems biology. A few popular RNA-Seq databases and analysis tools are also presented for each application. We began to witness the broader impacts of RNA-Seq in addressing complex biological questions in food and agriculture.

scholarly journals scHLAcount: Allele-specific HLA expression from single-cell gene expression data

2019 ◽  
Author(s):  
Charlotte A. Darby ◽  
Michael J. T. Stubbington ◽  
Patrick J. Marks ◽  
Álvaro Martínez Barrio ◽  
Ian T. Fiddes
Keyword(s):  
Single Cells ◽  
Expression Patterns ◽  
Allelic Expression ◽  
Loss Of Function ◽  
Cell Type ◽  
Sequencing Data ◽  
Cell Type Specificity ◽  
Specific Expression ◽  
Hla Genes ◽  
Allele Specific

AbstractStudies in bulk RNA sequencing data suggest cell-type and allele-specific expression of the human leukocyte antigen (HLA) genes. These loci are extremely diverse and they function as part of the major histocompatibility complex (MHC) which is responsible for antigen presentation. Mutation and or misregulation of expression of HLA genes has implications in diseases, especially cancer. Immune responses to tumor cells can be evaded through HLA loss of function. However, bulk RNA-seq does not fully disentangle cell type specificity and allelic expression. Here we present scHLAcount, a workflow for computing allele-specific molecule counts of the HLA genes in single cells an individualized reference. We demonstrate that scHLAcount can be used to find cell-type specific allelic expression of HLA genes in blood cells, and detect different allelic expression patterns between tumor and normal cells in patient biopsies. scHLAcount is available at https://github.com/10XGenomics/scHLAcount.

scholarly journals Accurate quantitation of allele-specific expression patterns by analysis of DNA melting

2007 ◽  
Vol 17 (7) ◽  
pp. 1093-1100 ◽  
Author(s):  
S. Jeong ◽  
Y. Hahn ◽  
Q. Rong ◽  
K. Pfeifer
Keyword(s):  
Expression Patterns ◽  
Dna Melting ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

scholarly journals Spatially varying cis-regulatory divergence inDrosophilaembryos elucidates cis-regulatory logic

2017 ◽  
Author(s):  
Peter A. Combs ◽  
Hunter B. Fraser
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Raw Material ◽  
Spatial Patterning ◽  
Rna Seq ◽  
Specific Expression ◽  
Complex Interactions ◽  
Allele Specific ◽  
Spatially Varying ◽  
Cis And Trans

AbstractSpatial patterning of gene expression is a key process in development—responsible for the incredible diversity of animal body plans—yet how it evolves is still poorly understood. Both cis- and trans-acting changes could accumulate and participate in complex interactions, so to isolate the cis-regulatory component of patterning evolution, we measured allele-specific spatial gene expression patterns inD. melanogaster×D. simulanshybrid embryos. RNA-seq of cryosectioned slices revealed 55 genes with strong spatially varying allele-specific expression, and several hundred more with weaker but significant spatial divergence. For example, we found thathunchback (hb), a major regulator of developmental patterning, had reduced expression specifically in the anterior tip ofD. simulansembryos. Mathematical modeling ofhbcis-regulation suggested that a mutation in a Bicoid binding site was responsible, which we verified using CRISPR-Cas9 genome editing. In sum, even comparing morphologically near-identical species we identified a substantial amount of spatial variation in gene expression, suggesting that development is robust to many such changes, but also that natural selection may have ample raw material for evolving new body plans via cis-regulatory divergence.

scholarly journals Allele specific expression in worker reproduction genes in the bumblebee Bombus terrestris

2015 ◽  
Author(s):  
Harindra E Amarasinghe ◽  
Bradley J Toghill ◽  
Despina Nathanael ◽  
Eamonn B Mallon
Keyword(s):  
Bombus Terrestris ◽  
Expression Patterns ◽  
Worker Reproduction ◽  
Imprinted Genes ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

Methylation has previously been associated with allele specific expression in ants. Recently, we found methylation is important in worker reproduction in the bumblebee Bombus terrestris. Here we searched for allele specific expression in twelve genes associated with worker reproduction in bees. We found allele specific expression in Ecdysone 20 monooxygenase and IMP-L2-like. Although we were unable to confirm a genetic or epigenetic cause for this allele specific expression, the expression patterns of the two genes match those predicted for imprinted genes.

scholarly journals Highly Genotype- and Tissue-specific Single-Parent Expression Drives Dynamic Gene Expression Complementation in Maize Hybrids

2019 ◽  
Author(s):  
Zhi Li ◽  
Peng Zhou ◽  
Rafael Della Coletta ◽  
Tifu Zhang ◽  
Alex B. Brohammer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Single Parent ◽  
Specific Expression ◽  
Data Set ◽  
Tissue Specific ◽  
Allele Specific ◽  
Silent Allele ◽  
Almost All

AbstractMaize exhibits tremendous gene expression variation between different lines. Complementation of diverse gene expression patterns in hybrids could play an important role in the manifestation of heterosis. In this study, we used transcriptome data of five different tissues from 33 maize inbreds and 89 hybrids (430 samples in total) to survey the global gene expression landscape of F1-hybrids relative to their inbred parents. Analysis of this data set revealed that single parent expression (SPE), which is defined as gene expression in only one of the two parents, while commonly observed, is highly genotype- and tissue-specific. Genes that have SPE in at least one pair of inbreds also tend to be tissue-specific. Genes with SPE caused by genomic presence/absence variation (PAV SPE) are much more frequently expressed in hybrids than genes that are present in the genome of both inbreds, but expressed in only a single-parent (non-PAV SPE) (74.7% vs. 59.7%). For non-PAV SPE genes, allele specific expression was used to investigate whether parental alleles not expressed in the inbred line (“silent allele”) can be actively transcribed in the hybrid. We found that expression of the silent allele in the hybrid is relatively rare (∼6.3% of non-PAV SPE genes), but is observed in almost all hybrids and tissues. Non-PAV SPE genes with expression of the silent allele in the hybrid are more likely to exhibit above high-parent expression level in the hybrid than those that do not express the silent allele. Finally, both PAV SPE and non-PAV SPE genes are highly enriched for being classified as non-syntenic, but depleted for curated genes with experimentally determined functions. This study provides a more comprehensive understanding of the potential role of non-PAV SPE and PAV SPE genes in heterosis.

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