Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat

Andrea Louise Harper; Martin Trick; Zhesi He; Leah Clissold; Alison Fellgett; Simon Griffiths; Ian Bancroft

doi:10.1111/pbi.12486

Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat

Andrea Louise Harper, Martin Trick, Zhesi He, Leah Clissold, Alison Fellgett, Simon Griffiths, Ian Bancroft

Research output: Contribution to journal › Article › peer-review

Abstract

Using a combination of de novo transcriptome assembly, a newly-developed 9495-marker transcriptome SNP genetic linkage map and comparative genomics approaches, we developed an ordered set of non-redundant transcripts for each of the sub-genomes of hexaploid wheat: A (47,160 unigenes), B (59,663 unigenes) and D (40,588 unigenes). We used these as reference sequences against which to map Illumina mRNA-seq reads derived from young leaf tissue. Transcript abundance was quantified for each unigene. Using a 3-way reciprocal BLAST approach, 15,527 triplet sets of homoeologues (one from each genome) were identified. Differential expression (P<0.05) was identified for 5,248 unigenes, with 2906 represented at greater abundance than their two homoeologues and 2342 represented at lower abundance than their two homoeologues. Analysis of gene ontology terms revealed no biases between homoeologues. There was no evidence of genome-wide dominance effects, rather the more highly transcribed individual genes were distributed throughout all three genomes. Transcriptome Display Tile Plot (TDTP), a visualization approach based on CMYK colourspace, was developed and used to assess the genome for regions of skewed homoeologue transcript abundance. Extensive striation was revealed, indicative of many small regions of genome dominance (transcripts of homoeologues from one genome more abundant than the others) and many larger regions of genome repression (transcripts of homoeologues from one genome less abundant than the others).

Original language	English
Number of pages	8
Journal	Plant biotechnology journal
Early online date	7 Oct 2015
DOIs	https://doi.org/10.1111/pbi.12486
Publication status	Published - 2015

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10.1111/pbi.12486

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title = "Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat",

abstract = "Using a combination of de novo transcriptome assembly, a newly-developed 9495-marker transcriptome SNP genetic linkage map and comparative genomics approaches, we developed an ordered set of non-redundant transcripts for each of the sub-genomes of hexaploid wheat: A (47,160 unigenes), B (59,663 unigenes) and D (40,588 unigenes). We used these as reference sequences against which to map Illumina mRNA-seq reads derived from young leaf tissue. Transcript abundance was quantified for each unigene. Using a 3-way reciprocal BLAST approach, 15,527 triplet sets of homoeologues (one from each genome) were identified. Differential expression (P<0.05) was identified for 5,248 unigenes, with 2906 represented at greater abundance than their two homoeologues and 2342 represented at lower abundance than their two homoeologues. Analysis of gene ontology terms revealed no biases between homoeologues. There was no evidence of genome-wide dominance effects, rather the more highly transcribed individual genes were distributed throughout all three genomes. Transcriptome Display Tile Plot (TDTP), a visualization approach based on CMYK colourspace, was developed and used to assess the genome for regions of skewed homoeologue transcript abundance. Extensive striation was revealed, indicative of many small regions of genome dominance (transcripts of homoeologues from one genome more abundant than the others) and many larger regions of genome repression (transcripts of homoeologues from one genome less abundant than the others).",

author = "Harper, {Andrea Louise} and Martin Trick and Zhesi He and Leah Clissold and Alison Fellgett and Simon Griffiths and Ian Bancroft",

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T1 - Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat

AU - Harper, Andrea Louise

AU - Trick, Martin

AU - He, Zhesi

AU - Clissold, Leah

AU - Fellgett, Alison

AU - Griffiths, Simon

AU - Bancroft, Ian

PY - 2015

Y1 - 2015

N2 - Using a combination of de novo transcriptome assembly, a newly-developed 9495-marker transcriptome SNP genetic linkage map and comparative genomics approaches, we developed an ordered set of non-redundant transcripts for each of the sub-genomes of hexaploid wheat: A (47,160 unigenes), B (59,663 unigenes) and D (40,588 unigenes). We used these as reference sequences against which to map Illumina mRNA-seq reads derived from young leaf tissue. Transcript abundance was quantified for each unigene. Using a 3-way reciprocal BLAST approach, 15,527 triplet sets of homoeologues (one from each genome) were identified. Differential expression (P<0.05) was identified for 5,248 unigenes, with 2906 represented at greater abundance than their two homoeologues and 2342 represented at lower abundance than their two homoeologues. Analysis of gene ontology terms revealed no biases between homoeologues. There was no evidence of genome-wide dominance effects, rather the more highly transcribed individual genes were distributed throughout all three genomes. Transcriptome Display Tile Plot (TDTP), a visualization approach based on CMYK colourspace, was developed and used to assess the genome for regions of skewed homoeologue transcript abundance. Extensive striation was revealed, indicative of many small regions of genome dominance (transcripts of homoeologues from one genome more abundant than the others) and many larger regions of genome repression (transcripts of homoeologues from one genome less abundant than the others).

AB - Using a combination of de novo transcriptome assembly, a newly-developed 9495-marker transcriptome SNP genetic linkage map and comparative genomics approaches, we developed an ordered set of non-redundant transcripts for each of the sub-genomes of hexaploid wheat: A (47,160 unigenes), B (59,663 unigenes) and D (40,588 unigenes). We used these as reference sequences against which to map Illumina mRNA-seq reads derived from young leaf tissue. Transcript abundance was quantified for each unigene. Using a 3-way reciprocal BLAST approach, 15,527 triplet sets of homoeologues (one from each genome) were identified. Differential expression (P<0.05) was identified for 5,248 unigenes, with 2906 represented at greater abundance than their two homoeologues and 2342 represented at lower abundance than their two homoeologues. Analysis of gene ontology terms revealed no biases between homoeologues. There was no evidence of genome-wide dominance effects, rather the more highly transcribed individual genes were distributed throughout all three genomes. Transcriptome Display Tile Plot (TDTP), a visualization approach based on CMYK colourspace, was developed and used to assess the genome for regions of skewed homoeologue transcript abundance. Extensive striation was revealed, indicative of many small regions of genome dominance (transcripts of homoeologues from one genome more abundant than the others) and many larger regions of genome repression (transcripts of homoeologues from one genome less abundant than the others).

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