The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

Katie Baker, Micha Bayer, Nicola Cook, Steven Dreißig, Taniya Dhillon, Joanne Russell, Pete E Hedley, Jenny Morris, Luke Ramsay, Isabelle Colas, Robbie Waugh, Brian Steffenson, Iain Milne, Gordon Stephen, David Marshall, Andrew J. Flavell*

*Corresponding author for this work

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

The low‐recombining pericentromeric region of the barley genome contains roughly a quarter of the genes of the species, embedded in low‐recombining DNA that is rich in repeats and repressive chromatin signatures. We have investigated the effects of pericentromeric region residency upon the expression, diversity and evolution of these genes. We observe no significant difference in average transcript level or developmental RNA specificity between the barley pericentromeric region and the rest of the genome. In contrast, all of the evolutionary parameters studied here show evidence of compromised gene evolution in this region. First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome. Second, gene duplicates (ohnolog pairs) derived from the cereal whole‐genome duplication event ca. 60MYa have been completely eliminated from the barley pericentromeric region. Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome. Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes.
Original languageEnglish
Pages (from-to)981-992
JournalPlant Journal
Volume79
Issue number6
Early online date20 Jun 2014
DOIs
Publication statusPrint publication - Sep 2014
Externally publishedYes

Fingerprint

Hordeum
barley
Gene Expression
gene expression
Genome
Genes
genome
genes
Duplicate Genes
duplicate genes
Gene Duplication
gene duplication
Internship and Residency
Chromatin
chromatin
RNA
DNA

Cite this

Baker, K., Bayer, M., Cook, N., Dreißig, S., Dhillon, T., Russell, J., ... Flavell, A. J. (2014). The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression. Plant Journal, 79(6), 981-992. https://doi.org/10.1111/tpj.12600
Baker, Katie ; Bayer, Micha ; Cook, Nicola ; Dreißig, Steven ; Dhillon, Taniya ; Russell, Joanne ; Hedley, Pete E ; Morris, Jenny ; Ramsay, Luke ; Colas, Isabelle ; Waugh, Robbie ; Steffenson, Brian ; Milne, Iain ; Stephen, Gordon ; Marshall, David ; Flavell, Andrew J. / The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression. In: Plant Journal. 2014 ; Vol. 79, No. 6. pp. 981-992.
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abstract = "The low‐recombining pericentromeric region of the barley genome contains roughly a quarter of the genes of the species, embedded in low‐recombining DNA that is rich in repeats and repressive chromatin signatures. We have investigated the effects of pericentromeric region residency upon the expression, diversity and evolution of these genes. We observe no significant difference in average transcript level or developmental RNA specificity between the barley pericentromeric region and the rest of the genome. In contrast, all of the evolutionary parameters studied here show evidence of compromised gene evolution in this region. First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome. Second, gene duplicates (ohnolog pairs) derived from the cereal whole‐genome duplication event ca. 60MYa have been completely eliminated from the barley pericentromeric region. Third, local gene duplication in the pericentromeric region is reduced by 29{\%} relative to the rest of the genome. Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes.",
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Baker, K, Bayer, M, Cook, N, Dreißig, S, Dhillon, T, Russell, J, Hedley, PE, Morris, J, Ramsay, L, Colas, I, Waugh, R, Steffenson, B, Milne, I, Stephen, G, Marshall, D & Flavell, AJ 2014, 'The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression', Plant Journal, vol. 79, no. 6, pp. 981-992. https://doi.org/10.1111/tpj.12600

The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression. / Baker, Katie; Bayer, Micha; Cook, Nicola; Dreißig, Steven; Dhillon, Taniya; Russell, Joanne; Hedley, Pete E; Morris, Jenny; Ramsay, Luke; Colas, Isabelle; Waugh, Robbie; Steffenson, Brian; Milne, Iain; Stephen, Gordon; Marshall, David; Flavell, Andrew J.

In: Plant Journal, Vol. 79, No. 6, 09.2014, p. 981-992.

Research output: Contribution to journalArticle

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T1 - The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

AU - Baker, Katie

AU - Bayer, Micha

AU - Cook, Nicola

AU - Dreißig, Steven

AU - Dhillon, Taniya

AU - Russell, Joanne

AU - Hedley, Pete E

AU - Morris, Jenny

AU - Ramsay, Luke

AU - Colas, Isabelle

AU - Waugh, Robbie

AU - Steffenson, Brian

AU - Milne, Iain

AU - Stephen, Gordon

AU - Marshall, David

AU - Flavell, Andrew J.

PY - 2014/9

Y1 - 2014/9

N2 - The low‐recombining pericentromeric region of the barley genome contains roughly a quarter of the genes of the species, embedded in low‐recombining DNA that is rich in repeats and repressive chromatin signatures. We have investigated the effects of pericentromeric region residency upon the expression, diversity and evolution of these genes. We observe no significant difference in average transcript level or developmental RNA specificity between the barley pericentromeric region and the rest of the genome. In contrast, all of the evolutionary parameters studied here show evidence of compromised gene evolution in this region. First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome. Second, gene duplicates (ohnolog pairs) derived from the cereal whole‐genome duplication event ca. 60MYa have been completely eliminated from the barley pericentromeric region. Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome. Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes.

AB - The low‐recombining pericentromeric region of the barley genome contains roughly a quarter of the genes of the species, embedded in low‐recombining DNA that is rich in repeats and repressive chromatin signatures. We have investigated the effects of pericentromeric region residency upon the expression, diversity and evolution of these genes. We observe no significant difference in average transcript level or developmental RNA specificity between the barley pericentromeric region and the rest of the genome. In contrast, all of the evolutionary parameters studied here show evidence of compromised gene evolution in this region. First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome. Second, gene duplicates (ohnolog pairs) derived from the cereal whole‐genome duplication event ca. 60MYa have been completely eliminated from the barley pericentromeric region. Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome. Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes.

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SN - 0960-7412

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