Comparative analysis of the genetic variability within the Q-type C2H2 zinc-finger transcription factors in the economically important cabbage, canola and ... View Full Text


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Article Info

DATE

2018-12

AUTHORS

Susan D. Lawrence, Nicole G. Novak

ABSTRACT

Background: Brassica oleracea, B. rapa and B. napus encompass many economically important vegetable and oil crops; such as cabbage, broccoli, canola and Chinese cabbage. The genome sequencing of these species allows for gene discovery with an eye towards discerning the natural variability available for future breeding. The Q-type C2H2 zinc-finger protein (ZFP) transcription factors contain zinc finger motifs with a conserved QALGGH as part of the motif and they may play a critical role in the plants response to stress. While they may contain from one to five ZF domains (ZFD) this work focuses on the ZFPs that contain two zinc-fingers, which bind to the promoter of genes, and negatively regulate transcription via the EAR motif. B. oleracea and rapa are diploid and evolved into distinct species about 3.7 million years ago. B. napus is polyploid and formed by fusion of the diploids about 7500 years ago. Results: This work identifies a total of 146 Q-type C2H2-ZFPs with 37 in B. oleracea, 35 in B. rapa and 74 in B. napus. The level of sequence similarity and arrangement of these genes on their chromosomes have mostly remained intact in B. napus, when compared to the chromosomes inherited from either B. rapa or oleracea. In contrast, the difference between the protein sequences of the orthologs of B. rapa and oleracea is greater and their organization on the chromosomes is much more divergent. In general, the 146 proteins are highly conserved especially within the known motifs. Differences within subgroups of ZFPs were identified. Considering that B. napus has twice the number of these proteins in its genome, RNA-Seq data was mined and the expression of 68 of the 74 genes was confirmed. Conclusion: Alignment of these proteins gives a snapshot of the variability that may be available naturally in Brassica species. The aim is to study how different ZFPs bind different genes or how dissimilar EAR motifs alter the negative regulation of the genes bound to the ZFP. Results from such studies could be used to enhance tolerance in future Brassica breeding programs. More... »

PAGES

29

References to SciGraph publications

  • 2013-12. Bolbase: a comprehensive genomics database for Brassica oleracea in BMC GENOMICS
  • 2004-12. Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome in BMC GENOMICS
  • 2015-10. Mining the Brassica oleracea Genome for Q-type C2H2 Zinc Finger Transcription Factor Genes in PLANT MOLECULAR BIOLOGY REPORTER
  • 2014-12. Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana in BMC GENOMICS
  • 2014-12. Tolerance induction to human stem cell transplants with extension to their differentiated progeny in NATURE COMMUNICATIONS
  • 2011-10. The genome of the mesopolyploid crop species Brassica rapa in NATURE GENETICS
  • 2014-06. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea in GENOME BIOLOGY
  • 2016-04. Genome wide identification of C1-2i zinc finger proteins and their response to abiotic stress in hexaploid wheat in MOLECULAR GENETICS AND GENOMICS
  • 1999-04. Zinc-finger proteins: the classical zinc finger emerges in contemporary plant science in PLANT MOLECULAR BIOLOGY
  • 2014-09. C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses in FUNCTIONAL & INTEGRATIVE GENOMICS
  • 2014-12. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes in NATURE COMMUNICATIONS
  • 2017-06. Transcriptome wide identification, phylogenetic analysis, and expression profiling of zinc-finger transcription factors from Crocus sativus L. in MOLECULAR GENETICS AND GENOMICS
  • 2007-11. Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis in PLANT MOLECULAR BIOLOGY
  • 2008-04. The zinc finger network of plants in CELLULAR AND MOLECULAR LIFE SCIENCES
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    49 schema:description Background: Brassica oleracea, B. rapa and B. napus encompass many economically important vegetable and oil crops; such as cabbage, broccoli, canola and Chinese cabbage. The genome sequencing of these species allows for gene discovery with an eye towards discerning the natural variability available for future breeding. The Q-type C2H2 zinc-finger protein (ZFP) transcription factors contain zinc finger motifs with a conserved QALGGH as part of the motif and they may play a critical role in the plants response to stress. While they may contain from one to five ZF domains (ZFD) this work focuses on the ZFPs that contain two zinc-fingers, which bind to the promoter of genes, and negatively regulate transcription via the EAR motif. B. oleracea and rapa are diploid and evolved into distinct species about 3.7 million years ago. B. napus is polyploid and formed by fusion of the diploids about 7500 years ago. Results: This work identifies a total of 146 Q-type C2H2-ZFPs with 37 in B. oleracea, 35 in B. rapa and 74 in B. napus. The level of sequence similarity and arrangement of these genes on their chromosomes have mostly remained intact in B. napus, when compared to the chromosomes inherited from either B. rapa or oleracea. In contrast, the difference between the protein sequences of the orthologs of B. rapa and oleracea is greater and their organization on the chromosomes is much more divergent. In general, the 146 proteins are highly conserved especially within the known motifs. Differences within subgroups of ZFPs were identified. Considering that B. napus has twice the number of these proteins in its genome, RNA-Seq data was mined and the expression of 68 of the 74 genes was confirmed. Conclusion: Alignment of these proteins gives a snapshot of the variability that may be available naturally in Brassica species. The aim is to study how different ZFPs bind different genes or how dissimilar EAR motifs alter the negative regulation of the genes bound to the ZFP. Results from such studies could be used to enhance tolerance in future Brassica breeding programs.
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