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Diversification of Lrk/Tak kinase gene clusters is associated with subfunctionalization and cultivar-specific transcript accumulation in barley

Abstract

Lrk (Lr10 receptor-like kinase) and Tak (Triticum aestivum kinase) belong to the receptor-like kinase (RLK) supergene family in higher plants. Three Lrk/Tak gene regions spanning greater than 600 kb were identified via a genome-wide survey of barley gene-rich BAC clones. Two Lrk/Tak gene clusters are positioned on barley chromosome 3 (3H) and another is localized on chromosome 5 (1H), with each Lrk and Tak open reading frame physically positioned in a back-to-back orientation. Thirteen new Lrk/Tak-like fragments were cloned from the two clusters on 3H and the single cluster on 1H, respectively, and compared phylogenetically with other grass Lrk/Tak-like genes, including a 280-kb Lrk/Tak cluster on rice chromosome 1S. Physically clustered Lrk/Tak-like genes always form monophyletic groups; this suggests that the primary mechanism of expansion of the Lrk/Tak RLK super family was by tandem duplication, of which most members were duplicated after speciation of the Poaceae. Cultivar-dependent transcript accumulation of some Lrk/Tak family members on 3H, as revealed via Barley1 GeneChip microarray analysis, is consistent with the hypothesis of subfunctionalization of Lrk/Tak members following tandem duplication.

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Acknowledgments

The authors thank Matt Moscou for assistance with the GeneChip expression data and Andris Kleinhofs for providing the MapManager files with the accumulated map data for the Steptoe x Morex mini-mapper set. This research was supported by USDA-National Research Initiative 99-35300-7694 and USDA Initiative for Future Agriculture and Food Systems 2001-52100-11346. This article is a joint contribution of the Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, and The Iowa Agriculture and Home Economics Experiment Station. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.

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Correspondence to Roger P. Wise.

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Supplementary Table 1

Barley ESTs used for overgo development (PDF 54.7 kb)

Supplementary Table 2

Eleven overgo pools and the identification of hybridizing Morex BACS (PDF 123 kb)

Supplementary Fig. 1

NJ tree (unrooted) of representative genes in Lrk, Tak, PR5K-like, and lectin families from rice, barley, wheat, and Arabidopsis. Kinase domain peptides were used to construct the tree with 1,000 bootstrap replicates. Four well-supported major clades belong to the four gene families, which are indicated on the left. Bootstrap values are shown at nodes. Branch length represents number of amino acid substitutions per site. Red arrow indicates a rice Lectin gene, which are within the rice Lrk/Tak gene cluster loci (PDF 14.1 kb)

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Hu, P., Wise, R.P. Diversification of Lrk/Tak kinase gene clusters is associated with subfunctionalization and cultivar-specific transcript accumulation in barley. Funct Integr Genomics 8, 199–209 (2008). https://doi.org/10.1007/s10142-008-0077-8

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  • DOI: https://doi.org/10.1007/s10142-008-0077-8

Keywords

  • Lrk/Tak
  • Duplication
  • Evolution
  • Gene cluster