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The amplification and evolution of orthologous 22-kDa α-prolamin tandemly arrayed genes in coix, sorghum and maize genomes

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Abstract

Tandemly arrayed genes (TAGs) account for about one-third of the duplicated genes in eukaryotic genomes. They provide raw genetic material for biological evolution, and play important roles in genome evolution. The 22-kDa prolamin genes in cereal genomes represent typical TAG organization, and provide the good material to investigate gene amplification of TAGs in closely related grass genomes. Here, we isolated and sequenced the Coix 22-kDa prolamin (coixin) gene cluster (283 kb), and carried out a comparative analysis with orthologous 22-kDa prolamin gene clusters from maize and sorghum. The 22-kDa prolamin gene clusters descended from orthologous ancestor genes, but underwent independent gene amplification paths after the separation of these species, therefore varied dramatically in sequence and organization. Our analysis indicated that the gene amplification model of 22-kDa prolamin gene clusters can be divided into three major stages. In the first stage, rare gene duplications occurred from the ancestor gene copy accidentally. In the second stage, rounds of gene amplification occurred by unequal crossing over to form tandem gene array(s). In the third stage, gene array was further diverged by other genomic activities, such as transposon insertions, segmental rearrangements, etc. Unlike their highly conserved sequences, the amplified 22-kDa prolamin genes diverged rapidly at their expression capacities and expression levels. Such processes had no apparent correlation to age or order of amplified genes within TAG cluster, suggesting a fast evolving nature of TAGs after gene amplification. These results provided insights into the amplification and evolution of TAG families in grasses.

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Abbreviations

TAGs:

Tandemly arrayed genes

UCO:

Unequal crossing over

TEs:

Transposable elements

LTR:

Long terminal repeat

MITEs:

Miniature inverted repeat transposable elements

SINEs:

Short interspersed repetitive elements

mya:

Million years ago

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Acknowledgments

We would like thank Yiwei Yuan for technical support on sequencing analysis, Yuanping Tang for sequence analysis. This work was supported by National Natural Sciences Foundation of China (30671303, 30700472), Ministry of Education of China (NCET-06-0435, 206048), Ministry of Science and Technology of China (2006AA10Z148, 2006AA10A107, 2009CB118400), Fok Ying Tung Education Foundation (101024), Science and Technology Commission of Shanghai Municipality (05PJ14049, 05QMX1424, 09DZ2271800), Education Commission of Shanghai Municipality (05ZZ02), and Shanghai Education Foundation (04SG40).

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  1. Shanghai Key Laboratory of Bio-energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444, Shanghai, People’s Republic of China

    Liangliang Zhou, Binbin Huang, Xiangzong Meng, Gang Wang, Fei Wang, Zhengkai Xu & Rentao Song

  2. Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, People’s Republic of China

    Xiangzong Meng

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  1. Liangliang Zhou
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Correspondence to Rentao Song.

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Zhou, L., Huang, B., Meng, X. et al. The amplification and evolution of orthologous 22-kDa α-prolamin tandemly arrayed genes in coix, sorghum and maize genomes. Plant Mol Biol 74, 631–643 (2010). https://doi.org/10.1007/s11103-010-9705-5

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