Numbers of Genes in the NBS and RLK Families Vary by More than Four-Fold Within a Plant Species and are Regulated by Multiple Factors

Authors: ZHANG, MEIPING - Texas A&M University; WU, YEN-HSUAN - Texas A&M University; LEE, MI-KYUNG - Texas A&M University; LIU, YUN-HUA - Texas A&M University; RONG, YING - Texas A&M University; SANTOS, TEOFILA - Texas A&M University; WU, CHENGCANG - Texas A&M University; XIE, FANGMING - International Rice Research Institute; Nelson, Randall; ZHANG, HONG-BIN - Texas A&M University

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/21/2010
Publication Date: 6/11/2010
Citation: Zhang, M., Wu, Y., Lee, M., Liu, Y., Rong, Y., Santos, T.S., Wu, C., Xie, F., Nelson, R.L., Zhang, H. 2010. Numbers of Genes in the NBS and RLK Families Vary by More than Four-Fold Within a Plant Species and are Regulated by Multiple Factors. Nucleic Acids Research. Available: doi:10.1093/nar/gkq524.

Interpretive Summary: There are sets of genes that are similar in both form and function and are grouped together into gene families. Nucleotide-binding site-encoding gene (NBS) family and receptor-like kinase (RLK) family are two large gene families with many members involved in disease resistance. Very little is know about the amount of variation in size of these gene families either within or between species. In this research we compared the size of these two gene families among and within three important crop species: rice, soybean and cotton. This study shows that the number of genes in a gene family may vary by multiple fold not only among species, but also among cultivars within species. As expected, the inter-specific variation of the NBS and RLK family sizes agree with those of other gene families observed among species of archaea, bacteria, insects and mammals; however, the intra-specific variation of the gene family sizes provides novel insights into the roles of the gene family size variation in the observed genetic variation. Our data also show that the size variation of one gene family may be correlated with those of other families and these changes could be regulated by a number of factors including natural and human selection. In cotton and soybean, the wild species had more genes in each family but surprisingly in rice the cultivated species had more genes, which may indicate the influence of human selection. These results will be of use to scientists interested in genetic diversity and factors that affect diversity over time and space.

Technical Abstract: Many genes exist in the form of families; however, little is known about their size variation, evolution and biology. Here, we present the size variation and evolution of the nucleotide-binding site (NBS)- encoding gene family and receptor-like kinase (RLK) gene family in Oryza, Glycine and Gossypium. The sizes of both families vary by numeral fold, not only among species, surprisingly, also within a species. The size variations of the gene families are shown to correlate with each other, indicating their interactions, and driven by natural selection, artificial selection and genome size variation, but likely not by polyploidization. The numbers of genes in the families in a polyploid species are similar to those of one of its diploid donors, suggesting that polyploidization plays little roles in the expansion of the gene families and that organisms tend not to maintain their ‘surplus’ genes in the course of evolution. Furthermore, it is found that the size variations of both gene families are associated with organisms’ phylogeny, suggesting their roles in speciation and evolution. Since both selection and speciation act on organism’s morphological, physiological and biological variation, our results indicate that the variation of gene family size provides a source of genetic variation and evolution.