2012年1月11日星期三

gene family evolution - two papers


1

Unusual signatures of highly adaptable R-loci in closely-related Arabidopsis species.

Source

State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, China.

Abstract

Plant resistance genes (R-genes) evolve rapidly in response to changing environments. What are the most remarkable signatures of fast adaptive genes, besides the commonly revealed rapid divergence and high non-synonymous substitution rate? Here we investigated these changes in five R-loci following recent differentiation between Arabidopsis thaliana and Arabidopsis lyrataExtremedifferences in evolutionary rates were observede.g., an overall 5.46-9.83-fold different nucleotide diversity at two R-loci betweenspeciesten-fold higher non-synonymous substitution rates within one species versus the othersignificantly different Ka/Ks ratiosbetween species for the same R-geneand high interspecific divergence at one R-locusParticularlywe observed an elevated level oftrans-specific polymorphism at one R-locus and a differentially maintained presence/absence polymorphism at anotherThe highfrequency of ancestral polymorphisms amongst R-genes suggests that the persistence of some functional variation is an importantevolutionary mechanism shaping genetic variation in R-geneswhile the variation of presence/absence polymorphisms provides apotential mechanism for malleable activation of adaptive resistance response pathwaysThe distinct patterns among R-genes suggestthat the same R-gene ortholog can be quickly shaped by different evolutionary processese.g., purifying selection in one species butpositive selection in a closely-related species.
Copyright © 2011 Elsevier B.V. All rights reserved.
PMID:
 
21664259
 
[PubMed - indexed for MEDLINE]
Click here to read
2
J Mol Evol. 2011 Jun;72(5-6):498-509. doi: 10.1007/s00239-011-9448-1. Epub 2011 May 31.

Co-variation among major classes of LRR-encoding genes in two pairs of plant species.

Source

State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, China.

Abstract

NBS-LRR (nucleotide-binding site-leucine-rich repeat), LRR-RLK (LRR-receptor-like kinase), and LRR-only are the three major LRR-encoding genes. Owing to the crucial role played by them in plant resistance, development, and growth, extensive studies have been performed on the NBS-LRR and LRR-RLK genes. However, few studies have focused on these genes collectively; they may co-vary as all of them contain LRR motifs. To investigate their common evolutionary patterns, all major classes of LRR-encoding genes were identified in 12 plant species, and particularly compared in two pairs of close relatives, Arabidopsis thaliana-A. lyrata (At-Al) and Zea mays-Sorghum bicolor. Our results showed that these genes co-vary significantly in terms of their numbers between species and that the genes with certain evolutionary parameters are most likely to have similar functions. The development-related genes have clear orthologous relationships between closely related species, as well as lower nucleotide divergence, and Ka/Ks ratio. In contrast, resistance-related genes have exactly opposite characteristics and favor 11-15 LRRs per gene. This association could be very useful in predicting the function of LRR-encoding genes. The presence of co-variation suggests that LRRs, combined with other domains, can work better in some common functions. In order to cooperate efficiently, there should be balanced gene numbers among the different gene classes.
PMID:
 
21626302
 
[PubMed - indexed for MEDLINE]
Click here to read

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