**5. References**


Gene duplication is rampant. It should be noted that the products depicted above show considerable variation both in number of, and distances between, the LRR domains. Where, when and how do the genes listed here function? For most of them there is no evidence that they deliver innate immunity in the plant. Of course, some of them do! For many the function is not known. Gene duplications, carrying amino acid changes resulting from mutations, often end in neofunctionalization even though duplicate genes may also merely provide tissue specific expression for the original ancestral gene. Subsequent alternate splicing of genes, in turn, might also give new roles to the genes. But if domains are the units that built proteins, then domain shuffling provides a more efficient source for expressed gene versatility: (Thereby, nature promotes evolution of disparate proteins for novel functions.) Most of the genes listed in this chapter certainly exist because of duplication. These genes could be grouped further, however, because another domain had first been added for the projected protein molecules, long before the gene duplications occurred. Possibly, domains represent the evolutionary building blocks for all proteins. At present we can only speculate as to the mechanism of such random multi-domain protein formation. Were transposons involved? (Retroprocession, the process that is responsible for pseudogene formation, possibly could have also facilitated the creation of new disparate proteins!). Specific domain combinations might have been built randomly – maybe sometimes just once during the evolution of an organism – and then sometimes only to be rearranged during duplication or even to loose domains by

mutating them away thereafter. (.See e.g..the Strubbelig family members 1-8.)

Amano Y, Tsubouchi H, Shinohara H. et al. Tyrosine-sulfated glycopeptides involved in cellular proliferation and expansion in Arabidopsis, PNAS (2007) 104: 18333-8. Bhave NS, Veley KM, Nadeau JA, et al. Mutations of TMM causes stomatal patterning

Ceserani T, Trofka A, Gandora N, et al. VH1/BRL2 receptor-like kinase interacts with

Chevalier D, Batoux M, Fulton L, et al. Strubbelig defines a receptor kinase mediating

Clark SE, Williams RW, Myerowitz EM, The Clavata 1 gene encodes a putative receptor

Dangl JL, Jones JDG, Plant pathogens and integrated defence responses to infection, Nature

DeYoung BJ, Clark SE, Signalling through the Clavata 1 Receptor complex, Plant Mol Biol

defects in leaves and eliminates stomata formation in stems, Planta (2009) 229: 357-

vascular-specific adaptor proteins VIT and VIK to influence leaf venation, Plant J

signaling pathway regulating organ development in Arabidopsis, PNAS (2005) 102:

kinase that controls shoot and floral meristem size in Arabidopsis, Cell (1997)

**4. Conclusion** 

**5. References** 

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**6** 

*Spain* 

**Partial Gene Duplication and the** 

*Fabra (UPF) - Institut Municipal d'Investigació Mèdica (IMIM)* 

*2Catalan Institution for Research and Advanced Studies (ICREA), Barcelona* 

Macarena Toll-Riera1, Steve Laurie1, Núria Radó-Trilla1 and M.Mar Albà1,2 *1Evolutionary Genomics Group, Biomedical Informatics Programme, Universitat Pompeu* 

The publication of the first fully sequenced genomes represented a landmark in the biological sciences. The comparison of genomes from different organisms provides us with unprecedented opportunities to address many long-standing evolutionary questions in a

The availability of several genomes from related organisms permits the identification of newly evolved genes in different lineages or species, the study of their mechanisms of formation and the investigation of their role in adapting to new environments or physiological conditions (Domazet-Loso & Tautz, 2003; Guo et al., 2007; Khalturin et al., 2009; Kuo & Kissinger, 2008; Siepel, 2009; Toll-Riera et al., 2009a; Zhou et al., 2008). Recently formed genes give us the opportunity to study the action of natural selection in recent times

The number of species-specific genes, or orphan genes, is not insignificant. They represent around 14% of the genes in 60 fully sequenced microbial genomes (Siew & Fischer, 2003) and between 20-30% in *Drosophila* species (Domazet-Loso & Tautz, 2003; Drosophila 12 Genomes Consortium, 2007). Genes restricted to particular lineages include vomeronasal receptors and casein milk proteins in mammals, which are known to be involved in specific physiological adaptations in this lineage (International Chicken Genome Sequencing Consortium, 2004). Additionally, several lineage-specific genes have been found to be involved in defence against pathogens, such as dermcidin in primates (Toll-Riera et al., 2009a) and surface antigens in apicomplexan parasites (Kuo & Kissinger, 2008). Interestingly, it has been noticed that rice orphan genes are more often expressed under environmental pressure (injury and hormone treatment) than non-orphan genes, indicating

Many newly evolved genes are derived from partial or complete gene duplication of preexisting genes (Long et al., 2003; Marques et al., 2005; Toll-Riera et al., 2009a; Zhou et al., 2008). Alternative processes of gene formation include exaptation from mobile elements

and to investigate the processes associated with gene creation (Zhou & Wang, 2008).

that novel genes help in adaptation to changing conditions (Guo et al., 2007).

**1. Introduction** 

more comprehensive way.

**1.1 Lineage-specific genes** 

**Formation of Novel Genes** 

