Plant Molecular Biology 15: 437-448, 1990. © 1990 Kluwer Academic Publishers. Printed in Belgium. 437 Nomad DNA - A model for movement and duplication of DNA sequences in plant genomes Eran Pichersky Biology Department, University of Michigan, Ann Arbor, MI 48109, USA Received 20 April 1990; accepted in revised form 31 May 1990 Key words: chromosomes, DNA breaks, heteroduplex DNA, gene duplication, recombination Introduction reviewed and analyzed here, and a new mecha- nism, the 'Nomad DNA' model, for gene move- Virtually all genes originate from other genes by a ment and duplication in plants is proposed. process of gene duplication. Since most genes encode proteins which either are essential for the survival of the cell or confer some advantage to it, Models of gene duplications duplication of a gene and subsequent divergence of one duplicate copy provide a way of keeping At least four different mechanisms can be invoked the old function and also acquiring a new one to explain the observed gene duplications in ani- [38]. Thus, the mechanisms by which gene dupli- mals and plants. These mechanisms are schemati- cations arise are of great interest. Whereas a sub- cally diagrammed in Fig. 1. Different mechanisms stantial body of work has accumulated con- lead to different results - e.g., linked vs. non- cerning the mechanisms of gene duplication in linked duplicate genes, large chromosomal seg- animals [25], little information concerning gene ments vs. short segments duplicated, etc. I first duplications in plants, especially on the molecular briefly describe these mechanisms and then dis- level, is available. Plant genomes display a mode cuss the evidence for them. of evolution with some distinct features as com- It is important to realize at the outset that most pared to animal genome evolution (e.g., much postulated mechanisms of gene duplication do lower level of conservation of synteny groups not result in 'instant' duplications, that is, an [ 53 ], 5-10 fold difference in amount of DNA even additional copy is not produced within the same among congeneric species [52], high incidence of cell in which the initial steps leading to gene dupli- polyploidy [21]), and it is thus not apriori cation have occurred. This is easily demonstrated obvious that most gene duplications in plants by the mechanism of unequal crossing-over, occur by the same mechanism(s) by which the which gives rise to tandemly linked duplications majority of gene duplications occur in animals. (mechanism # 1, Fig. 1A). In this case, the actual Although few molecular investigations of plant event of unequal crossing-over involving gene X genes and genomes have specifically addressed changes only the distribution of the two copies of the issue ofgene duplications per se, a substantial gene X, not the number ofgene copies. Instead of amount of data derived from experiments from one copy per homologous chromosome, after the gene cloning, sequencing and mapping in plants crossing-over two copies are present on one chro- has recently become available. These data are mosome and none on the other. During meiosis, 438 A MECHANISM #1 B MECHANISM #2 II I II I,, I, I,, I, B A C A A z p A B X D X B ~ x S B C MECHANISM #3 D MECHANISM #4 I II I II I II II C C X A X D X b B B D Fig. 1. Hypothetical mechanisms of gene duplications (see text). each chromosome is segregated to a separate DNA segment bearing gene X has been trans- gamete. Following fertilization, a diploid cell may ferred is included in a gamete which fuses with be produced with one homologous chromosome another gamete having the normal chromosomal with the two copies of the X gene (tandemly- complement, an amphi-duplication results. In linked) and the homologous chromosome, de- subsequent generations, through the appropriate rived from a meiosis which did not involve an crosses, an individual may be obtained which is unequal crossing-over, with a single X gene. In homozygous for the presence of gene X on two subsequent generations, a diploid cell may be pro- different, non-homologous chromosomes. It duced with two homologous chromosomes each should be noted that this mechanism and the carrying two tandemly linked X genes. This result previously described one could also lead, in a may be favored in plants because many of them similar way, to deletions (which may or may not have the ability to self-pollinate. be lethal). Another phenomenon which initially affects A third mechanism in which a gene duplication only the distribution of genes but eventually may may be achieved is when a DNA fragment is lead to gene duplications is translocation between removed from its internal location on a chromo- non-homologous chromosomes (mechanism # 2, some and is reintegrated at a different site, either Fig. 1B) [19]. If the chromosome to which the on the same or another chromosome (mechanism 439 #3, Fig. 1C; see below for discussion of the ment of the homologous chromosomes at meiosis details of this possible mechanism). Such an in- [25]. The extent of misalignment determines the terstitial translocation is analogous to the move- size of the segment which is made into tandem ment of a transposable element in a conservative repeats. Once a tandem repeat which includes the transposition event. Again, a gene duplication gene itself is created, misalignment can bring may result by the fusing of the appropriate about recombination between the first and the gametes. Note that in this case, as well as in the second blocks of homologous sequences, thus previously described one, a broken chromosome leading to further duplications. Because these ho- could occur from the process and not be repaired, mology blocks can be extensive, this event may be but this may not matter: a gamete containing a more frequent than the event creating the first pair broken chromosome may not be viable but the of tandemly linked genes. Consistent with this other gametes, including the one with the extra postulate, plant loci which consist of tandemly DNA on one of its chromosomes, should not be linked genes generally contain more than two affected. copies of the genes: for example, a CAB locus A fourth model is analogous to the replicative containing four genes has been identified in transposition of transposable elements, in which tomato [41], and a CAB locus with three tandem- a duplicated element is created and at the same ly linked genes is present in Arabidopsis thaliana time inserted at a different location in the genome [30]. An A. thaliana RBCS locus contains three (mechanism #4, Fig. 1D). Even in this case of tandemly linked genes [ 28 ], a tomato RBCS locus 'instant' duplication, homozygosity of the dupli- also contains three tandemly linked genes [49], cation still requires additional generations. How- and its counterpart in petunia contains six [ 10]. ever, because plants do not have a germ line, a In some cases, the orientation of the genes may replicative transposition event in a somatic cell differ - there are head to head or tail-to-tail ar- that eventually gives rise to the reproductive tissue rangements, such as in two CAB loci in tobacco, in the flower may lead, upon selfing, to homozygo- each with four genes [6], and in a CAB locus in sity for the duplication in one generation. It is very tomato with three genes [41]. This can be ex- important to realize that this mechanism and the plained by 'flipping' of sequences (due to recombi- previous one may give the same results in the long nation at inverted repeats) after the duplications run even if the initial steps are not identical. This occurred [25]. Clusters of genes have been found follows because it is not necessary to maintain in many gene systems, although the orientation of one copy in the original locus in order for dupli- the genes has not always been determined (e.g., cation to occur; the gene in the original locus may actins [33]; histones [8], and additional examples be provided by the gamete from an individual in reviewed in [52]). Clusters of genes are common which no change in DNA (with respect to the gene in gene systems encoding abundant proteins (the in question) has occurred. most extensively studied plant gene systems) although gene dispersal is also found in these systems [ 11, 43]. Experimental evidence for these models Unequal crossing-over- Tandem duplication Translocations and gene duplications The original event creating a tandemly repeated Plants seem to tolerate translocations much more sequence by unequal crossing-over requires re- easily than animals, and, as a consequence, trans- combination outside the sequence in question. locations are common in plants [21]. Are they This is thought to occur at short sequences of involved in duplications [4]? If they were, one homologous, repetitive DNA, or at stretches with would expect to observe long segments of dupli- fortuitous sequence similarity, during misalign- cated DNA. In addition, duplicated sequences 440 will tend to reside at the ends of chromosomes pair of duplicate genes are not linked to each (terminal translocations are the most common other), no correlation is found with any of the type of translocation). In order to detect dupli- chromosomal translocations or the segmental du- cations of large chromosomal segments, it is ne- plication [ 53 ]. cessary to examine a well-developed genetic map based on DNA markers. (Only when the DNA of two loci hybridize with each other, is it possible Unlinked duplications to determine that the loci compared are homol- ogous; in plants, a complication is caused by the Most molecular investigations have studied genes lateral transfer of genes via the genome of the encoding abundant proteins, and linked gene photosynthetic endosymbiont [20, 55], but these duplications have often been found in these genes have been separated more than a billion systems.