Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements.

Chromosome organization and evolution in the Brassicaceae family was studied using comparative linkage mapping. A total of 160 mapped Arabidopsis thaliana DNA fragments identified 284 homologous loci covering 751 cM in Brassica nigra. The data support that modern diploid Brassica species are descended from a hexaploid ancestor, and that the A. thaliana genome is similar in structure and complexity to those of each of the hypothetical diploid progenitors of the proposed hexaploid. Thus, the Brassica lineage probably went through a triplication after the divergence of the lineages leading to A. thaliana and B. nigra. These duplications were also accompanied by an exceptionally high rate of chromosomal rearrangements. The average length of conserved segments between A. thaliana and B. nigra was estimated at 8 cM. This estimate corresponds to approximately 90 rearrangements since the divergence of the two species. The estimated rate of chromosomal rearrangements is higher than any previously reported data based on comparative mapping. Despite the large number of rearrangements, fine-scale comparative mapping between model plant A. thaliana and Brassica crops is likely to result in the identification of a large number of genes that affect important traits in Brassica crops.     

Contrasting genome organisation: two regions of the Brassica oleracea genome compared with collinear regions of the Arabidopsis thaliana genome.

Brassica crop species are of worldwide importance and are closely related to the model plant Arabidopsis thaliana for which the complete genome sequence has recently been established. We investigated collinearity of marker order by comparing two contrasting regions of the Brassica oleracea genome with homologous regions of A. thaliana. Although there is widespread replication of marker loci in both A. thaliana and B. oleracea, we found that a combination of genetic markers mapped in B. oleracea, including RFLPs, CAPS, and SSRs allowed comparison and interpretation of medium-scale chromosomal organisation and rearrangements. The interpretation of data was facilitated by hybridising probes onto the whole A. thaliana genome, as represented by BAC contigs. Twenty marker loci were sampled from the whole length of the shortest B. oleracea linkage group, 06, and 21 from a 30.4-cM section of the longest linkage group, 03. There is evidence of locus duplication on linkage group 06. Locus order is well conserved between a putative duplicated region of 10.5 cM and a discrete region comprising 25 cM of A. thaliana chromosome I. This was supported by evidence from seven paralogous loci, three of which were duplicated in a 30.6-cM region of linkage group 06. The pattern of locus order for the remainder of linkage group 06 and the sampled section of linkage group 03 was more complex when compared with the A. thaliana genome. Although there was some conservation of locus order between markers on linkage group 03 and approximately 9 cM of A. thaliana chromosome I, this was superimposed upon a complex pattern of additional loci that were replicated in both A. thaliana and B. oleracea. The results are discussed in the context of the ability to use collinear information to assist map-based cloning.     

Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana

Over 1000 genetically linked RFLP loci in Brassica napus were mapped to homologous positions in the Arabidopsis genome on the basis of sequence similarity. Blocks of genetically linked loci in B. napus frequently corresponded to physically linked markers in Arabidopsis. This comparative analysis allowed the identification of a minimum of 21 conserved genomic units within the Arabidopsis genome, which can be duplicated and rearranged to generate the present-day B. napus genome. The conserved regions extended over lengths as great as 50 cM in the B. napus genetic map, equivalent to approximately 9 Mb of contiguous sequence in the Arabidopsis genome. There was also evidence for conservation of chromosome landmarks, particularly centromeric regions, between the two species. The observed segmental structure of the Brassica genome strongly suggests that the extant Brassica diploid species evolved from a hexaploid ancestor. The comparative map assists in exploiting the Arabidopsis genomic sequence for marker and candidate gene identification within the larger, intractable genomes of the Brassica polyploids.     

Conserved patterns of chromosome pairing and recombination in Brassica napus crosses.

The patterns of chromosome pairing and recombination in two contrasting Brassica napus F1 hybrids were deduced. One hybrid was from a winter oilseed rape (WOSR) x spring oilseed rape cross, the other from a resynthesized B. napus x WOSR cross. Segregation at 211 equivalent loci assayed in the population derived from each hybrid produced two collinear genetic maps. Alignment of the maps indicated that B. napus chromosomes behaved reproducibly as 19 homologous pairs and that the 19 distinct chromosomes of B. napus each recombined with unique chromosomes from the interspecific hybrid between Brassica rapa and Brassica oleracea. This result indicated that the genomes of the diploid progenitors of amphidiploid B. napus have remained essentially unaltered since the formation of the species and that the progenitor genomes were similar to those of modern-day B. rapa and B. oleracea. The frequency and distribution of crossovers were almost indistinguishable in the two populations, suggesting that the recombination machinery of B. napus could cope easily with different degrees of genetic divergence between homologous chromosomes. Efficient recombination in wide crosses will facilitate the introgression of novel alleles into oilseed rape from B. rapa and B. oleracea (via resynthesized B. napus) and reduce linkage drag.     

Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time

The model dicotyledonous plant, Arabidopsis thaliana , is closely related to Brassica crop species. It is intended that information concerning the genetic control of basic biological processes in Arabidopsis will be transferable to other species. Genome collinearity and its potential to facilitate the identification of candidate genes in Arabidopsis homologous to genes controlling important agronomic traits in Brassica was investigated. Genetic mapping in B. nigra identified two loci influencing flowering time (FT), with loci on linkage groups 2 and 8 explaining 53% and 12% of the total variation in FT, respectively. The CO gene exerts an important control over FT in A. thaliana , and B. nigra homologues of CO probably also play an important role in regulating FT. B. nigra homologues of CO were identified on linkage groups 2 and 8, the homologue on group 2 was coincident with the major locus controlling FT while the homologue on group 8 was within the 90% confidence interval of the weaker FT gene. The CO homologue on group 2 exhibits abundant allelic variation suggesting that it naturally controls a wide range of flowering times. Fine-scale A. thaliana/B. nigra comparative mapping demonstrated short-range collinearity between the genomes of Arabidopsis and Brassica . Eleven DNA fragments spaced over a 1.5 Mb contig in A. thaliana were used as RFLP probes in B. nigra . Three collinear representations of the A. thaliana contig were identified in B. nigra , with one interrupted by a large chromosomal inversion. Collinearity over this range will allow the resources generated by the Arabidopsis genome project to facilitate map-based cloning in Brassica crops.     

Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana

Brassica oleracea is closely related to the model plant, Arabidopsis thaliana. Despite this relationship, it has been difficult to both identify the most closely related segments between the genomes and determine the degree of genome replication within B. oleracea relative to A. thaliana. These difficulties have arisen in part because both species have replicated genomes, and the criteria used to identify orthologous regions between the genomes are often ambiguous. In this report, we compare the positions of sequenced Brassica loci with a known position on a B. oleracea genetic map to the positions of their putative orthologs within the A. thaliana genome. We use explicit criteria to distinguish orthologous from paralogous loci. In addition, we develop a conservative algorithm to identify collinear loci between the genomes and a permutation test to evaluate the significance of these regions. The algorithm identified 34 significant A. thaliana regions that are collinear with >28% of the B. oleracea genetic map. These regions have a mean of 3.3 markers spanning 2.1 Mbp of the A. thaliana genome and 2.5 cM of the B. oleracea genetic map. Our findings are consistent with the hypothesis that the B. oleracea genome has been highly rearranged since divergence from A. thaliana, likely as a result of polyploidization.     

The mosaic of ancestral karyotype blocks in the Sinapis alba L. genome

The organisation of the Sinapis alba genome, comprising 12 linkage groups (n = 12), was compared with the Brassicaceae ancestral karyotype (AK) genomic blocks previously described in other crucifer species. Most of the S. alba genome falls into conserved triplicated genomic blocks that closely match the AK-defined genomic blocks found in other crucifer species including the A, B, and C genomes of closely related Brassica species. In one instance, an S. alba linkage group (S05) was completely collinear with one AK chromosome (AK1), the first time this has been observed in a member of the Brassiceae tribe. However, as observed for other members of the Brassiceae tribe, ancestral genomic blocks were fragmented in the S. alba genome, supporting previously reported comparative chromosome painting describing rearrangements of the AK karyotype prior to the divergence of the Brassiceae from other crucifers. The presented data also refute previous phylogenetic reports that suggest S. alba was more closely related to Brassica nigra (B genome) than to B. rapa (A genome) and B. oleracea (C genome). A comparison of the S. alba and Arabidopsis thaliana genomes revealed many regions of conserved gene order, which will facilitate access to the rich genomic resources available in the model species A. thaliana for genetic research in the less well-resourced crop species S. alba.     

A genetic linkage map of the baboon (Papio hamadryas) genome based on human microsatellite polymorphisms

A first-generation genetic linkage map of the baboon (Papio hamadryas) genome was developed for use in biomedical and evolutionary genetics. Pedigreed baboons (n = 694) were selected from the breeding colony maintained by the Southwest Foundation for Biomedical Research. To facilitate comparison with the human genome, the baboon linkage map consists primarily of human microsatellite loci amplified using published human PCR primers. Genotypes for 325 human microsatellites and 6 novel baboon microsatellites were used in linkage analyses performed with the MultiMap expert system. The resulting sex-averaged meiotic recombination map covers all 20 baboon autosomes, with average spacing among loci of 7.2 cM. Direct comparison among homologous (orthologous) loci reveals that, for 7 human autosomes, locus order is conserved between humans and baboons. For the other 15 autosomes, one or more rearrangements distinguish the two genomes. The total centimorgan distances among homologous markers are 28.0% longer in the human genome than in the baboon, suggesting that rates of recombination may be higher in humans. This baboon linkage map is the first reported for any nonhuman primate species and creates opportunities for mapping quantitative trait loci in baboons, as well as for comparative evolutionary analyses of genome structure.     

Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes.

The complex polyploid genomes of three Saccharum species have been aligned with the compact diploid genome of Sorghum (2n = 2x = 20). A set of 428 DNA probes from different Poaceae (grasses) detected 2460 loci in F1 progeny of the crosses Saccharum officinarum Green German x S. spontaneum IND 81-146, and S. spontaneum PIN 84-1 x S. officinarum Muntok Java. Thirty-one DNA probes detected 226 loci in S. officinarum LA Purple x S. robustum Molokai 5829. Genetic maps of the six Saccharum genotypes, including up to 72 linkage groups, were assembled into "homologous groups" based on parallel arrangements of duplicated loci. About 84% of the loci mapped by 242 common probes were homologous between Saccharum and Sorghum. Only one interchromosomal and two intrachromosomal rearrangements differentiated both S. officinarum and S. spontaneum from Sorghum, but 11 additional cases of chromosome structural polymorphism were found within Saccharum. Diploidization was advanced in S. robustum, incipient in S. officinarum, and absent in S. spontaneum, consistent with biogeographic data suggesting that S. robustum is the ancestor of S. officinarum, but raising new questions about the antiquity of S. spontaneum. The densely mapped Sorghum genome will be a valuable tool in ongoing molecular analysis of the complex Saccharum genome.     

Comparative analysis of diploid species of Avena l. using cytogenetic and biochemical markers: Avena canariensis baum et fedak and A. longiglumis dur

The diploid oat species containing the A genome of two types (Al and Ac) were studied by electrophoresis of grain storage proteins (avenins), chromosome C-banding, and in situ hybridization with probes pTa71 and pTa794. The karyotypes of the studied species displayed similar C-banding patterns but differed in size and morphology of several chromosomes, presumably, resulting from structural rearrangements that took place during the divergence of A genomes from a common ancestor. In situ hybridization demonstrated an identical location of the 45S and 5S rRNA gene loci in Avena canariensis and A. longiglumis similar to that in the A. strigosa genome. However, the 5S rDNA locus in A. longiglumis (5S rDNA1) was considerably decreased in the chromosome 3A1 long arm. The analysis demonstrated that these oat species were similar in the avenin component composition, although individual accessions differed in the electrophoretic mobilities of certain components. A considerable similarity of A. canariensis and A. longiglumis to the Avena diploid species carrying the As genome variant was demonstrated.     

Genetic map-based analysis of genome structure in the homosporous fern Ceratopteris richardii

Homosporous ferns have extremely high chromosome numbers relative to flowering plants, but the species with the lowest chromosome numbers show gene expression patterns typical of diploid organisms, suggesting that they may be diploidized ancient polyploids. To investigate the role of polyploidy in fern genome evolution, and to provide permanent genetic resources for this neglected group, we constructed a high-resolution genetic linkage map of the homosporous fern model species, Ceratopteris richardii (n = 39). Linkage map construction employed 488 doubled haploid lines (DHLs) that were genotyped for 368 RFLP, 358 AFLP, and 3 isozyme markers. Forty-one linkage groups were recovered, with average spacing between markers of 3.18 cM. Most loci (approximately 76%) are duplicated and most duplicates occur on different linkage groups, indicating that as in other eukaryotic genomes, gene duplication plays a prominent role in shaping the architecture of fern genomes. Although past polyploidization is a potential mechanism for the observed abundance of gene duplicates, a wide range in the number of gene duplicates as well as the absence of large syntenic regions consisting of duplicated gene copies implies that small-scale duplications may be the primary mode of gene duplication in C. richardii. Alternatively, evidence of past polyploidization(s) may be masked by extensive chromosomal rearrangements as well as smaller-scale duplications and deletions following polyploidization(s).     

Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication

Insertions and deletions (indels) in protein-coding genes are important sources of genetic variation. Their role in creating new proteins may be especially important after gene duplication. However, little is known about how indels affect the divergence of duplicate genes. We here study thousands of duplicate genes in five fish (teleost) species with completely sequenced genomes. The ancestor of these species has been subject to a fish-specific genome duplication (FSGD) event that occurred approximately 350 Ma. We find that duplicate genes contain at least 25% more indels than single-copy genes. These indels accumulated preferentially in the first 40 my after the FSGD. A lack of widespread asymmetric indel accumulation indicates that both members of a duplicate gene pair typically experience relaxed selection. Strikingly, we observe a 30-80% excess of deletions over insertions that is consistent for indels of various lengths and across the five genomes. We also find that indels preferentially accumulate inside loop regions of protein secondary structure and in regions where amino acids are exposed to solvent. We show that duplicate genes with high indel density also show high DNA sequence divergence. Indel density, but not amino acid divergence, can explain a large proportion of the tertiary structure divergence between proteins encoded by duplicate genes. Our observations are consistent across all five fish species. Taken together, they suggest a general pattern of duplicate gene evolution in which indels are important driving forces of evolutionary change.     

Assessing the level of collinearity between Arabidopsis thaliana and Brassica napus for A. thaliana chromosome 5.

This study describes a comprehensive comparison of chromosome 5 of the model crucifer Arabidopsis with the genome of its amphidiploid crop relative Brassica napus and introduces the use of in silico sequence homology to identify conserved loci between the two species. A region of chromosome 5, spanning 8 Mb, was found in six highly conserved copies in the B. napus genome. A single inversion appeared to be the predominant rearrangement that had separated the two lineages leading to the formation of Arabidopsis chromosome 5 and its homologues in B. napus. The observed results could be explained by the fusion of three ancestral genomes with strong similarities to modern-day Arabidopsis to generate the constituent diploid genomes of B. napus. This supports the hypothesis that the diploid Brassica genomes evolved from a common hexaploid ancestor. Alignment of the genetic linkage map of B. napus with the genomic sequence of Arabidopsis indicated that for specific regions a genetic distance of 1 cM in B. napus was equivalent to 285 Kb of Arabidopsis DNA sequence. This analysis strongly supports the application of Arabidopsis as a tool in marker development, map-based gene cloning, and candidate gene identification for the larger genomes of Brassica crop species.     

芸薹属植物起源，演化及分类的分子标记研究进展

本文概述了近几年来围绕芸薹屋植物的起源,演化和分类所进行的分子标记方面的研究进展,大量研究结果表明：芸薹属6个种基因组之间存在部分同源性,而且有大量的位点发生了重复,表明其是次生的多倍体种,是从一个染色体数目较少的祖选演化而来,在芸薹属基因组演化过程中发生了大量的染色体变异,如重复,易位,倒位,插入和缺失等。     

Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four triticeae genomes

Bread wheat (Triticum aestivum) is an allohexaploid species, consisting of three subgenomes (A, B, and D). To study the molecular evolution of these closely related genomes, we compared the sequence of a 307-kb physical contig covering the high molecular weight (HMW)-glutenin locus from the A genome of durum wheat (Triticum turgidum, AABB) with the orthologous regions from the B genome of the same wheat and the D genome of the diploid wheat Aegilops tauschii (Anderson et al., 2003; Kong et al., 2004). Although gene colinearity appears to be retained, four out of six genes including the two paralogous HMW-glutenin genes are disrupted in the orthologous region of the A genome. Mechanisms involved in gene disruption in the A genome include retroelement insertions, sequence deletions, and mutations causing in-frame stop codons in the coding sequences. Comparative sequence analysis also revealed that sequences in the colinear intergenic regions of these different genomes were generally not conserved. The rapid genome evolution in these regions is attributable mainly to the large number of retrotransposon insertions that occurred after the divergence of the three wheat genomes. Our comparative studies indicate that the B genome diverged prior to the separation of the A and D genomes. Furthermore, sequence comparison of two distinct types of allelic variations at the HMW-glutenin loci in the A genomes of different hexaploid wheat cultivars with the A genome locus of durum wheat indicates that hexaploid wheat may have more than one tetraploid ancestor.     

New evidence from Sinapis alba L. for ancestral triplication in a crucifer genome.

We present clear evidence of ancestral genome triplication in Sinapis alba, a close relative of the cultivated Brassica species. Exceptionally high levels of heterozygosity in the parents of an F1 intercross permitted the mapping of an estimated 87% of all detected restriction fragment length polymorphism (RFLP) loci, with each RFLP probe typically detecting 2 or 3 loci. These duplicated loci were arranged in 8 triplicated homologous linkage blocks and 2 small, duplicated, homologous linkage blocks covering the majority of the S. alba genome. Several large-scale inversions and translocations appear to have rearranged the order of loci within homologous blocks. The role of successive polyploidization events on the evolution of crucifer species is discussed.     

Identification of paralogous HERV-K LTRs on human chromosomes 3, 4, 7 and 11 in regions containing clusters of olfactory receptor genes

A locus harboring a human endogenous retroviral LTR (long terminal repeat) was mapped on the short arm of human chromosome 7 (7p22), and its evolutionary history was investigated. Sequences of two human genome fragments that were homologous to the LTR-flanking sequences were found in human genome databases: (1) an LTR-containing DNA fragment from region 3p13 of the human genome, which includes clusters of olfactory receptor genes and pseudogenes; and (2) a fragment of region 21q22.1 lacking LTR sequences. PCR analysis demonstrated that LTRs with highly homologous flanking sequences could be found in the genomes of human, chimp, gorilla, and orangutan, but were absent from the genomes of gibbon and New World monkeys. A PCR assay with a primer set corresponding to the sequence from human Chr 3 allowed us to detect LTR-containing paralogous sequences on human chromosomes 3, 4, 7, and 11. The divergence times for the LTR-flanking sequences on chromosomes 3 and 7, and the paralogous sequence on chromosome 21, were evaluated and used to reconstruct the order of duplication events and retroviral insertions. (1) An initial duplication event that occurred 14-17 Mya and before LTR insertion - produced two loci, one corresponding to that located on Chr 21, while the second was the ancestor of the loci on chromosomes 3 and 7. (2) Insertion of the LTR (most probably as a provirus) into this ancestral locus took place 13 Mya. (3) Duplication of the LTR-containing ancestral locus occurred 11 Mya, forming the paralogous modern loci on Chr 3 and 7.     

Genome Changes After Gene Duplication: Haploidy vs. Diploidy

Since genome size and the number of duplicate genes observed in genomes increase from haploid to diploid organisms, diploidy might provide more evolutionary probabilities through gene duplication. It is still unclear how diploidy promotes genomic evolution in detail. In this study, we explored the evolution of segmental gene duplication in haploid and diploid populations by analytical and simulation approaches. Results show that (1) under the double null recessive (DNR) selective model, given the same recombination rate, the evolutionary trajectories and consequences are very similar between the same-size gene-pool haploid vs. diploid populations; (2) recombination enlarges the probability of preservation of duplicate genes in either haploid or diploid large populations, and haplo-insufficiency reinforces this effect; and (3) the loss of duplicate genes at the ancestor locus is limited under recombination while under complete linkage the loss of duplicate genes is always random at the ancestor and newly duplicated loci. Therefore, we propose a model to explain the advantage of diploidy: diploidy might facilitate the increase of recombination rate, especially under sexual reproduction; more duplicate genes are preserved under more recombination by originalization (by which duplicate genes are preserved intact at a special quasi-mutation-selection balance under the DNR or haplo-insufficient selective model), so genome sizes and the number of duplicate genes in diploid organisms become larger. Additionally, it is suggested that small genomic rearrangements due to the random loss of duplicate genes might be limited under recombination.USUALLY genome size becomes larger from haploid to diploid organisms (Lynch and Conery 2003), and so does the number of duplicate genes observed in genomes (Zhang 2003). It is extensively hypothesized that diploidy might facilitate the preservation and accumulation of duplicate genes, but it is still unclear how diploidy supports the evolution of duplicate genes in detail. The superiority of diploidy is classically attributed to preventing expression of deleterious mutations (Crow and Kimura 1965), but it is also argued that the sheltering of deleterious mutations cannot adequately explain the advantages of diploidy (Perrot et al. 1991).Recombination is a common phenomenon in all three kingdoms of life, Bacteria, Eukarya, and Archaea. It has been reported that recombination influences the loss of duplicate genes (Zhang and Kishino 2004; Xue et al. 2010). In diploid organisms, if recombination between the ancestor locus and the newly duplicated locus is free, the rate of recombination is maximally 0.5, which is commonly observed especially when the two loci are located on different chromosomes. Although recombination should not be regarded as an exception in haploid organisms (Fraser et al. 2007), recombination events usually occur more frequently in diploid populations than they do in haploid populations. In other words, diploidy might facilitate the occurrence of recombination. The difference of recombination behaviors between haploid and diploid organisms is an obvious and important feature during genomic evolution.In our recent studies of genomic duplication, we proposed a new possible way of preserving and accumulating duplicate genes in genomes—originalization (Xue and Fu 2009a). As is well known, for a locus in an infinite diploid population, the frequencies of wild-type and degenerative alleles will move to an equilibrium under purifying selection and mutation, which is known as the mutation–selection balance. After genomic duplication, under two simple selective models, double null recessive (DNR, under which valid individuals require at least one active wild-type allele on the ancestor and newly duplicated loci) and haplo-insufficient (HI or partial dominant, under which valid individuals require at least two active wild-type alleles on both loci) models, a special equilibrium of allele frequencies at the ancestor and newly duplicated loci will be reached under recombination, in which the frequency of wild-type allele is kept high at both loci. Under the HI selective model this balance becomes so stable and flexible that the fixation of a degenerative allele at one of these two loci (or the balance being broken) becomes very difficult even in a modest population (Xue and Fu 2009a,b). However, if the two loci are tightly linked (recombination rate r = 0), this balance of allele frequencies does not appear. As r increases, the balance becomes more stable and the frequency of the wild-type allele at two loci becomes higher. High frequency of the wild-type allele at both loci means that duplicate genes are preserved intact in genomes, so this phenomenon was named originalization.Although many duplicate genes originated from genomic duplications in some species, such as yeast, maize, and fish (Li et al. 2005), those from segmental duplications are also very popular (Zhang et al. 2000; Leister 2004). In haploid populations, most duplication events are small segmental duplications. Therefore, to understand genomic evolution comprehensively, it is necessary to explore the evolution of segmental genomic duplication.Lynch et al. (2001) and Tanaka et al. (2009) have studied the evolution of segmental gene duplication in diploid populations theoretically. However, in this study, we further compared the evolution of segmental gene duplication in haploid vs. diploid populations by numerical and simulation approaches under the DNR and HI selective models. We observed that haploid and diploid populations with the same-size gene pool are very similar under the DNR model and the same recombination rate. Recombination enlarges the probability of preservation of duplicate genes in either haploid or diploid populations via originalization, and haplo-insufficiency reinforces this effect. The loss of duplicate genes at the ancestor locus might be limited under recombination, while under complete linkage, the loss of duplicate genes is random at the ancestor and newly duplicated loci. According to these results, we propose a model with which to explain the revolutionary genomic transition from haploidy to diploidy.     

Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region

The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurately assembly of its genome. To explore the utility of ancestral diploid species of polyploid wheat, sequence variation of T. urartu (A^uA^u) was analyzed by comparing its 277-kb large genomic region carrying the important Glu-1 locus with the homologous regions from the A genomes of the diploid T. monococcum (A^mA^m), tetraploid T. turgidum (AABB), and hexaploid T. aestivum (AABBDD). Our results revealed that in addition to a high degree of the gene collinearity, nested retroelement structures were also considerably conserved among the A^u genome and the A genomes in polyploid wheats, suggesting that the majority of the repetitive sequences in the A genomes of polyploid wheats originated from the diploid A^u genome. The difference in the compared region between A^u and A is mainly caused by four differential TE insertion and two deletion events between these genomes. The estimated divergence time of A genomes calculated on nucleotide substitution rate in both shared TEs and collinear genes further supports the closer evolutionary relationship of A to A^u than to A^m. The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the A^u sequence for mapping the A genome in hexaploid wheat. Eighty percent of these repeat junction markers were successfully mapped to the corresponding region in hexaploid wheat, suggesting that T. urartu could serve as a useful resource for developing molecular markers for genetic and breeding studies in hexaploid wheat.     

New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome

A unigene set of 1411 contigs was constructed from 2629 redundant maize expressed sequence tags (ESTs) mapped on the maizeDB genetic map. Rice orthologous sequences were identified by blast alignment against the rice genomic sequence. A total of 1046 (74%) maize contigs were associated with their corresponding homologues in the rice genome and 656 (47%) defined as potential orthologous relationships. One hundred and seventeen (8%) maize EST contigs mapped to two distinct loci on the maize genetic map, reflecting the tetraploid nature of the maize genome. Among 492 mono-locus contigs, 344 (484 redundant ESTs) identify collinear blocks between maize chromosomes 2 and 4 and a single rice chromosome, defining six new collinear regions. Fine-scale analysis of collinearity between rice chromosomes 1 and 5 with maize chromosomes 3, 6 and 8 shows the presence of internal rearrangements within collinear regions. Mapping of maize contigs to two distinct loci on the rice sequence identifies five new duplication events in rice. Detailed analysis of a duplication between rice chromosomes 1 and 5 shows that 11% of the annotated genes from the chromosome 1 locus are found duplicated on the chromosome 5 paralogous counterpart, indicating a high degree of re-organisations. The implications of these findings for map-based cloning in collinear regions are discussed.