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1.
Genetic mapping studies have suggested that diploid cotton (Gossypium) might be an ancient polyploid. However, further evidence is lacking due to the complexity of the genome and the lack of sequence resources. Here, we used the grape (Vitis vinifera) genome as an out-group in two different approaches to further explore evidence regarding ancient genome duplication (WGD) event(s) in the diploid Gossypium lineage and its (their) effects: a genome-level alignment analysis and a local-level sequence component analysis. Both studies suggest that at least one round of genome duplication occurred in the Gossypium lineage. Also, gene densities in corresponding regions from Gossypium raimondii, V. vinifera, Arabidopsis thaliana and Carica papaya genomes are similar, despite the huge difference in their genome sizes and the different number of WGDs each genome has experienced. These observations fit the model that differences in plant genome sizes are largely explained by transposon insertions into heterochromatic regions.  相似文献   

2.
The Hardness (Ha) locus controls grain hardness in hexaploid wheat (Triticum aestivum) and its relatives (Triticum and Aegilops species) and represents a classical example of a trait whose variation arose from gene loss after polyploidization. In this study, we investigated the molecular basis of the evolutionary events observed at this locus by comparing corresponding sequences of diploid, tertraploid, and hexaploid wheat species (Triticum and Aegilops). Genomic rearrangements, such as transposable element insertions, genomic deletions, duplications, and inversions, were shown to constitute the major differences when the same genomes (i.e., the A, B, or D genomes) were compared between species of different ploidy levels. The comparative analysis allowed us to determine the extent and sequences of the rearranged regions as well as rearrangement breakpoints and sequence motifs at their boundaries, which suggest rearrangement by illegitimate recombination. Among these genomic rearrangements, the previously reported Pina and Pinb genes loss from the Ha locus of polyploid wheat species was caused by a large genomic deletion that probably occurred independently in the A and B genomes. Moreover, the Ha locus in the D genome of hexaploid wheat (T. aestivum) is 29 kb smaller than in the D genome of its diploid progenitor Ae. tauschii, principally because of transposable element insertions and two large deletions caused by illegitimate recombination. Our data suggest that illegitimate DNA recombination, leading to various genomic rearrangements, constitutes one of the major evolutionary mechanisms in wheat species.  相似文献   

3.
The genus Gossypium, which comprises a divergent group of diploid species and several recently formed allotetraploids, offers an excellent opportunity to study polyploid genome evolution. In this study, chromosome structural variation among the A, At, and D genomes of Gossypium was evaluated by comparative genetic linkage mapping. We constructed a fully resolved RFLP linkage map for the diploid A genome consisting of 275 loci using an F2 interspecific Gossypium arboreum x Gossypium herbaceum family. The 13 chromosomes of the A genome are represented by 12 large linkage groups in our map, reflecting an expected interchromosomal translocation between G. arboreum and G. herbaceum. The A-genome chromosomes are largely collinear with the D genomes, save for a few small inversions. Although the 2 diploid mapping parents represent the closest living relatives of the allotetraploid At-genome progenitor, 2 translocations and 7 inversions were observed between the A and At genomes. The recombination rates are similar between the 2 diploid genomes; however, the At genome shows a 93% increase in recombination relative to its diploid progenitors. Elevated recombination in the Dt genome was reported previously. These data on the At genome thus indicate that elevated recombination was a general property of allotetraploidy in cotton.  相似文献   

4.
Nucleotide insertions and deletions (indels) are responsible for gaps in the sequence alignments. Indel is one of the major sources of evolutionary change at the molecular level. We have examined the patterns of insertions and deletions in the 19 mammalian genomes, and found that deletion events are more common than insertions in the mammalian genomes. Both the number of insertions and deletions decrease rapidly when the gap length increases and single nucleotide indel is the most frequent in all indel events. The frequencies of both insertions and deletions can be described well by power law.Key Words: Insertion, deletion, gap, indel, mammalian genome.  相似文献   

5.
Genome sizes vary by several orders of magnitude, driven by mechanisms such as illegitimate recombination and transposable element proliferation. Prior analysis of the CesA region in two cotton genomes that diverged 5–10 million years ago (Ma), and acquired a twofold difference in genome size, revealed extensive local conservation of genic and intergenic regions, with no evidence of the global genome size difference. The present study extends the comparison to include BAC sequences surrounding the gene encoding alcohol dehydrogenase A ( AdhA ) from four cotton genomes: the two co-resident genomes (AT and DT) of the allotetraploid, Gossypium hirsutum , as well as the model diploid progenitors, Gossypium arboreum (A) and Gossypium raimondii (D). In contrast to earlier work, evolution in the AdhA region reflects, in a microcosm, the overall difference in genome size, with a nearly twofold difference in aligned sequence length. Most size differences may be attributed to differential accumulation of retroelements during divergence of the genome diploids from their common ancestor, but in addition there has been a biased accumulation of small deletions, such that those in the smaller D genome are on average twice as large as those in the larger A genome. The data also provide evidence for the global phenomenon of 'genomic downsizing' in polyploids shortly after formation. This in part reflects a higher frequency of small deletions post-polyploidization, and increased illegitimate recombination. In conjunction with previous work, the data here confirm the conclusion that genome size evolution reflects many forces that collectively operate heterogeneously among genomic regions.  相似文献   

6.
To explore types, levels and patterns of genetic divergence among diploid Gossypium (cotton) genomes, 780 cDNA, genomic DNA and simple sequence repeat (SSR) loci were re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G. raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup, Gossypioides kirkii. Divergence among these genomes ranged from 7.32 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic sites per 100 base pairs, whereas expressed sequence tags are most conserved with 3.96 polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest percentage of 'extended polymorphisms' (spanning multiple consecutive nucleotides). The A genome lineage was particularly rapidly evolving, with the D genome also showing accelerated evolution relative to the C genome. Unexpected asymmetry in mutation rates was found, with much more transition than transversion mutation in the D genome after its divergence from a common ancestor shared with the A genome. This large quantity of orthologous DNA sequence strongly supports a phylogeny in which A-C divergence is more recent than A-D divergence, a subject that is of much importance in view of A-D polyploid formation being key to the evolution of the most productive and finest-quality cottons. Loci that are monomorphic within A or D genome types, but polymorphic between genome types, may be of practical importance for identifying locus-specific DNA markers in tetraploid cottons including leading cultivars.  相似文献   

7.
About 90 members of a major tandemly repeated DNA sequence family originally described in rye as pSc119.2 have been isolated from 11 diploid and polyploid Triticeae species using primers from along the length of the sequence for PCR amplification. Alignment and similarity analysis showed that the 120-bp repeat unit family is diverse with single nucleotide changes and few insertions and deletions occurring throughout the sequence, with no characteristic genome or species-specific variants having developed during evolution of the extant genomes. Fluorescent in situ hybridization showed that each of the large blocks of the repeat at chromosomal sites harboured many variants of the 120-bp repeat. There were substantial copy number differences between genomes, with abundant sub-terminal sites in rye, interstitial sites in the B genome of wheat, and relatively few sites in the A and D genome. We conclude that sequence homogenization events have not been operative in this repeat and that the common ancestor of the Triticeae tribe had multiple sequences of the 120-bp repeat with a range of variation not unlike that seen within and between species today. This diversity has been maintained when sites are moved within the genome and in all species since their divergence within the Triticeae.  相似文献   

8.
Evidence accumulated over the last decade has shown that allopolyploid genomes may undergo drastic reorganization. However, timing and mechanisms of structural diploidization over evolutionary timescales are still poorly known. As transposable elements (TEs) represent major and labile components of plant genomes, they likely play a pivotal role in fuelling genome changes leading to long-term diploidization. Here, we exploit the 4.5 MY old allopolyploid Nicotiana section Repandae to investigate the impact of TEs on the evolutionary dynamics of genomes. Sequence-specific amplified polymorphisms (SSAP) on seven TEs with expected contrasted dynamics were used to survey genome-wide TE insertion polymorphisms. Comparisons of TE insertions in the four allopolyploid species and descendents of the diploid species most closely related to their actual progenitors revealed that the polyploids showed considerable departure from predicted additivity of the diploids. Large numbers of new SSAP bands were observed in polyploids for two TEs, but restructuring for most TE families involved substantial loss of fragments relative to the genome of the diploid representing the paternal progenitor, which could be due to changes in allopolyploids, diploid progenitor lineages or both. The majority of non-additive bands were shared by all polyploid species, suggesting that significant restructuring occurred early after the allopolyploid event that gave rise to their common ancestor. Furthermore, several gains and losses of SSAP fragments were restricted to N. repanda, suggesting a unique evolutionary trajectory. This pattern of diploidization in TE genome fractions supports the hypothesis that TEs are central to long-term genome turnover and depends on both TE and the polyploid lineage considered.  相似文献   

9.
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.  相似文献   

10.
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 (AuAu) 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 (AmAm), 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 Au 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 Au genome. The difference in the compared region between Au 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 Au than to Am. The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the Au 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.  相似文献   

11.
Repetitive DNA variation and pivotal-differential evolution of wild wheats.   总被引:1,自引:0,他引:1  
Several polyploid species in the genus Triticum contain a U genome derived from the diploid T. umbellulatum. In these species, the U genome is considered to be unmodified from the diploid based on chromosome pairing analysis, and it is referred to as pivotal. The additional genome(s) are considered to be modified, and they are thus referred to as differential genomes. The M genome derived from the diploid T. comosum is found in many U genome polyploids. In this study, we cloned three repetitive DNA sequences found primarily in the U genome and two repetitive DNA sequences found primarily in the M genome. We used these to monitor variation for these sequences in a large set of species containing U and M genomes. Investigation of sympatric and allopatric accessions of polyploid species did not show repetitive DNA similarities among sympatric species. This result does not support the idea that the polyploid species are continually exchanging genetic information through introgression. However, it is also possible that repetitive DNA is not a suitable means of addressing the question of introgression. The U genomes of both diploid and polyploid U genome species were similar regarding hybridization patterns observed with U genome probes. Much more variation was found both among diploid T. comosum accessions and polyploids containing M genomes. The observed variation supports the cytogenetic evidence that the M genome is more variable than the U genome. It also raises the possibility that the differential nature of the M genome may be due to variation within the diploid T. comosum, as well as among polyploid M genome species and accessions.  相似文献   

12.
An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements(TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes.Gypsy was the most abundant TE type and most TEs were located $500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs(siRNAs) that targeted TEs. TEs,particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.  相似文献   

13.
Dvorak J  Akhunov ED 《Genetics》2005,171(1):323-332
The origin of tetraploid wheat and the divergence of diploid ancestors of wheat A and D genomes were estimated to have occurred 0.36 and 2.7 million years ago, respectively. These estimates and the evolutionary history of 3159 gene loci were used to estimate the rates with which gene loci have been deleted and duplicated during the evolution of wheat diploid ancestors and during the evolution of polyploid wheat. During diploid evolution, the deletion rate was 2.1 x 10(-3) locus(-1) MY(-1) for single-copy loci and 1.0 x 10(-2) locus(-1) MY(-1) for loci in paralogous sets. Loci were duplicated with a rate of 2.9 x 10(-3) locus(-1) MY(-1) during diploid evolution. During polyploid evolution, locus deletion and locus duplication rates were 1.8 x 10(-2) and 1.8 x 10(-3) locus(-1) MY(-1), respectively. Locus deletion and duplication rates correlated positively with the distance of the locus from the centromere and the recombination rate during diploid evolution. The functions of deleted and duplicated loci were inferred to gain insight into the surprisingly high rate of deletions of loci present apparently only once in a genome. The significance of these findings for genome evolution at the diploid and polyploid level is discussed.  相似文献   

14.
MOTIVATION: The two mutation processes that have the largest impact on genome evolution at small scales are substitutions, and sequence insertions and deletions (indels). While the former have been studied extensively, indels have received less attention, and in particular, the problem of inferring indel rates between pairs of divergent sequence remains unsolved. Here, I describe a novel and accurate method for estimating neutral indel rates between divergent pairs of genomes. RESULTS: Simulations suggest that new method for estimating indel rates is accurate to within 2%, at divergences corresponding to that of human and mouse. Applying the method to these species, I show that indel rates are up to twice higher than is apparent from alignments, and depend strongly on the local G + C content. These results indicate that at these evolutionary distances, the contribution of indels to sequence divergence is much larger than hitherto appreciated. In particular, the ratio of substitution to indel rates between human and mouse appears to be around gamma = 8, rather than the currently accepted value of about gamma = 14.  相似文献   

15.
Nam K  Ellegren H 《PLoS genetics》2012,8(5):e1002680
Selective and/or neutral processes may govern variation in DNA content and, ultimately, genome size. The observation in several organisms of a negative correlation between recombination rate and intron size could be compatible with a neutral model in which recombination is mutagenic for length changes. We used whole-genome data on small insertions and deletions within transposable elements from chicken and zebra finch to demonstrate clear links between recombination rate and a number of attributes of reduced DNA content. Recombination rate was negatively correlated with the length of introns, transposable elements, and intergenic spacer and with the rate of short insertions. Importantly, it was positively correlated with gene density, the rate of short deletions, the deletion bias, and the net change in sequence length. All these observations point at a pattern of more condensed genome structure in regions of high recombination. Based on the observed rates of small insertions and deletions and assuming that these rates are representative for the whole genome, we estimate that the genome of the most recent common ancestor of birds and lizards has lost nearly 20% of its DNA content up until the present. Expansion of transposable elements can counteract the effect of deletions in an equilibrium mutation model; however, since the activity of transposable elements has been low in the avian lineage, the deletion bias is likely to have had a significant effect on genome size evolution in dinosaurs and birds, contributing to the maintenance of a small genome. We also demonstrate that most of the observed correlations between recombination rate and genome contraction parameters are seen in the human genome, including for segregating indel polymorphisms. Our data are compatible with a neutral model in which recombination drives vertebrate genome size evolution and gives no direct support for a role of natural selection in this process.  相似文献   

16.
Bread wheat (Triticum aestivum, AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path (MTP) of 3176 BAC clones from the short arm of Ae. tauschii chromosome 3 (At3DS). The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B (Ta3BS) is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element (TE) bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D (Ta3DS), there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.  相似文献   

17.
Li W  Huang L  Gill BS 《Plant physiology》2008,146(1):200-212
Polyploidy is known to induce numerous genetic and epigenetic changes but little is known about their physiological bases. In wheat, grain texture is mainly determined by the Hardness (Ha) locus consisting of genes Puroindoline a (Pina) and b (Pinb). These genes are conserved in diploid progenitors but were deleted from the A and B genomes of tetraploid Triticum turgidum (AB). We now report the recurrent deletions of Pina-Pinb in other lineages of polyploid wheat. We analyzed the Ha haplotype structure in 90 diploid and 300 polyploid accessions of Triticum and Aegilops spp. Pin genes were conserved in all diploid species and deletion haplotypes were detected in all polyploid Triticum and most of the polyploid Aegilops spp. Two Pina-Pinb deletion haplotypes were found in hexaploid wheat (Triticum aestivum; ABD). Pina and Pinb were eliminated from the G genome, but maintained in the A genome of tetraploid Triticum timopheevii (AG). Subsequently, Pina and Pinb were deleted from the A genome but retained in the A(m) genome of hexaploid Triticum zhukovskyi (A(m)AG). Comparison of deletion breakpoints demonstrated that the Pina-Pinb deletion occurred independently and recurrently in the four polyploid wheat species. The implications of Pina-Pinb deletions for polyploid-driven evolution of gene and genome and its possible physiological significance are discussed.  相似文献   

18.
Nucleotide substitution, insertion and deletion (indel) events are the major driving forces that have shaped genomes. Using the recently identified human ribosomal protein (RP) pseudogene sequences, we have thoroughly studied DNA mutation patterns in the human genome. We analyzed a total of 1726 processed RP pseudogene sequences, comprising more than 700 000 bases. To be sure to differentiate the sequence changes occurring in the functional genes during evolution from those occurring in pseudogenes after they were fixed in the genome, we used only pseudogene sequences originating from parts of RP genes that are identical in human and mouse. Overall, we found that nucleotide transitions are more common than transversions, by roughly a factor of two. Moreover, the substitution rates amongst the 12 possible nucleotide pairs are not homogeneous as they are affected by the type of immediately neighboring nucleotides and the overall local G+C content. Finally, our dataset is large enough that it has many indels, thus allowing for the first time statistically robust analysis of these events. Overall, we found that deletions are about three times more common than insertions (3740 versus 1291). The frequencies of both these events follow characteristic power–law behavior associated with the size of the indel. However, unexpectedly, the frequency of 3 bp deletions (in contrast to 3 bp insertions) violates this trend, being considerably higher than that of 2 bp deletions. The possible biological implications of such a 3 bp bias are discussed.  相似文献   

19.
A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S-5.8S-26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A-C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C-A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S-5.8S-26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.  相似文献   

20.
利用SSR标记技术研究棉属A、D染色体组的进化   总被引:14,自引:0,他引:14  
郭旺珍  王凯  张天真 《遗传学报》2003,30(2):183-188
利用SSR分子标记技术,对棉属A、D染色体二倍体及四倍体代表棉种进行了遗传多样性分析。供试的10个二倍体代表棉种间遗传多态性丰富,分子聚类结果与Fryxell棉属分类结果相同。分子水平上进一步揭示出属于D染色体组的拟似棉与其他D染色体组棉种的相似系数最低,A,D染色体组间相似系数很高,该结果支持拟全民族似棉是D染色体组最原始棉种,棉属不同染色体组是共同起源,单元进化的理论,利用栽培的异源四倍体棉种不太适于研究棉属A、D染色体组的进化。  相似文献   

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