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Syntenic Relationships between the U and M Genomes of Aegilops, Wheat and the Model Species Brachypodium and Rice as Revealed by COS Markers  [PDF]
István Molnár, Hana ?imková, Michelle Leverington-Waite, Richard Goram, András Cseh, Jan Vrána, András Farkas, Jaroslav Dole?el, Márta Molnár-Láng, Simon Griffiths
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0070844
Abstract: Diploid Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS) markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat-Aegilops chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to Aegilops chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to Brachypodium and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of Aegilops, wheat and the model species. Five syntenic regions of Brachypodium identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species Ae. biuncialis and Ae. geniculata. A certain level of wheat–Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.
A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
Yong Q Gu, Yaqin Ma, Naxin Huo, John P Vogel, Frank M You, Gerard R Lazo, William M Nelson, Carol Soderlund, Jan Dvorak, Olin D Anderson, Ming-Cheng Luo
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-496
Abstract: A total of 67,151 Brachypodium BAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of the Brachypodium genome was constructed. The map consisted of 671 contigs and 2,161 clones remained as singletons. The contigs and singletons spanned 414 Mb. A total of 13,970 gene-related sequences were detected in the BAC end sequences (BES). These gene tags aligned 345 contigs with 336 Mb of rice genome sequence, showing that Brachypodium and rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot of Brachypodium contigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum. Brachypodium contigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door to Brachypodium-Triticeae comparative genomics.The construction of the Brachypodium physical map, and its comparison with the rice genome sequence demonstrated the utility of the SNaPshot-HICF method in the construction of BAC-based physical maps. The map represents an important genomic resource for the completion of Brachypodium genome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available at http://phymap.ucdavis.edu/brachypodium/ webcite.Model systems play an important role in studies of genome structure and evolution, and are invaluable in gene isolation and functional characterization. The application of model systems toward the study of both basic and applied problems in plant biology has become routine. The model dicot Arabidopsis thaliana has been used in studies ranging from nutrient uptake and metabolism to plant-pathogen interactions. Unfortunately, due to its distant relationship to monocots, Arabidopsis is not an ideal model for grasses. Rice is being currently used as a grass model [1], but its primary ad
Fine Mapping of Wheat Stripe Rust Resistance Gene Yr26 Based on Collinearity of Wheat with Brachypodium distachyon and Rice  [PDF]
Xiaojuan Zhang, Dejun Han, Qingdong Zeng, Yinghui Duan, Fengping Yuan, Jingdong Shi, Qilin Wang, Jianhui Wu, Lili Huang, Zhensheng Kang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0057885
Abstract: The Yr26 gene, conferring resistance to all currently important races of Puccinia striiformis f. sp. tritici (Pst) in China, was previously mapped to wheat chromosome deletion bin C-1BL-6-0.32 with low-density markers. In this study, collinearity of wheat to Brachypodium distachyon and rice was used to develop markers to saturate the chromosomal region containing the Yr26 locus, and a total of 2,341 F2 plants and 551 F2:3 progenies derived from Avocet S×92R137 were used to develop a fine map of Yr26. Wheat expressed sequence tags (ESTs) located in deletion bin C-1BL-6-0.32 were used to develop sequence tagged site (STS) markers. The EST-STS markers flanking Yr26 were used to identify collinear regions of the rice and B. distachyon genomes. Wheat ESTs with significant similarities in the two collinear regions were selected to develop conserved markers for fine mapping of Yr26. Thirty-one markers were mapped to the Yr26 region, and six of them cosegregated with the resistance gene. Marker orders were highly conserved between rice and B. distachyon, but some rearrangements were observed between rice and wheat. Two flanking markers (CON-4 and CON-12) further narrowed the genomic region containing Yr26 to a 1.92 Mb region in B. distachyon chromosome 3 and a 1.17 Mb region in rice chromosome 10, and two putative resistance gene analogs were identified in the collinear region of B. distachyon. The markers developed in this study provide a potential target site for further map-based cloning of Yr26 and should be useful in marker assisted selection for pyramiding the gene with other resistance genes.
Brachypodium Genomics  [PDF]
Bahar Sogutmaz Ozdemir,Pilar Hernandez,Ertugrul Filiz,Hikmet Budak
International Journal of Plant Genomics , 2008, DOI: 10.1155/2008/536104
Abstract: Brachypodium distachyon (L.) Beauv. is a temperate wild grass species; its morphological and genomic characteristics make it a model system when compared to many other grass species. It has a small genome, short growth cycle, self-fertility, many diploid accessions, and simple growth requirements. In addition, it is phylogenetically close to economically important crops, like wheat and barley, and several potential biofuel grasses. It exhibits agricultural traits similar to those of these target crops. For cereal genomes, it is a better model than Arabidopsis thaliana and Oryza sativa (rice), the former used as a model for all flowering plants and the latter hitherto used as model for genomes of all temperate grass species including major cereals like barley and wheat. Increasing interest in this species has resulted in the development of a series of genomics resources, including nuclear sequences and BAC/EST libraries, together with the collection and characterization of other genetic resources. It is expected that the use of this model will allow rapid advances in generation of genomics information for the improvement of all temperate crops, particularly the cereals.
Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat
Jan Barto?, ?estmír Vl?ek, Frédéric Choulet, Mária D?unková, Kate?ina Cviková, Jan ?afá?, Hana ?imková, Jan Pa?es, Hynek Strnad, Pierre Sourdille, Hélène Bergès, Federica Cattonaro, Catherine Feuillet, Jaroslav Dole?el
BMC Plant Biology , 2012, DOI: 10.1186/1471-2229-12-155
Abstract: We used new-generation sequencing (NGS) to generate sequence of a Mb-sized region from wheat chromosome arm 3DS. Sequence assembly of 24 BAC clones resulted in two scaffolds of 1,264,820 and 333,768 bases. The sequence was annotated and compared to the homoeologous region on wheat chromosome 3B and orthologous loci of Brachypodium distachyon and rice. Among 39 coding sequences in the 3DS scaffolds, 32 have a homoeolog on chromosome 3B. In contrast, only fifteen and fourteen orthologs were identified in the corresponding regions in rice and Brachypodium, respectively. Interestingly, five pseudogenes were identified among the non-collinear coding sequences at the 3B locus, while none was found at the 3DS locus.Direct comparison of two Mb-sized regions of the B and D genomes of bread wheat revealed similar rates of non-collinear gene insertion in both genomes with a majority of gene duplications occurring before their divergence. Relatively low proportion of pseudogenes was identified among non-collinear coding sequences. Our data suggest that the pseudogenes did not originate from insertion of non-functional copies, but were formed later during the evolution of hexaploid wheat. Some evidence was found for gene erosion along the B genome locus.Polyploidy is considered one of the main driving forces of plant evolution and speciation. Whole genome duplication (WGD) provides a substrate for plant genome evolution, diversification and adaptation. The presence of two or more copies of the same gene reduces selection pressure and enables sub-functionalization and neo-functionalization. The analysis of whole-genome sequences revealed a frequent and often repeated occurrence of genome doubling during the evolution of higher plants. Even plants with relatively small genomes such as Arabidopsis thalianaBrachypodium distachyon and Malus domestica have experienced polyploidization events during their evolution [1-3].Some whole-genome duplication events occurred tens or even hundre
Phylogenetic, Molecular, and Biochemical Characterization of Caffeic Acid o-Methyltransferase Gene Family in Brachypodium distachyon  [PDF]
Xianting Wu,Jiajie Wu,Yangfan Luo,Jennifer Bragg,Olin Anderson,John Vogel,Yong Q. Gu
International Journal of Plant Genomics , 2013, DOI: 10.1155/2013/423189
Abstract: Caffeic acid o-methyltransferase (COMT) is one of the important enzymes controlling lignin monomer production in plant cell wall synthesis. Analysis of the genome sequence of the new grass model Brachypodium distachyon identified four COMT gene homologs, designated as BdCOMT1, BdCOMT2, BdCOMT3, and BdCOMT4. Phylogenetic analysis suggested that they belong to the COMT gene family, whereas syntenic analysis through comparisons with rice and sorghum revealed that BdCOMT4 on Chromosome 3 is the orthologous copy of the COMT genes well characterized in other grass species. The other three COMT genes are unique to Brachypodium since orthologous copies are not found in the collinear regions of rice and sorghum genomes. Expression studies indicated that all four Brachypodium COMT genes are transcribed but with distinct patterns of tissue specificity. Full-length cDNAs were cloned in frame into the pQE-T7 expression vector for the purification of recombinant Brachypodium COMT proteins. Biochemical characterization of enzyme activity and substrate specificity showed that BdCOMT4 has significant effect on a broad range of substrates with the highest preference for caffeic acid. The other three COMTs had low or no effect on these substrates, suggesting that a diversified evolution occurred on these duplicate genes that not only impacted their pattern of expression, but also altered their biochemical properties. 1. Introduction Temperate grains like wheat and barley, along with forage grasses, contribute greatly to the human food and animal feed supply. However, the large and complex genomes in these economically important grasses present challenges for genomics studies and map-based cloning of target genes for crop improvement. Similarly, although large perennial grasses like switchgrass and Miscanthus are being developed as dedicated herbaceous energy crops, our knowledge about the biological and genetic basis of important bioenergy traits remains limited [1–4]. Brachypodium distachyon (hereafter referred as Brachypodium) is an attractive experimental system and genomics model for grass research. It has many desirable attributes (small physical stature, short generation time, easy growth requirement, etc.) and numerous freely available genomics resources (high quality genome sequence, EST collection, large-insert BAC libraries, expression/tilling microarray, T-DNA mutant population, etc.) [5]. Thus, Brachypodium can serve as a useful model system to address issues unique to grasses ranging from grain improvement to the development of superior bioenergy crops [5–7].
The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes
Esteban Bortiri, Devin Coleman-Derr, Gerard R Lazo, Olin D Anderson, Yong Q Gu
BMC Research Notes , 2008, DOI: 10.1186/1756-0500-1-61
Abstract: The chloroplast genome of Brachypodium distachyon was sequenced by a combinational approach using BAC end and shotgun sequences derived from a selected BAC containing the entire chloroplast genome. Comparative analysis indicated that the chloroplast genome is conserved in gene number and organization with respect to those of other cereals. However, several Brachypodium genes evolve at a faster rate than those in other grasses. Sequence analysis reveals that rice and wheat have a ~2.1 kb deletion in their plastid genomes and this deletion must have occurred independently in both species.We demonstrate that BAC libraries can be used to sequence plastid, and likely other organellar, genomes. As expected, the Brachypodium chloroplast genome is very similar to those of other sequenced grasses. The phylogenetic analyses and the pattern of insertions and deletions in the chloroplast genome confirmed that Brachypodium is a close relative of the tribe Triticeae. Nevertheless, we show that some large indels can arise multiple times and may confound phylogenetic reconstruction.Plastids are key organelles of green plants, carrying out functions like photosynthesis, starch storage, nitrogen and sulfate metabolism, and synthesis of chlorophyll, carotenoids, fatty acids and nucleic acids [1]. Plastids have multiple copies of a circular, double-stranded DNA chromosome, each with a set of approximately 110 genes highly conserved in sequence and organization [2].In addition to their important biological roles, plastids have the potential to make a big impact on biotechnology. Plastid transformation, achieved via homologous recombination, is very advantageous compared to nuclear genome transformation mainly because it can generate high levels of gene expression and the recombinant DNA is more easily contained since chloroplasts are maternally inherited in most species of angiosperms [3].The family Poaceae, with approximately 10,000 species, contains the world's most important crops. T
Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources
Camille Rustenholz, Pete E Hedley, Jenny Morris, Frédéric Choulet, Catherine Feuillet, Robbie Waugh, Etienne Paux
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-714
Abstract: Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B.Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.The term "gene space" refers to the fraction of the genome corresponding to protein coding genes and, by extension, to the distribution of these genes [1]. In large genomes that contain abundant repetitive DNA, it encompasses also the notion of regions containing genes, the so-called gene-rich regions, surrounded by gene-poor regions composed of repeats [2].With the growing number of sequenced plant genomes, it becomes obvious that the distribution pattern of genes is far from random and not universal across the plant kingdom. Small plant genomes, such as Arabidopsis thaliana (125 Mb), Brachypodium distachyon (272 Mb) and Oryza sativa (389 Mb) exhibit fairly homogenous gene distribution along their chromosomes [3-5]. The transition from a homogenous to a non-homogenous gene distribution seems correlated to the genome size. Indeed, in intermediate size genome, such as Populus trichocarpa (485 Mb) and Vitis vinifera (487 Mb), large regions alternating between high and low gene density wer
First Survey of the Wheat Chromosome 5A Composition through a Next Generation Sequencing Approach  [PDF]
Nicola Vitulo, Alessandro Albiero, Claudio Forcato, Davide Campagna, Francesca Dal Pero, Paolo Bagnaresi, Moreno Colaiacovo, Primetta Faccioli, Antonella Lamontanara, Hana ?imková, Marie Kubaláková, Gaetano Perrotta, Paolo Facella, Loredana Lopez, Marco Pietrella, Giulio Gianese, Jaroslav Dole?el, Giovanni Giuliano, Luigi Cattivelli, Giorgio Valle, A. Michele Stanca
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026421
Abstract: Wheat is one of the world's most important crops and is characterized by a large polyploid genome. One way to reduce genome complexity is to isolate single chromosomes using flow cytometry. Low coverage DNA sequencing can provide a snapshot of individual chromosomes, allowing a fast characterization of their main features and comparison with other genomes. We used massively parallel 454 pyrosequencing to obtain a 2x coverage of wheat chromosome 5A. The resulting sequence assembly was used to identify TEs, genes and miRNAs, as well as to infer a virtual gene order based on the synteny with other grass genomes. Repetitive elements account for more than 75% of the genome. Gene content was estimated considering non-redundant reads showing at least one match to ESTs or proteins. The results indicate that the coding fraction represents 1.08% and 1.3% of the short and long arm respectively, projecting the number of genes of the whole chromosome to approximately 5,000. 195 candidate miRNA precursors belonging to 16 miRNA families were identified. The 5A genes were used to search for syntenic relationships between grass genomes. The short arm is closely related to Brachypodium chromosome 4, sorghum chromosome 8 and rice chromosome 12; the long arm to regions of Brachypodium chromosomes 4 and 1, sorghum chromosomes 1 and 2 and rice chromosomes 9 and 3. From these similarities it was possible to infer the virtual gene order of 392 (5AS) and 1,480 (5AL) genes of chromosome 5A, which was compared to, and found to be largely congruent with the available physical map of this chromosome.
Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS
Delphine Fleury, Ming-Cheng Luo, Jan Dvorak, Luke Ramsay, Bikram S Gill, Olin D Anderson, Frank M You, Zahra Shoaei, Karin R Deal, Peter Langridge
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-382
Abstract: We report the use of Ae. tauschii for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii with 85 EST on the Ae. tauschii and barley genetic maps. The 24 contigs were aligned to the rice and B. distachyon genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the Ae. tauschii-rice and Ae. tauschii-Brachypodium syntenies were identical. We observed chromosomal rearrangements between Ae. tauschii and barley. The comparison of Ae. tauschii physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs.The physical map reported here is the first physical map using fingerprinting of a complete Triticeae genome. This study demonstrates that global fingerprinting of the large plant genomes is a viable strategy for generating physical maps. Physical maps allow the description of the co-linearity between wheat and grass genomes and provide a powerful tool for positional cloning of new genes.Although wheat is a major food for the world population and the most extensively grown crop, progress in genomics had been slowed due to the size and the complexity of the genome. The hexaploid genome of common wheat (Triticum aestivum) contains 16,000 Mb of DNA organized into three genomes, A, B and D, with 7 chromosomes each. This makes the wheat genome far larger than the sequenced rice genome at 430 Mb [1] and Brachypodiu
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