2014 publications


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Authors

Mago R, Tabe L, Vautrin S, Imková H, Kubaláková M, Upadhyaya N, Berges H, Kong X, Breen J, Dole El J, Appels R, Ellis J, Spielmeyer W

BMC Plant Biol. 2014. 14(1):1585.

Abstract

The adult plant stem rust resistance gene Sr2 was introgressed into hexaploid wheat cultivar (cv) Marquis from tetraploid emmer wheat cv Yaroslav, to generate stem rust resistant cv Hope in the 1920s. Subsequently, Sr2 has been widely deployed and has provided durable partial resistance to all known races of Puccinia graminis f. sp. tritici. This report describes the physical map of the Sr2-carrying region on the short arm of chromosome 3B of cv Hope and compares the Hope haplotype with non-Sr2 wheat cv Chinese Spring.Results Sr2 was located to a region of 867 kb on chromosome 3B in Hope, which corresponded to a region of 567 kb in Chinese Spring. The Hope Sr2 region carried 34 putative genes but only 17 were annotated in the comparable region of Chinese Spring. The two haplotypes differed by extensive DNA sequence polymorphisms between flanking markers as well as by a major insertion/deletion event including ten Germin-Like Protein (GLP) genes in Hope that were absent in Chinese Spring. Haplotype analysis of a limited number of wheat genotypes of interest showed that all wheat genotypes carrying Sr2 possessed the GLP cluster; while, of those lacking Sr2, some, including Marquis, possessed the cluster, while some lacked it. Thus, this region represents a common presence-absence polymorphism in wheat, with presence of the cluster not correlated with presence of Sr2. Comparison of Hope and Marquis GLP genes on 3BS found no polymorphisms in the coding regions of the ten genes but several SNPs in the shared promoter of one divergently transcribed GLP gene pair and a single SNP downstream of the transcribed region of a second GLP.ConclusionPhysical mapping and sequence comparison showed major haplotype divergence at the Sr2 locus between Hope and Chinese Spring. Candidate genes within the Sr2 region of Hope are being evaluated for the ability to confer stem rust resistance. Based on the detailed mapping and sequencing of the locus, we predict that Sr2 does not belong to the NB-LRR gene family and is not related to previously cloned, race non-specific rust resistance genes Lr34 and Yr36.

Link : http://www.ncbi.nlm.nih.gov/pubmed/25547135 

Dominance hierarchy arising from the evolution of a complex small RNA regulatory network.

Science. 346(6214):1200-5. doi: 10.1126/science.1259442.

Added on : 15 December 2014

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Authors

Durand E1, Méheust R1, Soucaze M1, Goubet PM1, Gallina S1, Poux C1, Fobis-Loisy I2, Guillon E2, Gaude T2, Sarazin A3, Figeac M4, Prat E5, Marande W5, Bergès H5, Vekemans X1, Billiard S1, Castric V6.

Science. 346(6214):1200-5. doi: 10.1126/science.1259442.

Abstract

The prevention of fertilization through self-pollination (or pollination by a close relative) in the Brassicaceae plant family is determined by the genotype of the plant at the self-incompatibility locus (S locus). The many alleles at this locus exhibit a dominance hierarchy that determines which of the two allelic specificities of a heterozygous genotype is expressed at the phenotypic level. Here, we uncover the evolution of how at least 17 small RNA (sRNA)-producing loci and their multiple target sites collectively control the dominance hierarchy among alleles within the gene controlling the pollen S-locus phenotype in a self-incompatible Arabidopsis species. Selection has created a dynamic repertoire of sRNA-target interactions by jointly acting on sRNA genes and their target sites, which has resulted in a complex system of regulation among alleles.

Link : http://www.ncbi.nlm.nih.gov/pubmed/25477454

Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome.

BMC Genomics. 2014 Sep 26;15:816. doi: 10.1186/1471-2164-15-816

Added on : 06 October 2014

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Authors

Santos AA, Penha HA, Bellec A, Munhoz Cde F, Pedrosa-Harand A, Bergès H, Vieira ML.

BMC Genomics. 2014 Sep 26;15:816. doi: 10.1186/1471-2164-15-816

Abstract

Background:
The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource.

Results:
The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n = 9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%).

Conclusions:
We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome study. Remarkably, a number of BAC-end pair sequences could be mapped to intervals of the sequenced Arabidopsis thaliana, V. vinifera and P. trichocarpa chromosomes, and putative collinear microsyntenic regions were identified.

Link : http://www.ncbi.nlm.nih.gov/pubmed/25260959


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Authors

Makhloufi E, Yousfi FE, Marande W, Mila I, Hanana M, Bergès H, Mzid R, Bouzayen M.

J Exp Bot. 2014

Abstract

As food crop, wheat is of prime importance for human society. Nevertheless, our understanding of the genetic and molecular mechanisms controlling wheat productivity conditions has been, so far, hampered by the lack of sufficient genomic resources. The present work describes the isolation and characterization of TdERF1, an ERF gene from durum wheat (Triticum turgidum L. subsp. durum). The structural features of TdERF1 supported the hypothesis that it is a novel member of the ERF family in durum wheat and, considering its close similarity to TaERF1 of Triticum aestivum, it probably plays a similar role in mediating responses to environmental stresses. TdERF1 displayed an expression pattern that discriminated between two durum wheat genotypes contrasted with regard to salt-stress tolerance. The high number of cis-regulatory elements related to stress responses present in the TdERF1 promoter and the ability of TdERF1 to regulate the transcription of ethylene and drought-responsive promoters clearly indicated its potential role in mediating plant responses to a wide variety of environmental constrains. TdERF1 was also regulated by abscisic acid, ethylene, auxin, and salicylic acid, suggesting that it may be at the crossroads of multiple hormone signalling pathways. Four TdERF1 allelic variants have been identified in durum wheat genome, all shown to be transcriptionally active. Interestingly, the expression of one allelic form is specific to the tolerant genotype, further supporting the hypothesis that this gene is probably associated with the susceptibility/tolerance mechanism to salt stress. In this regard, the TdERF1 gene may provide a discriminating marker between tolerant and sensitive wheat varieties.

 

Link : http://www.ncbi.nlm.nih.gov/pubmed/25205575

Structural and functional partitioning of bread wheat chromosome 3B.

Science. 2014 Jul 18;345(6194):1249721. doi: 10.1126/science.1249721.

Added on : 02 September 2014

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Authors

Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C.

Science. 2014 Jul 18;345(6194):1249721. doi: 10.1126/science.1249721.

Abstract

We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.

http://www.ncbi.nlm.nih.gov/pubmed/25035497

Building the sugarcane genome for biotechnology and identifying evolutionary trends.

BMC Genomics. 2014 Jun 30;15(1):540.

Added on : 08 July 2014

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Authors

De Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GM, Del Bem LE, Vicentini R, Nogueira FT, Campos RA, Nunes SL, Turrini PC, Vieira AP, Ochoa Cruz EA, Corrêa TC, Hotta CT, de Mello Varani A, Vautrin S, da Trindade AS, de Mendonça Vilela M, Lembke CG, Sato PM, de Andrade RF, Nishiyama MY Jr, Cardoso-Silva CB, Scortecci KC, Garcia AA, Carneiro MS, Kim C, Paterson AH, Bergès H, D Hont A, de Souza AP, Souza GM, Vincentz M, Kitajima JP, Van Sluys MA.

BMC Genomics. 2014 Jun 30;15(1):540.

Abstract

BACKGROUND:
Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.

RESULTS:
Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.

CONCLUSIONS:
This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery.

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome.

Biology (Basel). 3(2):295-319. doi: 10.3390/biology3020295

Added on : 19 May 2014

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Authors

Gill N, Buti M, Kane N, Bellec A, Helmstetter N, Berges H, Rieseberg LH.

Biology (Basel). 3(2):295-319. doi: 10.3390/biology3020295

Abstract

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are "novel" to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.


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Authors

Shoeva OY, Khlestkina EK, Berges H, Salina EA.

Gene. 538(2):334-41. doi: 10.1016/j.gene.2014.01.008.

Abstract

Chalcone-flavanone isomerase (CHI; EC 5.5.1.6.) participates in the early step of flavonoid biosynthesis, related to plant adaptive and protective responses to environmental stress. The bread wheat genomic sequences encoding CHI were isolated, sequenced and mapped to the terminal segment of the long arms of chromosomes 5A, 5B and 5D. The loss of the final Chi intron and junction of the two last exons was found in the wheat A, B and D genomes compared to the Chi sequences of most other plant species. Each of the three diploid genomes of hexaploid wheat encodes functional CHI; however, transcription of the three homoeologous genes is not always co-regulated. In particular, the three genes demonstrated different response to salinity in roots: Chi-D1 was up-regulated, Chi-A1 responds medially, whereas Chi-B1 was not activated at all. The observed variation in transcriptional activity between the Chi homoeologs is in a good agreement with structural diversification of their promoter sequences. In addition, the correlation between Chi transcription and anthocyanin pigmentation in different parts of wheat plant has been studied. The regulatory genes controlling anthocyanin pigmentation of culm and pericarp modulated transcription of the Chi genes. However, in other organs, there was no strong relation between tissue pigmentation and the transcription of the Chi genes, suggesting complex regulation of the Chi expression in most parts of wheat plant.

Meiotic gene evolution: can you teach a new dog new tricks?

Mol Biol Evol. 2014

Added on : 17 April 2014

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Authors

Lloyd A, Ranoux M, Vautrin S, Glover N, Fourment J, Charif D, Choulet F, Lassalle G, Marande W, Tran J, Granier F, Pingault L, Remay A, Marquis C, Belcram H, Chalhoub B, Feuillet C, Bergès H, Sourdille P, Jenczewski E.

MolBiol Evol. 2014

Abstract

Meiosis, the basis of sex, evolved through iterative gene duplications. To understand whether subsequent duplications have further enriched the core meiotic "tool-kit", we investigated the fate of meiotic gene duplicates following Whole Genome Duplication (WGD), a common occurrence in eukaryotes. We show that meiotic genes return to a single copy more rapidly than genome-wide average in Angiosperms, one of the lineages in which WGD is most vividly exemplified. The rate at which duplicates are lost decreases through time, a tendency that is also observed genome-wide and may thus prove to be a general trend post-WGD. The sharpest decline is observed for the subset of genes mediating meiotic recombination; however, we found no evidence that the presence of these duplicates is counter-selected in two recent polyploid crops selected for fertility. We therefore propose that their loss is passive, highlighting how quickly WGDs are resolved in the absence of selective duplicate retention.

http://www.ncbi.nlm.nih.gov/pubmed/24694832


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Authors

Raats D, Frenkel Z, Krugman T, Dodek I, Sela H, Imková H, Magni F, Cattonaro F, Vautrin S, Bergès H, Wicker T, Keller B, Leroy P, Philippe R, Paux E, Dole El J, Feuillet C, Korol A, Fahima T

Genome Biol. 2013 Dec 20;14(12):R138.

Abstract

BACKGROUND:
The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution.

RESULTS:
Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. Chromosome 1BS gene space spans the entire length of the chromosome arm, with 76% of the genes organized in small gene-islands, accompanied by a two fold increase in gene density from the centromere to the telomere.

CONCLUSIONS:
This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes, and a non-uniform size expansion along the centromere-telomere axis, compared with other model cereal genomes. The high quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.

http://www.ncbi.nlm.nih.gov/pubmed/24359668