Diversity in the genus Saccharum and contribution to the genome of sugarcane cultivar R570

La canne à sucre (Saccharum spp.) est une culture majeure pour la production de sucre (80% de la production mondiale) et plus récemment pour la production de biocarburant ou de bioénergie. Les cultivars de canne à sucre sont hautement polyploïdes (2n = 100 à 130 chromosomes), aneuploïdes et dérivent essentiellement de croisements interspécifiques entre l'espèce domestiquée sucrée S. officinarum et l'espèce sauvage S. spontaneum. Dans le cadre de cette thèse, une première étude a concerné la caractérisation de l'origine de séries d'haplotypes homéologues (segments d'environ 100 kilobases) correspondant à deux régions du génome de R570. L'analyse de ces haplotypes a été réalisée sur la base de la comparaison de leurs SNP avec un échantillon représentatif de la diversité Saccharum. Les résultats suggèrent la présence de trois sous-génomes (A, B et C) au sein du cultivar R570 au lieu des deux attendus, avec les groupes d'haplotypes A et B qui auraient été contribués par S. officinarum et les haplotypes du groupe C par S. spontaneum. Une seconde étude a consisté en une analyse à une échelle plus globale de la diversité du genre Saccharum et de sa contribution aux génomes des cultivars modernes, en particulier le cultivar R570. Cette étude est basée sur un assemblage en cours de réalisation du génome polyploïde du cultivar R570 et de données de séquence Illumina du génome d'un panel d'accessions représentatives du genre Saccharum. Des groupes de k-mers répétés (potentiellement des segments d'éléments transposables), partagés entre certaines accessions de l'échantillon, ont été recherchés. La distribution de ces k-mers répétés a permis de différencier les espèces sauvages S. spontaneum et S. robustum, les espèces horticoles S. barberi et S. sinense et a mis en évidence des sous-groupes au sein de ces espèces ainsi que quelques accessions S. officinarum introgressées par un génome inconnu. La distribution des k-mers représentatifs des espèces et sous-groupes sur l'assemblage du génome du cultivar R570 confirme que les chromosomes de ce cultivar sont en majorité issus de l'espèce S. officinarum (77%). Cette distribution montre aussi que le cultivar R570 comporte des introgressions provenant d'au moins deux pôles de la diversité S. spontaneum (pôle Indien, 15%, et Indonésien, 7%) et du génome inconnu (1%). Enfin, des résultats très préliminaires suggèrent que les sous-génomes A et B détectés dans la première étude seraient possiblement liés à divers sous-groupes de S. robustum à partir desquels S. officinarum aurait été domestiquée.Sugarcane (Saccharum spp.) is a major crop for sugar production (80% of world production) and more recently, for biofuel or bioenergy production. Sugarcane cultivars are highly polyploid (2n = 100 to 130), aneuploid and derived from interspecific crosses, mainly between the sweet domesticated species S. officinarum and the wild species S. spontaneum. During this thesis, a first study focused on the characterization of the origin of a series of homoeologous haplotypes (segments of about 100 kilobases) corresponding to two genomic regions of cultivar R570. The analysis of these haplotypes was performed based on SNP comparison with a representative sample of the Saccharum diversity. The results suggested the presence of three subgenomes (A, B and C) within cultivar R570, instead of the expected two, with haplotypes from groups A and B contributed by S. officinarum and haplotypes from group C by S. spontaneum. A second study consisted in a more global analysis of the Saccharum genus diversity and its contribution to the genomes of modern cultivars, in particular cultivar R570. This study was based on an ongoing assembly of the polyploid genome of cultivar R570 and on Illumina whole genome sequence data from a panel of representative accessions of the genus Saccharum. Groups of repeated k-mers (potentially segments of transposable elements) shared between some accessions of the panel were searched. The distribution of these repeated k-mers allowed the differentiation of the wild species S. spontaneum and S. robustum, the horticultural species S. barberi and S. sinense. It also highlighted the existence of subgroups within these species and identified some S. officinarum accessions introgressed by an unknown genome. The distribution of k-mers representative of species and subgroups on the genome assembly of cultivar R570 confirmed that the chromosomes of cultivar R570 are mainly derived from S. officinarum (77%). This distribution also showed that cultivar R570 has introgressions from at least two different subgroups of S. spontaneum diversity (Indian, 15%, and Indonesian, 7%) and from the unknown genome (1%). Finally, very preliminary results suggested that the A and B subgenomes detected in the first study were possibly linked to various subgroups of S. robustum from which S. officinarum may have been domesticated

Aligning the unalignable: bacteriophage whole genome alignments

International audienceBackgroundIn recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences.ResultsIn this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressiveMauve aligner – which implements a partial order strategy, but whose alignments are linearized – shows a greatly improved interactive graphic display, while avoiding misalignments.ConclusionsMultiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains.A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://​bitbucket.​org/​thekswenson/​alpha)

Exploration of the supramolecular interactions involving tris-dipicolinate lanthanide complexes in protein crystals by a combined biostructural, computational and NMR study.

International audienceIncorporating in a non-covalent manner lanthanide derivatives into protein crystals has shown to be of prime interest for X-ray crystallography, insofar as these versatile compounds can co-crystallize with proteins through supramolecular interactions, in addition to being strong anomalous scatterers for anomalous-based diffraction techniques. In this paper, the selective affinity of tris-dipicolinate lanthanide complexes for cationic amino-acid residues is explored, using a panel of experimental (X-ray diffraction, NMR titration) and theoretical methods that provides access to an accurate description of the interaction process

Additional file 3 of Aligning the unalignable: bacteriophage whole genome alignments

Detailed comparison of Alpha and Mauve alignments for the four S. aureus phages phiETA3, phiNM2, phiNM1 and B236. (XLSX 83 kb

Three founding ancestral genomes involved in the origin of sugarcane

International audienceAbstract Background and Aims Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. Methods To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. Key Results The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. Conclusions This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity

Three founding ancestral genomes involved in the origin of sugarcane.

Background and aimsModern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum.MethodsTo analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus.Key resultsThe diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered.ConclusionsThis evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity

Crop Domestication in the Asia Pacific Region: A review

Understanding crop domestication provides a basis for ongoing genetic improvement of crops, especially in the utilization of wild crop relatives as a source of new variation and may guide the domestication of new crops. The Asia Pacific region is home to most of the world’s human population and is a region in which many important crops were domesticated. Here we review the domestication of banana, citrus, coconut, macadamia, mango, millet, mungbean, rice, sugarcane and taro in the Asia Pacific region. These examples illustrate the importance of this region in the development of agriculture. The challenges of conservation of the genetic resources for these crops are exacerbated by the large human population and rapid economic development in the region. Advances in genetic technologies provide an opportunity for accelerated genetic improvement of these crops and the domestication of new crops