Evolution of gene families involved in banana fruit development and ripening : W077

A reference genome sequence of banana was recently obtained from a Musa acuminata doubled-haploid accession (DH-Pahang, 523 Mb) and organized into eleven pseudomolecules. This genome opens brand new perspectives for the identification of genes underlying key physiological processes and agricultural traits in this economically important species. To identify genes involved in banana fruit development and ripening, we used a whole genome-scale approach combining phylogenomic analyses and gene expression profiling. Global analysis of gene expression in banana fruits in response to ethylenic treatment was performed using RNA-seq. In parallel, gene families involved in core ethylene biosynthesis/signaling pathways and starch/sucrose metabolism were identified in the Musa genome using comparative genomics and phylogenomic analyses with eleven plant species. Our results showed a progressive global reprogramming of banana fruits during ripening characterized by an inhibition of the downstream ethylene signaling pathway. In addition, we identified expansions of gene families encoding transcriptional regulation elements of the ethylene signaling pathway in Musa. These expansions are currently analyzed in relation to Musa whole genome duplications. Finally, the combined structural and gene expression analyses led to the identification of candidate genes and gene family members involved in banana fruit ripening. (Résumé d'auteur

Genomics of an ancient sex chromosome in Tilapia. W633

We have developed important genomic tools and methods of comparative genomics in the Nile tilapia, Oreochromis niloticus. The physical comparative map generated with BACs allowed us to calculate that there were about one rearrangement of intra-chromosomal every 3 Mb. For most chromosomes (about 40-48 Mb) there were about 16 breakpoints with ie eight inversions per chromosome. When extrapolated to the large bivalent chromosome Chr 1-LG3 (about 100-120 Mb), we estimate probably 40 breakpoints and 20 inversions. Our work suggests that intrachromosomal rearrangements with 160 inversions have occurred since the divergence of tilapia with stickleback, the species found to be closely related to tilapia. We have also developed a high resolution RH map containing 1296 markers distributed over the 22 chromosomes, that are now identifiable by cytogenetic analysis. The linkage groups of the genetic map were anchored with 149 microsatellites to chromosomes. A inverted zone was found by BAC-FISH close to the centromere in one of the Chr1-LG3 chromosomes of XY males and in 2 Chr1-LG3 chromosomes of YY males, but absent in XX females. This inversion is not in the region where recombination is suppressed. These results suggest that the Chr1-LG3 chromosome is still acting as a sex chromosome. The Nile tilapia appears to be in the midst of a transition between ZW to XY systems. In the Chr1-LG3 chromosome, 515 protein-encoding genes were found with 152 being tilapia-specific, while in the inversed region 19 genes were found including the gene dmrtA1. Highly conserved and ordered syntenies have been identified with the genes of the inversion zone, not only with the stickleback (Chr 7 and Chr9) but also with the chicken Z chromosome, the platypus X5 Chr and also with human Chr9, in which genes involved in sex determination are located. (Texte integral

Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods

Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa acuminata)

TARP as immunotherapeutic target in AML expressed in the LSC compartment

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The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications

Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes. Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested

BAC libraries construction from the ancestral diploid genomes of the allotetraploid cultivated peanut.

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Molecular Diagnostic of Both Brown and Orange Sugarcane Rust and Evaluation of Sugarcane Brown Rust Resistance in Tucuman, Argentina, Using Molecular Markers Associated with Bru1 a Broad-Range Resistance Allele

Brown rust (Puccinia melanocephala) and orange rust (P. kuehnii) cause important yield loss in global sugarcane production. Due to the difficulties of distinguishing between the two diseases to the naked eye, it is essential to use molecular techniques for an accurate rust diagnosis. A major gene, Bru1, which confers resistance to a broad spectrum of P.melanocephala strains in different parts of the world, has been described, and molecular markers closely associated with this allele have been developed. The aims of the present study were: (1) to optimise a PCR-based method to diagnose and characterise the causal agent of both rusts in Tucumán; (2) to determine the usefulness of the Bru1 gene in the Sugarcane Breeding Program of “Estación Experimental Agroindustrial Obispo Colombres” (EEAOC) by studying its association with resistant and susceptible phenotypes; and (3) to assess the frequency of the Bru1 allele in the sugarcane germplasm of the EEAOC. Conditions for both rust diagnoses were optimised. Out of 129 genotypes evaluated to study the usefulness of the Bru1 allele, 49 were found to be resistant to brown rust, but only eight of these resistant genotypes were positive for the Bru1 allele. Also frequency of appearance of the Bru1 allele was analysed in 191 sugarcane accessions of the EEAOC germplasm, and its presence was detected in only 7 % of the genotypes evaluated. In conclusion, although results showed that Bru1 markers enable positive selection of this character, additional source(s) of resistance are available in the EEAOC Sugarcane Breeding Program.Fil: Racedo, Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Gobierno de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial Obispo Colombres; ArgentinaFil: Perera, María Francisca. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Gobierno de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial Obispo Colombres; ArgentinaFil: Bertani, Romina Priscila. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Gobierno de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial Obispo Colombres; ArgentinaFil: Funes, C.. Gobierno de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial Obispo Colombres; ArgentinaFil: González, V.. Gobierno de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial Obispo Colombres; ArgentinaFil: Cuenya, María Inés. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Gobierno de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial Obispo Colombres; ArgentinaFil: D'Hont, A.. Centre de Coopération Internationale en Recherche Agronomique pour le Développement; FranciaFil: Welin, Bjorn. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Gobierno de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial Obispo Colombres; ArgentinaFil: Castagnaro, Atilio Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Gobierno de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial Obispo Colombres; Argentin

Genome structure and chromosome segregation in triploid interspecific plantain bananas (AAB) and breeding accessions (AAAB)

Many banana cultivars are triploid interspecific hybrids between M. acuminata (Genome A, 2n=22) and M. balbisiana (Genome B, 2n=22). They included the important group of Plantain cooking bananas classified as AAB that account for almost 20% of the bananas produced worldwide. Previous molecular analysis suggested that this group is genetically homogeneous but diversified phenotypically through somatic variations. To progress on the understanding of chromosome composition and segregation of the breeding material used to improve plantain bananas, we performed several analysis based on Genotyping By Sequencing (GBS) technologies. We analyzed the A/B chromosomes composition of a few plantain cultivars and discovered chromosome segments with AAA composition and one entire chromosome with ABB composition instead of the supposed general 'AAB' composition. We compared the global chromosome structure of A and B genomes through the construction a high density M. balbisiana genetic map and its comparison with the M. acuminata reference sequence assembly. We identified a large reciprocal translocation between a region of 0.6Mb at the beginning of chromosome 1 and a 8 Mb region at the end of chromosome 3. We also identified a large inversion of 9Mb within chromosome 5. We analyzed the A/B chromosomes segregation in a progeny from an 'AAAB' tetraploid breeding accession derived from a plantain. We revealed frequent recombination between A and B all along the genomes with a few exceptions. The exceptions consisted in the absence of recombination recorded in the inverted segment between A and B on chromosome 5 and a reduced recombination rate near the translocated regions on chromosome 1 and 3. We also observed 62% of aneuploids in the progeny involving mainly the three chromosomes that differed in their global structure between A and B genomes. Implication of these results on the origin of plantain banana cultivars and on breeding of allopolyploid bananas will be discussed based on the patterns of recombination revealed