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Background Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales. Findings Using Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The single 5S ribosomal DNA locus had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11. Conclusions The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence, and genomic location, critical to understanding its role in diversity and evolution.

International audience; Meningeal melanocytic tumors are rare. We report an exceptional case of transformation of a meningeal melanocytoma in a malignant melanoma. The course of the disease extents from 61-years to 85-years and ends with the death of the patient. Besides histopathological and immunohistochemical data, we also report the array CGH study of the melanocytoma and melanoma components suggesting the malignant transformation from whole chromosome gains in the melanocytoma to additional segmental aberrations in the malignant melanoma. Beyond the rarity of this tumor subtype, this case report highlights the potential interest of molecular analyses for diagnostic and prognostic purposes in the field of meningeal melanocytic tumors.

Polyploidisation is a key source of diversification and speciation in plants. Most researchers consider sexual polyploidisation leading to unreduced gamete as its main origin. Unreduced gametes are useful in several crop breeding schemes. Their formation mechanism, i.e., First-Division Restitution (FDR) or Second-Division Restitution (SDR), greatly impacts the gametic and population structures and, therefore, the breeding efficiency. Previous methods to identify the underlying mechanism required the analysis of a large set of markers over large progeny. This work develops a new maximum-likelihood method to identify the unreduced gamete formation mechanism both at the population and individual levels using independent centromeric markers. Knowledge of marker-centromere distances greatly improves the statistical power of the comparison between the SDR and FDR hypotheses. Simulating data demonstrated the importance of selecting markers very close to the centromere to obtain significant conclusions at individual level. This new method was used to identify the meiotic restitution mechanism in nineteen mandarin genotypes used as female parents in triploid citrus breeding. SDR was identified for 85.3% of 543 triploid hybrids and FDR for 0.6%. No significant conclusions were obtained for 14.1% of the hybrids. At population level SDR was the predominant mechanisms for the 19 parental mandarins.

Les auteurs ont produit et caractérisé la première banque de BAC (chromosome bactériens artificiels) chez une espèce de bananier (#Musa balbisiana# 'Pisang Klutuk Wulung', d'où le nom de la banque PKW). Un protocole nouveau et amélioré d'isolement des noyaux a été employé pour surmonter les problèmes causés par l'abondance de polyphénols et de polysaccharides dans les tissus foliaires. L'emploi de la cytométrie en flux pour purifier les noyaux a éliminé la contamination aux métabolites secondaires ainsi que l'ADN plastidique. De plus, l'utilité d'un vecteur inductible, pCC1BAC, en vue de l'obtention d'une plus grande quantité d'ADN de BAC a été démontrée. La banque PKW compte l'équivalent de neuf génomes du #M. balbisiana# et la taille moyenne des inserts est de 135 kb. Elle est composée de deux sous-banques; la première (la sous-banque SN avec 24 960 clones) ayant été préparée en suivant un protocole standard amélioré pour l'isolement des noyaux tandis que la seconde (sous-banque FN avec 11 904 clones) a été obtenue à partir des noyaux purifiés par cytométrie en flux. Le criblage de la banque avec 12 sondes RFLP, connues comme étant situées sur huit groupes de liaison chez le #Musa acuminata#, a permis d'identifier une moyenne de 11 clones par sonde. Cette observation permet de valider l'estimé quant à la couverture du génome et indique une forte conservation entre les génomes des deux espèces du genre #Musa#. La localisation sur les chromosomes mitotiques de clones BAC choisis au-moyen d'hybridations FISH a permis de montrer que cette banque de clones BAC constitue une ressource utile pour la cartographie cytogénétique. Dans le cadre d'une démarche de clonage positionne] d'un facteur génétique qui est impliqué dans l'activation de séquence pararétrovirales intégrées appartenant au virus de la striure du bananier genre badnavirus (BSV), le locus BSV exprimé (BEL; "BSV expressed locus") a été délimité physiquement. La banque BAC PKW constitue un outil disponible publiquement et est présentement employé pour révéler les mécanismes d'intégration et d'activation de séquences du BSV et pour étudier la structure et l'évolution du génome du bananier.

We compared the reproductive system of Rubus alceifolius in its native range in Southeast Asia, in Madagascar, where the plant was introduced apparently some centuries ago, and in La Reunion, an Indian Ocean island onto which R. alceifolius was introduced (from Madagascan source populations) around 1850. While tetraploidy makes it impossible to analyze variation in R. alceifolius using classical methods of population genetics, both the patterns of genetic diversity (as revealed by AFLP [amplified fragment length polymorphism] markers) and differences between half-sib progeny and their maternal parents (revealed by microsatellite markers) show that in the plant's native range in southeast Asia, seeds are produced sexually. In contrast, in Madagascar sexual reproduction cannot alone account for the genetic patterns observed with microsatellite markers. Over 85% of the half-sib progeny resulting from open pollination gave multilocus genotypes identical to those of their respective maternal parents, despite the fact that the latter had alleles that were rare in the population. The other progeny differed in having an allele with one motif more or less than that of the maternal parent. Seeds thus appear to be produced mostly or exclusively by apomixis in Madagascar. We present findings suggesting that Madagascan populations result from hybridization of introduced R. alceifolius and native populations of R. roridus, a closely related species of Rubus subgenus Malachobatus, and suggest that apomixis was a consequence of this hybridization. In Reunionese populations of R. alceifolius (derived from Madagascan populations), seeds obtained in controlled pollination experiments were all genetically identical to maternal parents. While genetic variation (microsatellite markers) in Reunionese populations was low, it was sufficient to allow us to demonstrate that seeds could not have resulted from fertilization by the pollen donors chosen for controlled pollinations, or from autogamy, and were produced exclusively by apomixis.

The characterization of the mitotic chromosomes of Helianthus argophyllus by means of Feulgen staining, Giemsa C-banding, and the usual DNA sequence-specific fluorochromes allows a chromosomal classification of this species, and shows that two kinds of heterochromatin co-exist equilocally in its chromosomes. One type is confined to the pericentromeric areas of all the chromosomes and the other is associated with the secondary constrictions of the satellite chromosomes. This species is evolutionarily very close to H. annuus with which it is involved in introgression breeding programs. Since these two species show no intra- or interspecific differences with the above treatments, we have used C-banding followed by DAPI, chromomycin A3 or Acridine Orange, and the fluorescent in situ hybridization (FISH) with 5S and 18S-25S ribosomal DNA probes to characterize further the chromosomes of both species in an attempt to find practically applicable chromosomal markers. Our results confirm the heterogeneity of the heterochromatin in these species and show that neither its distribution nor its response to distinct fluorochrome treatments allows better discrimination of the chromosomes within or between the species. On the other hand, the 18S-5.8S-25S rDNA arrays are located in the secondary constrictions of the satellited SM7, SM10, and ST13 pairs and the 5S-rDNA genes are interstitially placed on the short arm of the SM7 and SM11 chromosomes in both species. This permits these chromosomes to be distinguished and provides markers which may be helpful for further physical mapping of DNA sequences in these species.Key words: chromosome banding, sunflower cytogenetics, heterochromatin, ribosomal DNA mapping, FISH.

Beyond their own commercial potential, highland papayas (Vasconcellea spp.) bear genes for resistances against important diseases, cold hardiness, and monoecy, which are absent from the common papaya genome. While the two genera share many morphological traits, strong reproductive barriers have considerably limited the success of introgression programs, imposing the use of special techniques for hybridizations. In fact, all cytogenetic and genetic studies have consistently shown that Vasconcellea is relatively distant from Carica as compared to other Caricaceae genera. A few years after the first breakthrough obtained in the field, the present chapter reviews the potential of the different highland papaya species as sources of genes for papaya improvement, the considerable experience accumulated in the different hybridization programs, the advantages of this difficult approach, and its current perspectives. It also stresses the need for further exploration within Vasconcellea and closer genera of the Caricaceae. After the successful introgression of papaya ring spot virus resistance from V. quercifolia, the combination of marker-assisted selection, new breeding schemes (e.g., bridging species), and a deeper knowledge of Caricaceae gene pools should give access to more genes of considerable interest to the papaya industry.

Vasconcellea, comprising 21 species, is the largest genus of the Caricaceae, best known for the monotypic genus Carica, including papaya (C. papaya), one of the most important tropical fruit crops. It is distributed from Mexico to Chile, with the center of diversity in Ecuador and Colombia. Because of their preference for higher altitudes, most Vasconcellea species are referred to as highland or mountain papayas. Currently, five of them are threatened and red-listed and four are not found in protected areas, while none of them are currently present in seed collections, raising questions on their conservation and urging for rapid action. Some Vasconcellea species have potential as novel tropical fruits, particularly V.?×?heilbornii, V.?cundinamarcensis, and V. goudotiana, which are being used for a growing (niche) market for new exotic products. As a source of papain, several Vasconcellea species show proteolytic activity up to 17 times as high as that of papaya. Others are being used as a source of new genes for papaya breeding, particularly for disease resistance (especially against papaya ringspot virus), cold tolerance, and specific organoleptic traits. Optimal use of Vasconcellea genetic resources requires a better understanding of its genetic potential, as well as the development of technologies to create intergeneric hybrids with papaya, as conventional breeding faces significant barriers. Cytogenetic and molecular studies, based on AFLP, PCR-RFLP, and SRR analysis, have allowed a better understanding of the evolution of the main Vasconcellea species, indicating complex hybridization and introgression processes among multiple species, which contrasts with the straightforward domestication of the common papaya. Genomic research in Vasconcellea has been limited to the sequencing of some gene fragments and the development of BAC libraries for a few species. Recent progress on papaya genomics, the development of a high-density genetic map, and the sequencing of the genome will help in the identification of genes of interest in Vasconcellea, either for papaya breeding or for the development of Vasconcellea species as new crops.

Fluram (Fluorescamine; 4-phenylspiro(furan-2(3H),1′-phthalan)-3,3′-dione) is a fluorogenic reagent, which permits the detection of primary amines by forming highly fluorescent pyrrolinone derivatives. This reagent has been used on methanol – acetic acid fixed metaphase chromosomes of mouse and man and proved to be very effective in differentiating chromosome regions in both genomes. Mouse centromeric heterochromatin is highly reactive, showing intense fluorescence in all centromeric regions, whereas human chromosomes show no fluorescence in such regions. In addition, a G-like banding pattern is also obtained in both types of chromosomes. The differential reactivity of each chromosome region showed by this method demonstrates a heterogeneous distribution of chromosome proteins, resulting in a chromosome banding pattern, which is in this case species dependent.Key words: cytogenetics, chromosome banding, mammalian chromosomes, fluorescence microscopy, Fluram.

Dioscorea alata is a polyploid species with several ploidy levels and its basic chromosome number has been considered by most authors to be x = 10. Standard chromosome counting and flow cytometry analysis were used to determine the chromosome number of 110 D. alata accessions of the CIRAD germplasm collection. The results revealed that 76% of accessions have 2n = 40 chromosomes, 7% have 2n = 60 chromosomes and 17% have 2n = 80 chromosomes. Progenies were produced from 2n = 40 types of D. alata and the segregation patterns of six microsatellite markers in four different progenies were analysed. The Bayesian method was used to test for diploid versus tetraploid (allo- and autotetraploid) modes of inheritance. The results provided the genetic evidence to establish the diploidy of plants with 2n = 40 chromosomes and to support the hypothesis that plants with 2n = 40, 60 and 80 chromosomes are diploids, triploids and tetraploids, respectively, and that the basic chromosome number of D. alata is x = 20. The findings obtained in the present study are significant for effective breeding programs, genetic diversity analysis and elucidation of the phylogeny and the species origin of D. alata.

The African pygmy mice, subgenus Nannomys, constitute the most speciose lineage of the genus Mus with 19 recognized species. Although morphologically very similar, they exhibit considerable chromosomal diversity which is here confirmed and extended by the G-banding analysis of 65 mice from West and South Africa. On the basis of their karyotype and distribution area, the specimens were assigned to at least five species. Extensive differentiation both within and between species was observed that involved almost exclusively Robertsonian translocations, 23 of which are newly described. Two of the rearrangements were sex chromosome-autosome translocations, associated in some cases with partial deletions of the X or Y chromosomes. Several authors have predicted that the highly deleterious effect of this rearrangement would be reduced if the sex and autosomal segments were insulated by a block of centromeric heterochromatin. The C-banding analyses performed showed that among the species carrying X-autosome translocations, one followed the expected pattern, while the other did not. In this case, functional isolation of the sex and autosome compartments must involve other repetitive sequences or genomic traits that require further molecular characterization. Such studies will provide insight into the causes and consequences of the high diversity of sex chromosome rearrangements in this subgenus.

In the past few years, approaches such as molecular cytogenetics and the use of molecular markers have permitted significant advances in the establishment of the evolutionary origin and genome structure of sugarcane, an important polyploid crop. The availability of new resources, such as a bacterial artificial chromosome library and a huge collection of expressed sequence tags, has opened the gateway to promising functional analyses on a genomic scale.

International audience; Three bulls of the Montbéliarde breed that exhibited fertility rates lower than 30% following more than 400 artificial inseminations were examined. Semen quality (sperm motility and morphology) from these bulls was normal. Fertilizing ability estimated from in vitro embryo production results was studied for two of them. In vitro production rate was very low for one bull (A) and normal for the other (B). Cytogenetic analyses were carried out on the three bulls using chromosome banding techniques. These analyses revealed a reciprocal translocation (12;17)(q22;q14) in bull B. Based on family analyses, the hypothesis of a de novo origin of this rearrangement is proposed.; Une nouvelle translocation réciproque chez un taureau hypofertile. Trois taureaux de race Montbéliarde présentant une très faible fertilité ($< 30 \%$) après plus de 400 inséminations artificielles ont été étudiés. Les trois individus présentaient une qualité de semence (motilité et morphologie des spermatozoïdes) normale. La fécondance de la semence (aptitude à la production in vitro d'embryons) a été étudiée chez deux individus. Celle-ci a été faible pour un taureau (A) et normale pour l'autre (B). Des analyses cytogénétiques ont été réalisées dans tous les cas à l'aide de techniques de coloration en bandes des chromosomes. Elles ont révélé une translocation réciproque (12 ; 17)(q22 ; q14) chez le taureau B. Les analyses familiales réalisées permettent de faire l'hypothèse d'une apparition de novo du remaniement.

The aims of this PhD were to determine (1) the effects of the herbicide diuron on the genome of the oyster, Crassostrea gigas, (2) the possible transmission to the offspring of damaged DNA and (3) its consequences on oyster physiology. The genotoxicity of diuron and the vertical transmission of DNA damage were highlighted after parental exposure to environmental concentrations of diuron during the gametogenesis. Primary DNA lesions were detected in both somatic cells and germ cells of exposed genitors. Detection of the oxidized base 8-oxodGuo in gonads shows that exposure to diuron led to an oxidative stress which likely explains the observed DNA strand breaks in spermatozoa. The transmission of these DNA damage was confirmed by fluorescent in situ hybridization: aneuploid nuclei were detected in embryos from diuron-exposed genitors. This hyper- and hypodiploidy particularly concerns 5S and 18-5.8-28S ribosomal genes localized on chromosomes 4, 5 and 10. Flow cytometry analysis showed survival of hypodiploid individuals at spat stage. This vertical transmission of damaged genetic material is associated with deleterious effects on the physiology of the offspring (developmental defects, growth retardation). Data acquired during this PhD contribute to a better understanding of the long-term effects of exposure to genotoxic pollutants. In the context of massive mortality outbreaks, the presence of chemical pollutants may contribute to a weakening of oysters in case of the presence of pathogens or adverse physicochemical environmental conditions., les effets d’un herbicide, le diuron, sur le génome de l'huître creuse, (2) la possible transmission des dommages à l'ADN à la descendance ainsi que (3) les conséquences physiologiques associées. La génotoxicité du diuron et la transmission verticale des dommages à l'ADN ont été démontrées après une exposition parentale à des concentrations environnementales de diuron pendant la période de gamétogenèse. Des lésions primaires à l’ADN ont été détectées aussi bien dans les cellules somatiques que dans les cellules germinales des géniteurs exposés. La détection de la base oxydée 8-oxodGuo dans les gonades montre que l'exposition au diuron a conduit à un stress oxydant qui vraisemblablement explique les cassures à l’ADN observées dans les spermatozoïdes. La transmission de ces dommages à l’ADN a été confirmée par la technique d’hybridation in situ : des noyaux aneuploïdes ont été détectés chez les embryons issus des géniteurs exposés au diuron. Cette hyper- et hypodiploïdie concerne notamment les gènes ribosomaux 5S et 18-5.8-28S présents sur les chromosomes 4, 5 et 10. Les analyses de cytométrie en flux montrent la survie d’individus hypodiploïdes au stade naissain. Cette transmission verticale de matériel génétique endommagé s'accompagne d'effets délétères au niveau de la physiologie des descendants (anomalies de développement, retard de croissance). Les données acquises au cours de cette thèse contribuent à une meilleure connaissance des effets à long terme de l'exposition à des polluants génotoxiques. Dans le contexte des mortalités massives, la présence de polluants chimiques pourrait contribuer à un affaiblissement des huîtres face à la présence de pathogènes ou à des conditions physicochimiques du milieu défavorables

Les caryotypes de douze especes de Glossines ont ete decrits par differents auteurs, au cours des six dernieres annees. Toutefois, parmi celles-ci, sept especes seulement ont ete relativement bien etudiees: deux especes du groupe palpalis (G. fuscipes fuscipes et G. tachinoides), quatre especes du groupe morsitans (G. m. morsitans, G. m. centralis, G. m. submorsitans et G. austeni) et une espece du groupe fusca (G. fusca congolensis) La carte des chromosomes polyteniques a pu, en outre, etre etablie chez une espece (G. m. morsitans) (Resume d'auteur)