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Introduction Advances in plant genome sequencing have improved our understanding of DNA sequence organisation, distribution, and expression on chromosomes (Heng et al. 2018). DNA probes specific for fluorescence in situ [...], Coffea spp. chromosomes are very small and accumulate a variety of repetitive DNA families around the centromeres. However, the proximal regions of Coffea chromosomes remain poorly understood, especially regarding the nature and organisation of the sequences. Taking advantage of the genome sequences of C. arabica (2n = 44), C. canephora, and C. eugenioides (C. arabica progenitors with 2n = 22) and good coverage genome sequencing of dozens of other wild Coffea spp., repetitive DNA sequences were identified, and the genomes were compared to decipher particularities of pericentromeric structures. The searches revealed a short tandem repeat (82 bp length) typical of Gypsy/TAT LTR retrotransposons, named Coffea_sat11. This repeat organises clusters with fragments of other transposable elements, comprising regions of non-coding RNA production. Cytogenomic analyses showed that Coffea_sat11 extends from the pericentromeres towards the middle of the chromosomal arms. This arrangement was observed in the allotetraploid C. arabica chromosomes, as well as in its progenitors. This study improves our understanding of the role of the Gypsy/TAT LTR retrotransposon lineage in the organisation of Coffea pericentromeres, as well as the conservation of Coffea_sat11 within the genus. The relationships between fragments of other transposable elements and the functional aspects of these sequences on the pericentromere chromatin were also evaluated. Highlights: A scattered short tandem repeat, typical of Gypsy/TAT LTR retrotransposons, associated with several fragments of other transposable elements, accumulates in the pericentromeres of Coffea chromosomes. This arrangement is preserved in all clades of the genus and appears to have a strong regulatory role in the organisation of chromatin around centromeres. Key words: centromeric retrotransposons, chromocentres, Coffea genomes, FISH, Gypsy LTR retrotransposons. Les chromosomes des espèces du genre Coffea sont très petits et présentent une accumulation de familles d'ADN répétitif autour des centromères. Les régions proximales des chromosomes du genre Coffea demeurent mal caractérisées, particulièrement en ce qui regarde la nature et l'organisation des séquences. En s'appuyant sur les séquences des génomes du C. arabica (2n = 44), du C. canephora et du C. eugenioides (les espèces ancestrales du C. arabica, chacune à 2n = 22), ainsi que du séquençage de profondeur adéquate pour des douzaines d'autres espèces sauvages au sein du genre Coffea, les séquences répétitives ont été identifiées et les génomes ont été comparés pour décoder les particularités des structures péricentromériques. Ces investigations ont révélé une courte séquence répétée en tandem (longue de 82 pb) qui est typique des rétrotransposons à LTR de type Gypsy/TAT et qui a été nommée Coffea_sat11. Cette séquence répétée est organisée en amas incluant des fragments d'autres éléments transposables, lesquels constituent des régions produisant des ARN non-codants. Des analyses cytogénétiques ont montré que Coffea_sat11 s'étend des régions péricentromériques jusqu'au milieu des bras chromosomiques. Cette disposition est observée tant au sein des chromosomes allotétraploïdes du C. arabica que chez ses ancêtres. La présente étude contribue à la compréhension du rôle de la lignée des rétrotransposons à LTR Gypsy/TAT dans l'organisation des régions péricentromériques chez le genre Coffea, ainsi que dans la conservation de Coffea_sat11 au sein du genre. Les relations avec des fragments d'autres éléments transposables et les aspects fonctionnels de ces séquences sur la chromatine péricentromérique sont également évalués. Mots-clés : rétrotransposons centromériques, chromocentres, génomes du genre Coffea, FISH, rétrotransoposons à LTR Gypsy.

Introduction The genus Coffea L. (Rubiaceae) includes more than 100 species native to Africa and Madagascar (Davis et al. 2006; Maurin et al. 2007). Coffea arabica L. and Coffea canephora [...], The genus Coffea possesses about 100 species, and the most economically important are Coffea canephora and Coffea arabica. The latter is predominantly self-compatible with 2n = 4x = 44, while the others of the genus are diploid with 2n = 2x = 22 and mostly self-incompatible. Studies using molecular markers have been useful to detect differences between genomes in Coffea; however, molecular and cytogenetic studies have produced only limited information on the karyotypes organization. We used DOP-PCR to isolate repetitive elements from genome of Coffea arabica var. typica. The pCa06 clone, containing a fragment of 775 bp length, was characterized by sequencing and used as a probe in chromosomes of C. arabica and six other species: C. canephora, Coffea eugenioides, Coffea kapakata, Coffea liberica var. dewevrei, Coffea racemosa, and Coffea stenophylla. This insert shows similarities with a gag protein of the Ty3-gypjy-hke super-family. Dot blot and FISH analyses demonstrated that pCa06 is differentially accumulated between species and chromosomes. Signals appeared scattered and clustered on the chromosomes and were also associated with heterochromatic regions. While the literature shows that there is a high karyotype similarity between Coffea species, our results point out differences in the accumulation and dispersion of this Ty3-gypsy-like retrotransposon during karyotype differentiation of Coffea. Key words: Coffea, dot blot, FISH, gag sequence, retrotransposons, Ty3-gypsy-like. Le genre Coffea compte environ 100 especes dont les plus importantes au plan economique sont Coffea canephora et Coffea arabica. Cette derniere est principalement auto-compatible avec 2n = 4x = 44, tandis que les autres especes au sein du genre sont diploides avec 2n = 2x = 22 et sont majoritairement auto-incompatibles. Des etudes avec des marqueurs moleculaires ont ete utiles pour detecter les differences entre les genomes au sein du genre Coffea, mais les analyses en cytogenetique moleculaire ont produit peu d'information sur l'organisation des caryotypes. Les auteurs ont employe le DOP-PCR pour isoler des sequences repetees du genome du Coffea arabica var. typica. Le clone pCa06, porteur d'un insert de 775 pb, a ete sequence et employe comme sonde sur les chromosomes du C. arabica et de six autres especes : C. canephora, Coffea eugenioides, Coffea kapakata, Coffea liberica var. dewevrei, Coffea racemosa et Coffea stenophylla. Cet insert presente de la similarite avec la proteine gag des elements de la superfamille Ty3-gypsy. Des buvardages ponctuels et des analyses FISH ont montre que pCa06 est present en quantites variables entre especes et entre chromosomes. Les signaux semblaient epars et groupes sur les chromosomes, ainsi qu'associes aux regions heterochromatiques. Bien que la litterature rapporte qu'il y a une grande similarite des caryotypes entre les especes du genre Coffea, les resultats obtenus ici mettent en evidence des differences quant a l'accumulation et a la dispersion de ce retrotransposon de type Ty3-gypsy au cours de la differenciation carytoypique chez les Coffea. Mots-cles: Coffea, buvardage ponctuel, FISH, sequence gag, retrotransposon, element de type Ty3-gypsy.

Post-harvest processing (PHP) modifies the quality of the coffee and increases the value of coffee production. The choice of PHP to apply depends primarily on the available infrastructure, local climatic conditions and the desired end-value. The objective of this study was to evaluate the influence of PHP on the physico-chemical characteristics of green and roasted coffee beans and their sensory attributes. Coffee cherries from IAPAR 59 cultivar were processed as natural coffee (CN), semi-dry coffee (CD), de-pulped coffee (CP) and floating coffee (CF). Total and reducing sugars, phenolic compounds, chlorogenic acids, lipids, proteins, caffeine and water content were determined in coffee beans collected during (10thday) and at the end of each processing. The roasted beans and their sensory attributes were also analyzed. The greatest changes at the ending point of the processes were found in total and reducing sugars, phenolic compounds, chlorogenic acids and lipids contents. The PHP presented different weight loss to achieve the same visual brown color and luminosity. Beverage sensory attributes were influenced by the PHP: CN and CP coffees presented similar intensities of coffee aroma, but higher intensity of green grassy aroma, and taste were found in CF and CN coffees. Aroma and taste precursors were modified during the PHP and these were associated to husk removal of the coffee beans, suggesting an activation of the germination metabolism during the PHP. This study allowed the characterization of the effects of the different post-harvest processing on the roasted coffee beans and provides the foundations to monitor their efficiencies in the future. [ABSTRACT FROM AUTHOR]

This study evaluated the transcriptional profile of genes related to nitrogen (N) assimilation in coffee plants susceptible and resistant to rust fungi under N sufficiency and N suppression. For this purpose, we inoculated young coffee leaves with Hemileia vastatrix uredospores and collected them at 0, 12, 24 and 48 hours post-inoculation (HPI) to evaluate the relative expressions of genes encoding cytosolic glutamine synthetase (CaGS1), plastid glutamine synthetase (CaGS2), nitrate reductase (CaNR), and asparagine synthetase (CaAS). The genes exhibited distinct patterns of transcriptional modulation for the different genotypes and N nutritional regimes. The resistant genotype (I59) presented high levels of transcription in response to pathogen inoculation for CaNR and CaGS1 genes, evaluated under N sufficiency in the initial moments of infection (12 HPI). The gene CaGS1 also showed a peak at 48 HPI. The susceptible genotype (CV99) showed increased transcript rates of CaNR at 12 and 24 HPI in response to rust inoculation. The transcriptional patterns observed for CV99, under N suppression, were high levels for CaAS and CaGS2 at all post-inoculation times in response to coffee leaf rust disease. In addition, CaGS1 was up-regulated at 48 HPI for CV99. Cultivar I59 showed high transcript levels at 12 HPI for CaAS and peaks at 24 and 48 HPI for CaGS2 in inoculated samples. Consequently, total chlorophyl concentration was influenced by N suppression and by rust infection. Regarding enzyme activities in vitro for glutamine synthetase and CaNR, there was an increase in infected coffee leaves (I59) and under N sufficiency. Moreover, CV99 was modulated in both N nutritional regimes for GS activity in response to rust. Our results indicate that N transport genes trigger a differential modulation between genotypes through the action of rust disease. [ABSTRACT FROM AUTHOR]