Dihaploid Coffea arabica genome sequencing and assembly.

Coffea arabica which accounts for 70% of world coffee production is an allotetraploid with a genome size of approximately 1.3 Gb and is derived from the hybridization of C. canephora (710 Mb) and C. eugenioides (670 Mb). To elucidate the evolutionary history of C. arabica, and generate critical information for breeding programs, a sequencing project is underway to finalize a reference genome using a dihaploid line and a set of Menu Abstract: Dihaploid Coffea arabica Genome Sequencing and Assembly (Plant and Animal Genome XXIII Conference) https://pag.confex.com/pag/xxiii/webprogram/Paper16983.html [25/02/2015 15:00:12] 30 C. arabica accessions

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica

GBS data C49N4ACXX_3_fastq.gz

GBS data file (Illumina reads) for Coffea specie

Grau de umidade e temperatura na conservação de sementes de café Moisture content and temperature on the preservation of coffee seeds

O presente trabalho foi realizado com o objetivo de verificar as influências do grau de umidade e da temperatura de armazenamento na manutenção da qualidade de sementes de Coffea arabica L. Sementes com 51%, 41%, 34%, 23%, 16% e 10% de água, acondicionadas em sacos de polietileno e mantidas sob temperaturas de 30 °C, 20 °C e 10 °C, durante 48 semanas de armazenamento, foram submetidas a avaliações periódicas do grau de umidade, da germinação, do vigor e da sanidade. Foi constatado que as reduções do grau de umidade até 10% e da temperatura até 10 °C são favoráveis à manutenção da qualidade fisiológica das sementes, e que umidade próxima a 23% favorece o estabelecimento de Penicillium sp. e de Aspergillus sp. nas sementes.<br>The aim of this work was to verify the influences of the moisture content and storage temperature in the preservation of Coffea arabica L. seeds. Seeds with 51%, 41%, 34%, 23%, 16% and 10% moisture content were packed in polyethylene bags and stored at temperatures of 30 °C, 20 °C and 10 °C for forty-eight weeks, and submitted to periodic evaluations of moisture content, germination, vigour and sanity. Decreases in moisture content until 10% and temperature until 10 °C were favorable to the maintenance of seed physiological quality. Seed moisture content around 23% favor the establishment of Penicillium sp. and Aspergillus sp

Natural infection of several Coffea species and hybrids and Psilanthus ebracteolatus by the coffee ringspot virus (CoRSV)

Coffee ringspot is a minor coffee disease caused by the nuclear type of Brevipalpus mite-transmitted virus, Coffee ringspot virus (CoRSV). Recently outbreaks of the disease in some growing regions of the state of Minas Gerais, Brazil, were registered with qualitative and quantitative yield losses. Coffea arabica was the only species registered as natural host. A survey was made on a germplasm collection of Coffea and related species kept at the Centro de Café "Alcides Carvalho", Instituto Agronômico, Campinas, state of São Paulo (SP), Brazil, to assess natural susceptibility of Coffee species, other than C. arabica and some interspecific hybrids of Coffea as well as other non-Coffea plant species to the Coffee ringspot virus (CoRSV). The following plants were found with ringspot symptoms on their leaves and/or fruits besides C. arabica L.: C. kapakata (IAC 4511), C. dewevrei cv. Excelsa, C. canephora cv. Robusta, hybrid derivative of the C. arabica × C. racemosa (IAC1195-5-6-2), C. arabica × C. dewerei (Piatã IAC 387), Híbrido de Timor CIFC 832/1 (derivative from a natural crossing between C. arabica × C. canephora) and C. racemosa. Also Psilanthus ebracteolatus, a species close to the genus Coffee was also found with ringspot lesions on their leaves. All these plants were also found infested by Brevipalpus mites identified as B. phoenicis. Infection of these plants by CoRSV was confirmed by the observation of characteristic cytopathic effects in the tissues of the lesion and by RT-PCR using a pair of primer specific for CoRSV. Only with C. racemosa RT-PCR failed to amplify the CoRSV genome. The susceptibility of P. ebracteolatus to CoRSV adds new dimension regarding its controversial taxonomic position