MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceaefamily

Plechakova, Olga; Tranchant‐Dubreuil, Christine; Bénédet, Fabrice; Couderc, Marie; Tinaut, Alexandra; Viader, Véronique; Block, Petra De; Hamon, Perla; Campa, Claudine; Kochko, Alexandre de; Hamon, Serge; Poncet, Valérie

doi:10.1186/1471-2229-9-123

Cited by 24 publications

(18 citation statements)

References 24 publications

(30 reference statements)

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“…PCR conditions and all information on the markers are given in MoccaDB (http://moccadb.mpl.ird.fr; Plechakova et al. ) and in the coffee genome hub (Dereeper et al. ).…”

Section: Methodsmentioning

confidence: 99%

Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species

Despinoy

Hamon

et al. 2016

Ecology and Evolution

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The frequency of plant species introductions has increased in a highly connected world, modifying species distribution patterns to include areas outside their natural ranges. These introductions provide the opportunity to gain new insight into the importance of flowering phenology as a component of adaptation to a new environment. Three Coffea species, C. arabica, C. canephora (Robusta), and C. liberica, native to intertropical Africa have been introduced to New Caledonia. On this archipelago, a secondary contact zone has been characterized where these species coexist, persist, and hybridize spontaneously. We investigated the impact of environmental changes undergone by each species following its introduction in New Caledonia on flowering phenology and overcoming reproductive barriers between sister species. We developed species distribution models and compared both environmental envelopes and climatic niches between native and introduced hybrid zones. Flowering phenology was monitored in a population in the hybrid zone along with temperature and precipitation sequences recorded at a nearby weather station. The extent and nature of hybridization events were characterized using chloroplast and nuclear microsatellite markers. The three Coffea species encountered weak environmental suitability compared to their native ranges when introduced to New Caledonia, especially C. arabica and C. canephora. The niche of the New Caledonia hybrid zone was significantly different from all three species' native niches based on identity tests (I Similarity and D Schoener's Similarity Indexes). This area appeared to exhibit intermediate conditions between the native conditions of the three species for temperature‐related variables and divergent conditions for precipitation‐related ones. Flowering pattern in these Coffea species was shown to have a strong genetic component that determined the time between the triggering rain and anthesis (flower opening), specific to each species. However, a precipitation regime different from those in Africa was directly involved in generating partial flowering overlap between species and thus in allowing hybridization and interspecific gene flow. Interspecific hybrids accounted for 4% of the mature individuals in the sympatric population and occurred between each pair of species with various level of introgression. Adaptation to new environmental conditions following introduction of Coffea species to New Caledonia has resulted in a secondary contact between three related species, which would not have happened in their native ranges, leading to hybridization and gene flow.

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“…PCR conditions and all information on the markers are given in MoccaDB (http://moccadb.mpl.ird.fr; Plechakova et al. ) and in the coffee genome hub (Dereeper et al. ).…”

Section: Methodsmentioning

confidence: 99%

Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species

Despinoy

Hamon

et al. 2016

Ecology and Evolution

Self Cite

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“…More recently, as the ability to sequence plant and crop genomes via next generation sequencing has almost become common place and relatively inexpensive (Varshney et al, 2009), the requirement to correlate this data with detailed and quantitative pheno(chemo)typic data has become a requirement and has seen a significant ramping up of complementary 'omics efforts under the banner of systems biology to bridge the genotype-to-phenotype gap (Fiehn, 2002). Already we are beginning to see these highly detailed complementary analytical approaches being applied in our most common crops such as potato (Lehesranta et al, 2005;Shepherd et al, 2006;Lehesranta et al, 2006;van Dijk et al, 2009;Shepherd et al, 2010), tomato (Hoekenga, 2008;Matsukura et al, 2008;Barone et al, 2009;Gavai et al, 2009;Plechakova et al 2009;Sánchez Pérez et al, 2009), tomato (Hoekenga, 2008;Matsukura et al, 2008;Barone et al, 2009;Gavai et al, 2009;Plechakova et al 2009;Sánchez Pérez et al, 2009) and to a lesser degree soft fruit such as raspberry Mazzitelli et al, 2007;Stewart et al, 2007;McDougall et al 2008). The crops addressed by this unified approach will undoubtedly broaden as the approaches become more common place and the technologies, and associated data handling software, more accessible.…”

Section: The Future Importance Of Metabolomics In Crop Researchmentioning

confidence: 99%

Crops and Tasty, Nutritious Food – How Can Metabolomics Help?

Stewart¹,

Shepherd²,

Hall

et al. 2011

Annual Plant Reviews Volume 43

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Food quality, security and safety have become topics of considerable recent interest. With a rapidly growing world population, entailing an everexpanding requirement for food, and with the global consumer making higher and better-informed demands on our crop and food producers, much attention is being given to how we can meet all these growing needs. Crop growers and food processors alike are already looking at state-of-the-art technologies such as metabolomics as a source of new inroads into the generation of detailed knowledge on the biochemical composition of crop products and how they change during transport, storage and industrial processing. All the steps in the food production chain, from the moment the plant breeder makes the first cross to the canning factory delivering to the supermarket distributor, have potentially significant influence on the quality of the final product the consumer places on the kitchen table. Metabolomics of crop plants and plant products is already being widely applied and is generating new information on the complexity of food composition. In this chapter, some of the main subjects of recent research, concerning both fresh and processed materials, are covered. Emphasis has been laid on technological

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“…When the marker is selected, the web site can display this marker in pre-computed multiple sequence alignments using the Look-Align viewer . MoccaDB (http://moccadb.mpl.ird.fr) is an integrative database for functional, comparative and diversity studies in the Rubiaceae family which includes coffee (Plechakova et al, 2009). It provides an easy access to markers, such as SSR, SNP and RFLP and related information data such as PCR assay conditions, cross amplification within related species, locus position on different linkage maps and diversity parameters.…”

Section: Molecular Databasesmentioning

confidence: 99%

Genome diversity in Triticum aestivum

Lai¹

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The aims of this PhD research are to identify and characterise genome diversity in Triticum aestivum (bread wheat).This research will establish a process for the identification of large numbers of single nucleotide polymorphisms (SNPs) and other genetic variations in Triticum aestivum.Single nucleotide polymorphisms (SNPs) are the most abundant type of molecular genetic marker and can be used for producing high-resolution genetic maps, marker-trait association studies and marker assisted breeding. Large polyploid genomes, such as wheat, present a challenge for SNP discovery due to the potential presence of multiple homoeologues for each gene.AutoSNPdb has been successfully applied to identify SNPs from Sanger sequence data for several species, including barley, rice and Brassica, but the volume of data required to accurately call SNPs in the complex genome of wheat has prevented its application to this important crop. DNA sequencing technology has been revolutionised by the introduction of next generation sequencing, and it is now possible to generate several million sequence reads in a timely and cost effective manner.Wheat transcriptome sequence data has been generated using Roche 454 Life Sciences technology. This data has been applied for SNP discovery using a modified autoSNPdb method, which integrates SNP and gene annotation information with a graphical viewer. A total of 4,694,141 sequence reads from three bread wheat varieties were assembled to identify a total of 38,928 candidate SNPs. Each SNP is within an assembly complete with annotation, enabling the selection of polymorphism within genes of interest.The discovery of large numbers of genomic SNPs across 16 Australian diverse bread wheat varieties has been completed using a novel algorithm SGSautoSNP. More than 10x whole genome shotgun Illumina paired read sequence data was generated through a bioplatforms collaboration and the data mapped to the draft assemblies of chromosomes ii 7A, 7B and 7D. Over 4 million inter-varietal SNPs were identified. SNP density varied along the lengths chromosome syntenic builds as well as between genomes.SNP density analysis and SNP transition/transversion ratio analysis provide insights into the evolution and breeding history of this important crop. Both the SNP density and SNP transition/transversion ratios across the D genome are significantly lower than across the A and B genomes. This difference reflects the evolutionary history of this crop. In addition, genes within low SNP density regions may have been selected during domestication and breeding. Furthermore, this SNP resource permits the application of high resolution skim based genotyping by sequencing (GBS), trait association and analysis of structural variation in populations.An integrated database and portal for wheat genome resource, WheatGenome.info, has been established and published online. This portal provides a variety of web-based systems hosting wheat genome and genomic data, including genomic SNPs, to support wheat research and crop improve...

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MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceaefamily

Cited by 24 publications

References 24 publications

Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species

Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species

Crops and Tasty, Nutritious Food – How Can Metabolomics Help?

Genome diversity in Triticum aestivum

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