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COFFEA CANEPHORA GENOME Presentation Report Coffea canephora is a coffee plant that belongs to Rubiaceae family and Coffea genus [1]. There are more than 100 species under the genus Coffea but most coffee productions are Coffea arabica and Coffea canephora [4]. Around the world, 70% of caffe productions are Coffea arabica and rest 30% productions are Coffea canephora [3]. Coffea sessiliflora, Coffea eugeniodies and Coffea pseudozangubariae are some examples of Coffees that found under the genus Coffea . Arabica consumed more than Canephora because, arabica is more tasty than Canephora, Aroma of the Arabica is better and Canephora have bitter taste [2,3,4]. Coffee is chosen to sequence the genome because there are several reasons. It is consumed 2.25 billion cups per day all around the world [3]. Approximately 12 billion dollars income per year [4]. 26 million employees in coffee sector in 52 countries [3]. Another goal for sequencing is understanding pathway and production of caffeine molecules which is very important our life [5]. One of the reason was understand Coffea arabica genome. Coffea canephora and Coffea eugeniodies hybridizations forms Coffea arabica. Coffea canephora and Coffea eugenioides are diploids, but Coffea Canephora is allotetraploid (4X) [1]. There are several platforms and methods for genome sequencing. Denoued et al., used whole genome sequencing strategy for coffee genome sequencing. Illumina GAIIx and Roche/454 GSFLX next generation sequencing platforms used to generate datas. They extracted DNA from coffee leaves. Also, they extracted RNA for transcriptome sequencing. RNA sequences read by Illumina GAII. BWA algorithm technology used for alignment of RNA reads to produce contigs. Coffea canephora genome assembled by using Solexa/Illumina platform and GapCloser Software used for fillingg Gaps between the contigs [5]. From these datas some specific databases generated for coffee such as Coffee Genome Hub (http://coffee-genome.org). Also, some informations included in some familiar databases such as NCBI Map Viewer (http://www.ncbi.nlm.nih.gov/mapview/).
Coffea canephora has 11 chromosomes [6] and 50% of the genome is transposable elements [5]. 130,305 Coding sequence and 25,574 protein coding gene is exist in genome. Also, it has high amount of intronless genes around 5,004. MicroRNA precursors are around 92 in the genome. 13,345 scaffolds with total length 586.6 Mb generated from 25,216 contigs [5]. Table 1: Chromosome overview of Coffea Canephora [7]. Results showed that from studies, Coffea canephora genome shows similarity to Solanum lycopersicum (tomato) and Vitis (grape). Also, canephora genome have syntenic relations with other asteroid species [5]. 155,283 proteins matched between Coffee, Gentianales, Arabidopsis, Solanum tubercosum, Solanum lycopersicum and Vitis [5].
Figure 1: Syntenic regions between Grape, Tomato and Coffee [5]. Genes of Coffea canephora named systematically. For example Cc01_g00020 is one of the gene name and it means that this gene is Coffea canephora gene which is located in first chromosome with region 00020. Cc02_g16990 and Cc06_g16090 are another examples of genes [5]. Cc01_g00020 gene is 5023 base pair long with 10877 nucleotides. It is coded for 171 amino acid. Another name for this gene is ‘Translation elongation factor activity’. Function of this gene is chain elongation at the ribosome [5,7,8]. Figure 2: Chromosomal location of Cc01_g00020 gene. Showed with red line on chromosome 1 [8].
63 different different transcription factor found in the genome. CPP, GRAS and SBP are just three examples for these transcription factors. CPP involved in Cc03_g04130 gene which has function in flower development. GRAS transcription factor involved in Cc00_g06820 gene and SBP involved in Cc00_g14640 gene which they have function in cell division and early flower development respectively [5]. Also, some biosynthesis genes are exist in the Coffea canephora genome such as isoflavones, alkaloids, monoterpenes, caffeine [5]. Isoflavones synthesis dietary oestrogen and antigen [9], alkaloids synthesis morphine [10], and monoterpenes forms aerosol which have role in climate change [11]. Caffeine is a central nervous system stimulant which is synthesised in leaves, seeds and fruits in Coffea canephora . Biosynthesis is controlled by series of genes which are called NMT genes [5]. Figure 3: Biosynthesis of caffeine. Xanthosine molecule can converted caffeine with just three methylation steps [5].
NMTs or N-methyltransferase is an enzyme that produces coffee. 23 NMT genes found in Coffea canephora [5]. Generally, some N-methyltransferase genes have same structure with 4 exons and 3 exons [5]. Some of the NMT genes are listed below in Table 2. Table 2: Some NMT genes in Coffea canephora genome [5]. Studies suggest that NMT genes mostly expressed in leaf than other parts of the canephora species. Also, researchers state that caffeine production is more expressed in coffee rather than other caffeine-producer species such as Camellia and Theobroma [5]. Figure 4: Expression profile of NMT genes in Coffea canephora .
Another study, Mohanan et al., discovered that NMT genes are similar in their coding genes. They have polymorphism in their untranslated regions such as 3’ UTR, promotors and introns [12]. Coffea canephora genome studies helps us to understand caffeine biosynthesis and it is the first step to study with other coffea species in molecular level. Researchers wants to study with arabica genome now based on canephora genome. REFERENCES
[1] ICGN Coffee Genomics Workshops, Plant and Animal Genome Meeting (PAG) , San Diego, California, USA, January 10-14, 2009 [2] International Coffee Genomics Network, Report 7th Coffee Genomics Workshop held at the XXII Plant and Animal Genome Meeting, San Diego, California January 11-15, 2014 [3] Coffee genome sheds light on the evolution of caffeine (2014, September 4) retrieved 17 October 2014 from http://phys.org/news/2014-09-coffee-genome-evolution- caffeine.html [4] Brazilian Coffee genome project : an EST-based genomic resource, Braz. J., Plant Physiol., 18(1):95-108, 2006 [5] The coffee genome provides insight into the convergent evolution of caffeine biosynthesis, France Denied et. al., Science 345, 1181 (2014); DOI: 10.1126/science. 1255274 [6] NCBI Map Viewer Database : http://www.ncbi.nlm.nih.gov/projects/mapview/ map_search.cgi?taxid=49390&query= [7] Ptools database : http://ptools.cirad.fr [8] Coffee-genome hub database : http://coffee-genome.org [9] Heber, D (2008). Berdanier, C.D, Dwyer, J.T., Feldman, E.B., ed. Plant Foods and Phytochemicals in human health . CRC Press. pp. 176–181. [10]Andreas Luch (2009). Molecular, clinical and environmental toxicology . Springer. p. 20. ISBN 3-7643-8335-6. [11]D. V. Spracklen, B. Bonn, K. S. Carslaw (2008). "Boreal forests, aerosols and the impacts on clouds and climate". Philosophical Transactions of the Royal Society A 366 (1885): 4613–26. Bibcode:2008RSPTA.366.4613S. doi:10.1098/rsta.2008.0201. PMID 18826917. [12]Shibin Mohanan (2013). “Involvement of a novel intronic microRNA in cross regulation of N-methytransferase genes involved in caffeine biosynthesis in Coffea canephora”. ScienceDriect. Gene 519(2013) 107-112. View publication stats View publication stats
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