Overview

The coffee is a perennial evergreen shrub or small tree of the Rubiaceae family. Coffee for daily consumption is a beverage made from coffee beans with various cooking utensils, and as one of the three major beverages in the world, it is popular as a major drink in the world along with cocoa and tea. Coffee is dark, bitter, slightly acidic and has a stimulating effect on the human body, mainly due to its caffeine content.

Geographical Distribution

The coffee tree is native to the highlands of southwestern Ethiopia in Africa.In the 13th century, Ethiopian troops invaded Yemen and brought coffee to the Arab world. By the 16th century, coffee had spread to other parts of the Middle East, Persia, Turkey and North Africa. In 1727, coffee was introduced to Brazil, where the climate was highly conducive to its growth, leading to rapid expansion throughout South America.

After more than a hundred years since coffee was introduced to China in 1898 and planted in the town of Wenchang Mai, Hainan, coffee cultivation has entered a period of rapid development. Currently, coffee is grown in various regions of China, including Fujian, Taiwan, Guangdong, Hainan, Guangxi, Sichuan, Guizhou, and Yunnan.

Application

• Drinking use: Coffee, made from roasted coffee beans, is one of the world's three major beverages, alongside cocoa and tea. It is widely enjoyed worldwide.
• Medicinal use: Coffee beans contain complex chemical components and possess various biological activities, making them highly valuable in medicine. They have shown potential in neuroprotection, combating hyperglycemia and hyperlipidemia, anti-cancer effects, anti-inflammatory properties, antioxidant activity, and hepatoprotection, among others.

Genome sequencing

In 2014, the French Institute of Genomics conducted sequencing of Coffea canephora, an outcrossing and highly heterozygous diploid species. They generated a total of 54.4 million reads from Roche 454 single and mate-pair sequencing, along with 143,605 reads from Sanger bacterial artificial chromosome-end sequencing. This achieved a genome coverage of approximately 30×. Additionally, Illumina sequencing data (60×) was used to improve the assembly. The resulting genome assembly consisted of 25,216 contigs and 13,345 scaffolds, with a total length of 568.6 Mb and a scaffold N50 of 1.26 Mb. Moreover, a high-density genetic map was constructed, encompassing 349 scaffolds and covering around 64% of the assembly (364 Mb), as well as 86% of the annotated genes. The genetic map was anchored to the 11 chromosomes of C. canephora. The researchers successfully annotated a total of 25,574 protein-coding genes, 92 microRNA precursors, and 2,573 organellar-to-nuclear genometransfers.

Coffea arabica is a heterotetraploid resulting from a cross between Coffea eugenioides and Coffea canephora. The reference genome was completed under the joint leadership of the World Coffee Research Center and IGA Technical Services Srl. The researchers assembled a genome with a total length of 1.536 Gbp, predicted 46,562 gene models, and compared it to the genomes of two other coffee species.

The Coffea humblotiana, a wild and endangered species from the Comoros Islands, naturally lacks caffeine. The reference genome was completed through the collaborative efforts of the Nestlé Research - Plant Sciences Research Unit and the University of Montpellier's School of Development Studies. For the de novo genome assembly, 48 Gb of PacBio SMRT reads were utilized, providing a coverage of approximately 102X. This assembly produced 783 contigs for a total of 422 Mb with an N50 of 1.5 Mb. To improve the contiguity of the assembly, a Hi-C scaffolding assembly was conducted using 90 million paired-end reads of 150 bp. Finally, 390 scaffolds were obtained, with an N50 of 29.6 Mb. A total of 32,874 genes were predicted, and 88.7% of the sequences were anchored to 11 chromosomes.

Reference

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2.李文俊.浅谈云南小粒咖啡及其种植技术[J].上海农业科技,2014(5):90-91,79. DOI:10.3969/j.issn.1001-0106.2014.05.062.

3.张柂儇,吴国泰,王晓禹,等.咖啡豆化学成分发现及药用价值研究现状[J].中国野生植物资源,2022,41(5):57-66. DOI:10.3969/j.issn.1006-9690.2022.05.009.

4.Denoeud F, Carretero-Paulet L, Dereeper A, et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science. 2014;345(6201):1181-1184. [OpenLBID: OLB-PM-25190796]

5.Scalabrin S, Toniutti L, Di Gaspero G, et al. A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm. Sci Rep. 2020;10(1):4642. [OpenLBID: OLB-PM-32170172]

6.Raharimalala N, Rombauts S, McCarthy A, et al. The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago. Sci Rep. 2021;11(1):8119. [OpenLBID: OLB-PM-33854089]