Institut de Recherche pour le Développement (IRD), UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394, Montpellier Cedex 5, France.
Plant Mol Biol. 2013 Oct;83(3):177-89. doi: 10.1007/s11103-013-0077-5. Epub 2013 May 25.
Coffee is one of the world's most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome.
咖啡是世界上最重要的农产品之一。咖啡属于茜草科（Rubiaceae），在双子叶植物真双子叶植物分支中与茄科（Solanaceae）同属一科。为构建同质双单倍体植株咖啡的两个细菌人工染色体（BAC）文库，我们使用了 HindIII 和 BstYI 两种酶。从两个文库的 73728 个克隆中总共生成了 134827 个高质量的 BAC 末端序列（BESs），经过排除质体和线粒体序列后，有 131412 个 BESs 被保留下来用于进一步分析。这几乎相当于咖啡预估基因组大小的 13%。BESs 中有 6.7%包含简单重复序列，其中最丰富的（47.8%）是单核苷酸基序。这些序列允许开发出许多有用的标记位点。潜在的转座元件（TEs）占全长 BESs 的 11.9%。BstYI 和 HindIII 文库之间存在差异（14.9%比 8.8%）。针对已知 TEs 编码序列对 BESs 的分析表明，11.9%的基因组对应于已知的重复序列，就像其他开花植物一样。咖啡基因组中的基因数量估计为 41973 个，这可能被高估了。比较基因组作图表明，咖啡和葡萄之间的微同线比咖啡和番茄或拟南芥之间的微同线更高。BESs 是咖啡全基因组首次调查的宝贵资源，为咖啡基因组的组成和进化提供了新的见解。
