Guyot Romain, Darré Thibaud, Dupeyron Mathilde, de Kochko Alexandre, Hamon Serge, Couturon Emmanuel, Crouzillat Dominique, Rigoreau Michel, Rakotomalala Jean-Jacques, Raharimalala Nathalie E, Akaffou Sélastique Doffou, Hamon Perla
IRD UMR IPME, CoffeeAdapt, BP 64501, 34394, Montpellier Cedex 5, France.
IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France.
Mol Genet Genomics. 2016 Oct;291(5):1979-90. doi: 10.1007/s00438-016-1235-7. Epub 2016 Jul 28.
The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994 Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7 %. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53 % of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes.
咖啡属有124个已描述的物种，其自然分布范围从热带非洲延伸至西印度洋岛屿、印度、亚洲直至澳大拉西亚。两种栽培种，即阿拉伯咖啡和卡内弗拉咖啡，受到了深入研究，而所有野生种的育种潜力和基因组组成仍鲜为人知。在此，我们报告了代表自然生物地理分布的11个咖啡物种中高度重复转座元件含量的特征及比较情况。通过454测序共产生了994兆碱基的序列，基因组覆盖度在3.2%至15.7%之间。分析表明，高度重复转座元件，主要是长末端重复反转录转座子（LTR-RT），占咖啡基因组的32%至53%，这取决于它们的生物地理位置和基因组大小。来自西非和中非的物种（真咖啡）含有最高的LTR-RT含量，但相对于其基因组大小没有强烈变化。相反，对于岛屿物种（马斯卡林咖啡），观察到LTR-RT有强烈变化，表明这些元件在该组中有不同的动态变化。两个LTR-RT谱系，SIRE和Del在非洲物种和岛屿物种之间明显有差异地积累，表明这些谱系与非洲咖啡物种的基因组分化有关。总之，本研究获得的信息增进了我们的认识，并为野生咖啡基因组的组成、进化和分化带来了新的数据。
