UMR CNRS 6553 ECOBIO, OSUR, University of Rennes 1, Bât 14A Campus Scientifique de Beaulieu, 35042, Rennes Cedex, France.
Plant Mol Biol. 2013 Dec;83(6):591-606. doi: 10.1007/s11103-013-0111-7. Epub 2013 Jul 23.
Spartina species play an important ecological role on salt marshes. Spartina maritima is an Old-World species distributed along the European and North-African Atlantic coasts. This hexaploid species (2n = 6x = 60, 2C = 3,700 Mb) hybridized with different Spartina species introduced from the American coasts, which resulted in the formation of new invasive hybrids and allopolyploids. Thus, S. maritima raises evolutionary and ecological interests. However, genomic information is dramatically lacking in this genus. In an effort to develop genomic resources, we analysed 40,641 high-quality bacterial artificial chromosome-end sequences (BESs), representing 26.7 Mb of the S. maritima genome. BESs were searched for sequence homology against known databases. A fraction of 16.91% of the BESs represents known repeats including a majority of long terminal repeat (LTR) retrotransposons (13.67%). Non-LTR retrotransposons represent 0.75%, DNA transposons 0.99%, whereas small RNA, simple repeats and low-complexity sequences account for 1.38% of the analysed BESs. In addition, 4,285 simple sequence repeats were detected. Using the coding sequence database of Sorghum bicolor, 6,809 BESs found homology accounting for 17.1% of all BESs. Comparative genomics with related genera reveals that the microsynteny is better conserved with S. bicolor compared to other sequenced Poaceae, where 37.6% of the paired matching BESs are correctly orientated on the chromosomes. We did not observe large macrosyntenic rearrangements using the mapping strategy employed. However, some regions appeared to have experienced rearrangements when comparing Spartina to Sorghum and to Oryza. This work represents the first overview of S. maritima genome regarding the respective coding and repetitive components. The syntenic relationships with other grass genomes examined here help clarifying evolution in Poaceae, S. maritima being a part of the poorly-known Chloridoideae sub-family.
米草属物种在盐沼生态系统中发挥着重要作用。米草是一种旧世界物种，分布于欧洲和北非大西洋沿岸。这种六倍体物种（2n = 6x = 60，2C = 3700Mb）与从美洲海岸引入的不同米草物种杂交，形成了新的入侵杂种和异源多倍体。因此，米草引起了进化和生态方面的兴趣。然而，该属的基因组信息严重缺乏。为了开发基因组资源，我们分析了 40641 个高质量的细菌人工染色体末端序列（BES），代表了米草基因组的 26.7Mb。BES 被搜索与已知数据库的序列同源性。BES 的 16.91%代表已知重复序列，包括大多数长末端重复（LTR）反转录转座子（13.67%）。非 LTR 反转录转座子占 0.75%，DNA 转座子占 0.99%，而小 RNA、简单重复序列和低复杂度序列占分析 BES 的 1.38%。此外，还检测到 4285 个简单重复序列。使用高粱的编码序列数据库，发现 6809 个 BES 与同源性，占所有 BES 的 17.1%。与相关属的比较基因组学表明，与其他已测序的禾本科植物相比，米草的微同线性更好地保守，其中 37.6%的配对匹配 BES 正确定向在染色体上。使用所采用的映射策略，我们没有观察到大的宏同线性重排。然而，当将米草与高粱和水稻进行比较时，一些区域似乎经历了重排。这项工作代表了米草基因组在编码和重复成分方面的首次概述。与这里检查的其他禾本科基因组的同线性关系有助于澄清禾本科的进化，米草是鲜为人知的 Chloridoideae 亚科的一部分。
