Department of Plant Sciences, University of California, Davis, CA 95616, USA.
Plant Mol Biol. 2012 Jan;78(1-2):95-107. doi: 10.1007/s11103-011-9849-y. Epub 2011 Nov 19.
Persian walnut (Juglans regia L.) is an economically important tree for its nut crop and timber. To gain insight into the structure and evolution of the walnut genome, we constructed two bacterial artificial chromosome (BAC) libraries, containing a total of 129,024 clones, from in vitro-grown shoots of J. regia cv. Chandler using the HindIII and MboI cloning sites. A total of 48,218 high-quality BAC end sequences (BESs) were generated, with an accumulated sequence length of 31.2 Mb, representing approximately 5.1% of the walnut genome. Analysis of repeat DNA content in BESs revealed that approximately 15.42% of the genome consists of known repetitive DNA, while walnut-unique repetitive DNA identified in this study constitutes 13.5% of the genome. Among the walnut-unique repetitive DNA, Julia SINE and JrTRIM elements represent the first identified walnut short interspersed element (SINE) and terminal-repeat retrotransposon in miniature (TRIM) element, respectively; both types of elements are abundant in the genome. As in other species, these SINEs and TRIM elements could be exploited for developing repeat DNA-based molecular markers in walnut. Simple sequence repeats (SSR) from BESs were analyzed and found to be more abundant in BESs than in expressed sequence tags. The density of SSR in the walnut genome analyzed was also slightly higher than that in poplar and papaya. Sequence analysis of BESs indicated that approximately 11.5% of the walnut genome represents a coding sequence. This study is an initial characterization of the walnut genome and provides the largest genomic resource currently available; as such, it will be a valuable tool in studies aimed at genetically improving walnut.
巴旦木（Juglans regia L.）是一种经济上重要的树种，其坚果和木材都具有重要价值。为了深入了解巴旦木基因组的结构和演化，我们利用 HindIII 和 MboI 克隆位点，从体外生长的 Chandler 品种巴旦木芽中构建了两个细菌人工染色体（BAC）文库，共包含 129024 个克隆。总共生成了 48218 个高质量的 BAC 末端序列（BES），累计序列长度为 31.2 Mb，约占巴旦木基因组的 5.1%。对 BES 中重复 DNA 含量的分析表明，基因组中约有 15.42%由已知重复 DNA 组成，而本研究中鉴定的巴旦木特有重复 DNA 构成了基因组的 13.5%。在巴旦木特有的重复 DNA 中，Julia SINE 和 JrTRIM 元件分别代表了第一个鉴定出的巴旦木短散在元件（SINE）和末端重复反转录转座子微型（TRIM）元件；这两种元件在基因组中都很丰富。与其他物种一样，这些 SINE 和 TRIM 元件可用于开发巴旦木基于重复 DNA 的分子标记。对 BES 中的简单序列重复（SSR）进行了分析，发现它们在 BES 中的丰度高于表达序列标签。分析的巴旦木基因组中 SSR 的密度也略高于杨树和木瓜。BES 序列分析表明，约 11.5%的巴旦木基因组代表编码序列。本研究是对巴旦木基因组的初步特征描述，提供了目前可用的最大基因组资源；因此，它将成为遗传改良巴旦木研究的宝贵工具。
