Reeve Wayne, van Berkum Peter, Ardley Julie, Tian Rui, Gollagher Margaret, Marinova Dora, Elia Patrick, Reddy T B K, Pillay Manoj, Varghese Neha, Seshadri Rekha, Ivanova Natalia, Woyke Tanja, Baeshen Mohamed N, Baeshen Nabih A, Kyrpides Nikos
School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia.
U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA.
Stand Genomic Sci. 2017 Mar 4;12:26. doi: 10.1186/s40793-017-0238-2. eCollection 2017.
USDA 76 (INSCD = ARAG00000000), the type strain for , is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume, USDA 76 was selected as part of the DOE Joint Genome Institute 2010 sequencing project. Here the symbiotic abilities of USDA 76 are described, together with its genome sequence information and annotation. The 9,484,767 bp high-quality draft genome is arranged in 2 scaffolds of 25 contigs, containing 9060 protein-coding genes and 91 RNA-only encoding genes. The USDA 76 genome contains a low GC content region with symbiotic and genes, indicating the presence of a symbiotic island integration. A comparison of five genomes that formed a clique revealed that 356 of the 9060 protein coding genes of USDA 76 were unique, including 22 genes of an intact resident prophage. A conserved set of 7556 genes were also identified for this species, including genes encoding a general secretion pathway as well as type II, III, IV and VI secretion system proteins. The type III secretion system has previously been characterized as a host determinant for and/or soybean cultivars. Here we show that the USDA 76 genome contains genes encoding all the type III secretion system components, including a translocon complex protein NopX required for the introduction of effector proteins into host cells. While many bradyrhizobial strains are unable to nodulate the soybean cultivar Clark (), USDA 76 was able to elicit nodules on Clark (), although in reduced numbers, when plants were grown in Leonard jars containing sand or vermiculite. In these conditions, we postulate that the presence of NopX allows USDA 76 to introduce various effector molecules into this host to enable nodulation.
USDA 76（INSCD = ARAG00000000）是该菌株的模式菌株，是一种需氧、运动、革兰氏阴性、不形成芽孢的杆菌，从生长在美国的（L. Merr）有效固氮根瘤中分离得到。由于其作为这种经济上重要的豆科植物的微共生体具有重要意义，USDA 76被选为美国能源部联合基因组研究所2010年测序项目的一部分。这里描述了USDA 76的共生能力，以及其基因组序列信息和注释。9484767 bp的高质量草图基因组排列在2个支架的25个重叠群中，包含9060个蛋白质编码基因和91个仅编码RNA的基因。USDA 76基因组包含一个低GC含量区域，带有共生和基因，表明存在共生岛整合。对形成一个类群的五个基因组的比较显示，USDA 76的9060个蛋白质编码基因中有356个是独特的，包括一个完整的常驻原噬菌体的22个基因。还为该物种鉴定了一组7556个保守基因，包括编码一般分泌途径以及II型、III型、IV型和VI型分泌系统蛋白的基因。III型分泌系统先前已被表征为大豆品种和/或的宿主决定因素。在这里我们表明，USDA 76基因组包含编码所有III型分泌系统组件的基因，包括将效应蛋白导入宿主细胞所需的转位孔复合体蛋白NopX。虽然许多慢生根瘤菌菌株不能使大豆品种Clark（）结瘤，但当植物种植在含有沙子或蛭石的伦纳德罐中时，USDA 76能够在Clark（）上诱导结瘤，尽管数量减少。在这些条件下，我们推测NopX的存在使USDA 76能够将各种效应分子导入该宿主以实现结瘤。
