A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research
A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research
复制标题
DOI：
10.1094/mpmi-06-12-0148-ta
复制
发表时间：
2012-12-01
影响因子：
3.5
通讯作者：
Martin, Gregory B.
中科院分区：
文献类型：
--
作者：
Bombarely, Aureliano;Rosli, Hernan G.;Martin, Gregory B.
benthamiana是一种被广泛用于研究分子植物-微生物相互作用和其他植物生物学领域基本问题的模式植物物种。这种流行源于它对多种病原体的易感性，特别是它对病毒诱导的基因沉默和瞬时蛋白表达方法的适应性。在这里，我们报告了N. benthamiana 63倍覆盖的草图基因组序列的生成，以及它在Sol Genomics Network上的可用性，用于BLAST搜索和下载到本地服务器。估计benthamiana的基因组大小为3gb （gigabases）。目前的组装由大约141,000个支架组成，跨度为2.6 Gb，其中50%的基因组序列包含在支架内的bb0 - 89千碱基。在GenBank中可获得的大约16,000个benthamiana的独特基因中，bbb90 %在该集合中有代表。通过检索其他物种的24个免疫相关基因，包括Ago2、Ago7、Bak1、Bik1、Crt1、Fls2、Pto、Prf、Rar1和丝裂原活化蛋白激酶，证明了该序列的有效性。该序列也将对茄科的比较基因组学有用，如在这里发现的N. benthamiana和番茄在Pto和Prf基因区域之间的微共生性。
Nicotiana benthamiana is a widely used model plant species for the study of fundamental questions in molecular plant-microbe interactions and other areas of plant biology. This popularity derives from its well-characterized susceptibility to diverse pathogens and, especially, its amenability to virus-induced gene silencing and transient protein expression methods. Here, we report the generation of a 63-fold coverage draft genome sequence of N. benthamiana and its availability on the Sol Genomics Network for both BLAST searches and for downloading to local servers. The estimated genome size of N. benthamiana is 3 Gb (gigabases). The current assembly consists of approximately 141,000 scaffolds, spanning 2.6 Gb with 50% of the genome sequence contained within scaffolds >89 kilobases. Of the approximately 16,000 N. benthamiana unigenes available in GenBank, >90% are represented in the assembly. The usefulness of the sequence was demonstrated by the retrieval of N. benthamiana orthologs for 24 immunity-associated genes from other species including Ago2, Ago7, Bak1, Bik1, Crt1, Fls2, Pto, Prf, Rar1, and mitogen-activated protein kinases. The sequence will also be useful for comparative genomics in the Solanaceae family as shown here by the discovery of microsynteny between N. benthamiana and tomato in the region encompassing the Pto and Prf genes.