Cao Zhe, Deng Zhanao
Gulf Coast Research and Education Center, Department of Environmental Horticulture, IFAS, University of Florida, 14625 County Road 672, Wimauma, FL 33598, USA.
Int J Mol Sci. 2017 Mar 27;18(4):712. doi: 10.3390/ijms18040712.
Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars ( × ) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance to , the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome. De novo assembly of the reads resulted in approximately 130,000 unigenes. Based on bioinformatic analysis, 71,825 (52.3%) caladium unigenes were annotated for putative functions, 48,417 (67.4%) and 31,417 (72.7%) were assigned to Gene Ontology (GO) and Clusters of Orthologous Groups (COG), respectively, and 46,406 (64.6%) unigenes were assigned to 128 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 4518 distinct unigenes were observed only in -resistant "Candidum" roots, of which 98 seemed to be involved in disease resistance and defense responses. In addition, 28,837 simple sequence repeat sites and 44,628 single nucleotide polymorphism sites were identified among the three caladium cultivars. These root transcriptome data will be valuable for further genetic improvement of caladium and related aroids.
根系对植物存活和作物产量至关重要，但在非模式植物根系（根转录组）中表达基因的特征描述方面所做的工作甚少。本研究利用RNA测序对三个粗肋草品种（×）的根转录组进行测序、组装、注释和特征描述。本研究中使用的粗肋草品种对粗肋草根最具破坏性的坏死营养型病原菌具有不同程度的抗性。每个粗肋草根转录组获得了4600万至6100万个 clean reads。对这些 reads 进行从头组装得到了约130,000个单基因。基于生物信息学分析，71,825个（52.3%）粗肋草单基因被注释了推定功能，48,417个（67.4%）和31,417个（72.7%）分别被归类到基因本体论（GO）和直系同源基因簇（COG），46,406个（64.6%）单基因被归类到128条京都基因与基因组百科全书（KEGG）通路。仅在抗[病原菌名称未给出]的“Candidum”根系中观察到总共4518个不同的单基因，其中98个似乎参与抗病和防御反应。此外，在三个粗肋草品种中鉴定出28,837个简单序列重复位点和44,628个单核苷酸多态性位点。这些根转录组数据对于粗肋草及相关天南星科植物的进一步遗传改良将具有重要价值。
