Lemos Samara M C, Fonçatti Luiz F C, Guyot Romain, Paschoal Alexandre R, Domingues Douglas S
Department of Computer Science, Federal University of Technology-Parana, Cornelio Procopio 86300-000, Brazil.
Group of Genomics and Transcriptomes in Plants, São Paulo State University, Rio Claro, Sao Paulo 13506-900, Brazil.
Noncoding RNA. 2020 Sep 11;6(3):39. doi: 10.3390/ncrna6030039.
grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the genome. This study aimed to provide a curated characterization of six ncRNA classes in the genome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in the genome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity.
谷物是全球交易活跃的商品。非编码RNA（ncRNA）是参与基因组调控、环境响应和植物发育的转录产物。目前尚未有全面的全基因组分析来揭示基因组中的ncRNA部分。本研究旨在对基因组中的六类ncRNA进行精准表征。为此，我们采用了基于相似性和基于结构的计算方法相结合，并进行严格筛选。利用小RNA测序文库对候选ncRNA基因座的表达证据进行了分析。我们在基因组中鉴定出7455个ncRNA基因座（6976个有转录证据）。其中包括115个小核RNA（snRNA）、1031个核仁小RNA（snoRNA）、92个微小RNA（miRNA）前体、602个转运RNA（tRNA）、72个核糖体RNA（rRNA）和5064个长链非编码RNA（lncRNA）。对于miRNA，我们鉴定出159个假定的高可信度靶标。本研究是咖啡属中最全面的ncRNA基因组编目。这些数据可能有助于在未来的比较基因组研究以及基因调控和基因组动态研究中提出更可靠的假设，有助于理解驯化、环境适应、抗病虫害和咖啡产量的分子基础。
