MtSSPdb: The Medicago truncatula Small Secreted Peptide Database
MtSSPdb: The Medicago truncatula Small Secreted Peptide Database
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DOI：
10.1104/pp.19.01088
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发表时间：
2020-05-01
期刊：
影响因子：
7.4
通讯作者：
Zhao, Patrick Xuechun
中科院分区：
文献类型：
--
作者：
Boschiero, Clarissa;Dai, Xinbin;Zhao, Patrick Xuechun
MtSSPdb是一个基于RNA-seq的蒺藜苜蓿小分泌肽基因表达图谱的数据库，它是一个预测植物小分泌肽的工具，也是植物合成肽筛选的表型数据库。和病原体防御最近的发现进一步暗示SSP在调节根瘤发育，这是特别重要的豆科植物。SSP编码基因经常被忽视，因为基因组注释管道通常忽略小的开放阅读框，这是那些最有可能编码SSP的。此外，SSP编码的小开放阅读框通常以低水平或仅在特定条件下表达，因此在非组织靶向或非条件优化的RNA测序项目中代表性不足。我们以前确定了4,439 SSP编码基因的模式豆科植物蒺藜苜蓿。为了支持这些推定的SSP编码基因的系统表征和注释，我们开发了M。蒺藜小分泌肽数据库（MtSSPdb;）。MtSSPdb目前拥有（1）M.（2）一个大规模的M.（3）在线植物SSP预测工具，其能够使用与鉴定SSP基因相同的方案在基因组规模上分析蛋白质序列;和（4）关于合成肽文库的信息以及来自植物中合成肽筛选的根和根瘤表型数据。这些数据集和分析工具使MtSSPdb成为植物研究界独特而宝贵的资源。MtSSPdb也有可能成为植物中最完整的SSP数据库。
MtSSPdb hosts a compendium of small secreted peptide sequences with annotations and an RNA-seq-based gene expression atlas for Medicago truncatula, a plant small secreted peptide prediction tool, and phenotyping data from synthetic peptide screens in planta.A growing number of small secreted peptides (SSPs) in plants are recognized as important regulatory molecules with roles in processes such as growth, development, reproduction, stress tolerance, and pathogen defense. Recent discoveries further implicate SSPs in regulating root nodule development, which is of particular significance for legumes. SSP-coding genes are frequently overlooked, because genome annotation pipelines generally ignore small open reading frames, which are those most likely to encode SSPs. Also, SSP-coding small open reading frames are often expressed at low levels or only under specific conditions, and thus are underrepresented in non-tissue-targeted or non-condition-optimized RNA-sequencing projects. We previously identified 4,439 SSP-encoding genes in the model legume Medicago truncatula. To support systematic characterization and annotation of these putative SSP-encoding genes, we developed the M. truncatula Small Secreted Peptide Database (MtSSPdb; ). MtSSPdb currently hosts (1) a compendium of M. truncatula SSP candidates with putative function and family annotations; (2) a large-scale M. truncatula RNA-sequencing-based gene expression atlas integrated with various analytical tools, including differential expression, coexpression, and pathway enrichment analyses; (3) an online plant SSP prediction tool capable of analyzing protein sequences at the genome scale using the same protocol as for the identification of SSP genes; and (4) information about a library of synthetic peptides and root and nodule phenotyping data from synthetic peptide screens in planta. These datasets and analytical tools make MtSSPdb a unique and valuable resource for the plant research community. MtSSPdb also has the potential to become the most complete database of SSPs in plants.