CANTATAdb 3.0: An Updated Repository of Plant Long Non-Coding RNAs.

IF 3.9 2区生物学 Q2 CELL BIOLOGY

Plant and Cell Physiology Pub Date : 2024-10-03 DOI:10.1093/pcp/pcae081

Michał Wojciech Szcześniak, Elżbieta Wanowska

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引用次数: 0

Abstract

CANTATAdb 3.0 is an updated database of plant long non-coding RNAs (lncRNAs), containing 571,688 lncRNAs identified across 108 species, including 100 Magnoliopsida (flowering plants), a significant expansion from the previous version. A notable feature is the inclusion of 112,980 lncRNAs that are expressed specifically in certain plant organs or embryos, indicating their potential role in development and organ-specific processes. In addition, CANTATAdb 3.0 includes 74,886 pairs of evolutionarily conserved lncRNAs found across 47 species and inferred from genome-genome alignments as well as conserved lncRNAs obtained using a similarity search approach in 5,479 species pairs, which would further aid in the selection of lncRNAs for functional studies. Interestingly, we find that conserved lncRNAs with tissue-specific expression patterns tend to occupy the same plant organ across different species, pointing toward conserved biological roles. The database now offers extended search capabilities and downloadable data in popular formats, further facilitating research on plant lncRNAs.

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CANTATAdb 3.0：植物长非编码 RNA 的最新资料库。

CANTATAdb 3.0 是一个更新的植物长非编码 RNA（lncRNA）数据库，包含在 108 个物种中鉴定出的 571,688 个 lncRNA，其中包括 100 种木兰纲（开花植物），比上一版本有了显著扩展。其中一个显著特点是收录了 112,980 个在某些植物器官或胚胎中特异表达的 lncRNA，表明它们在发育和器官特异过程中的潜在作用。此外，CANTATAdb 3.0 还收录了从基因组-基因组比对中推断出的 47 个物种中的 74,886 对进化保守的 lncRNA，以及通过相似性搜索法在 5,479 个物种对中获得的保守的 lncRNA，这将进一步帮助选择 lncRNA 进行功能研究。有趣的是，我们发现具有组织特异性表达模式的保守lncRNA往往在不同物种中占据相同的植物器官，这表明它们具有保守的生物学作用。该数据库现在提供了扩展搜索功能和流行格式的可下载数据，进一步促进了对植物 lncRNAs 的研究。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Plant and Cell Physiology 生物-细胞生物学

CiteScore

8.40

自引率

4.10%

发文量

166

审稿时长

1.7 months

期刊介绍： Plant & Cell Physiology (PCP) was established in 1959 and is the official journal of the Japanese Society of Plant Physiologists (JSPP). The title reflects the journal''s original interest and scope to encompass research not just at the whole-organism level but also at the cellular and subcellular levels. Amongst the broad range of topics covered by this international journal, readers will find the very best original research on plant physiology, biochemistry, cell biology, molecular genetics, epigenetics, biotechnology, bioinformatics and –omics; as well as how plants respond to and interact with their environment (abiotic and biotic factors), and the biology of photosynthetic microorganisms.