CAFRI-Arabidopsis: An Intuitive Web-Based Functional Redundancy Inspector in Arabidopsis

IF 2.2 4区生物学 Q2 PLANT SCIENCES

Journal of Plant Biology Pub Date : 2024-02-21 DOI:10.1007/s12374-024-09421-z

Woo-Jong Hong, Hongman Moon, Chanseok Shin, Ki-Hong Jung

{"title":"CAFRI-Arabidopsis: An Intuitive Web-Based Functional Redundancy Inspector in Arabidopsis","authors":"Woo-Jong Hong, Hongman Moon, Chanseok Shin, Ki-Hong Jung","doi":"10.1007/s12374-024-09421-z","DOIUrl":null,"url":null,"abstract":"<p>Plants, being sessile organisms, are exposed to a diverse range of environmental challenge. Over time, they have evolved various mechanisms to withstand these harsh conditions, often acquiring functional redundancy in genes with similar sequence. This genetic redundancy, while advantageous for the plant's adaptability, poses challenges in functional genomics research. To address this issue, we developed CAFRI-Arabidopsis (https://cafri.khu.ac.kr/arabidopsis/), a web resource designed to intuitively explore functional redundancy in Arabidopsis, a model plant that has significantly contributed to understanding the morphological and physiological traits. Our tool combines transcriptome data with Pfam-based phylogenetic data across 33 tissues/organs to visualize and quantify functional redundancy. Its effectiveness has been validated through a comprehensive literature review. User-friendly in design, CAFRI-Arabidopsis allows users to quickly generate results by inputting the desired locus. We anticipate that this tool will be invaluable in uncovering new insights in plant developmental and physiological studies that have been previously obscured due to functional redundancy.</p>","PeriodicalId":16762,"journal":{"name":"Journal of Plant Biology","volume":"37 1","pages":""},"PeriodicalIF":2.2000,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Plant Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s12374-024-09421-z","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"PLANT SCIENCES","Score":null,"Total":0}

引用次数: 0

Abstract

Plants, being sessile organisms, are exposed to a diverse range of environmental challenge. Over time, they have evolved various mechanisms to withstand these harsh conditions, often acquiring functional redundancy in genes with similar sequence. This genetic redundancy, while advantageous for the plant's adaptability, poses challenges in functional genomics research. To address this issue, we developed CAFRI-Arabidopsis (https://cafri.khu.ac.kr/arabidopsis/), a web resource designed to intuitively explore functional redundancy in Arabidopsis, a model plant that has significantly contributed to understanding the morphological and physiological traits. Our tool combines transcriptome data with Pfam-based phylogenetic data across 33 tissues/organs to visualize and quantify functional redundancy. Its effectiveness has been validated through a comprehensive literature review. User-friendly in design, CAFRI-Arabidopsis allows users to quickly generate results by inputting the desired locus. We anticipate that this tool will be invaluable in uncovering new insights in plant developmental and physiological studies that have been previously obscured due to functional redundancy.

Abstract Image

查看原文本刊更多论文

CAFRI-Arabidopsis：基于网络的拟南芥功能冗余直观检查器

植物作为无柄生物，面临着各种环境挑战。随着时间的推移，它们进化出了各种机制来抵御这些严酷的条件，往往在序列相似的基因中获得功能冗余。这种基因冗余虽然有利于植物的适应性，但却给功能基因组学研究带来了挑战。为了解决这个问题，我们开发了 CAFRI-Arabidopsis (https://cafri.khu.ac.kr/arabidopsis/)，这是一个网络资源，旨在直观地探索拟南芥的功能冗余，拟南芥是一种模式植物，对了解其形态和生理性状做出了重大贡献。我们的工具将转录组数据与 33 个组织/器官中基于 Pfam 的系统发育数据相结合，对功能冗余进行可视化和量化。该工具的有效性已通过全面的文献综述得到验证。CAFRI-Arabidopsis 的设计非常人性化，用户只需输入所需的基因座，就能快速生成结果。我们预计，这一工具将在植物发育和生理研究中发挥无价之宝的作用，揭示以前由于功能冗余而被掩盖的新见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Journal of Plant Biology 生物-植物科学

CiteScore

5.40

自引率

3.40%

发文量

审稿时长

1 months

期刊介绍： Journal of Plant Biology, an official publication of the Botanical Society of Korea, is an international journal devoted to basic researches in biochemistry, cellular biology, development, ecology, genetics, molecular biology, physiology, and systematics of plants. The Journal publishes the following categories of paper: Original articles -- For publication in Journal of Plant Biology the manuscript must provide a significant new contribution to our understanding of plants. All areas of plant biology are welcome. No limit on the length, but a concise presentation is encouraged. Reviews -- Invited by the EiC. Brief Communications -- Concise but independent report representing significant contribution to plant science. The Botanical Society of Korea was founded on November 30, 1957 to promote studies, disseminate and exchange information on the field of plant biology. The first issue of The Korean Journal of Botany, the official publication of the society, was published on April 1, 1958. It was published twice a year, but quarterly from 5th volume in 1962. In 1994, it was renamed to Journal of Plant Biology and published in English since 1996. The journal entered its 50th year of publication in 2007.