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

被引：2

作者：

Hong, Woo-Jong ^{[1
]}

Moon, Hongman ^{[2
]}

Shin, Chanseok ^{[2
,3
,4
,5
]}

Jung, Ki-Hong ^{[5
,6
]}

机构：

[1] Kyung Hee Univ, Dept Smart Farm Sci, Yongin 17104, South Korea

[2] Seoul Natl Univ, Dept Agr Biotechnol, Seoul 08826, South Korea

[3] Seoul Natl Univ, Res Inst Agr & Life Sci, Seoul 08826, South Korea

[4] Seoul Natl Univ, Plant Genom & Breeding Inst, Seoul 08826, South Korea

[5] Seoul Natl Univ, Res Ctr Plant Plast, Seoul 08826, South Korea

[6] Kyung Hee Univ, Green Bio Sci & Crop Biotech Inst, Grad Sch, Yongin 17104, South Korea

来源：

JOURNAL OF PLANT BIOLOGY | 2024年 / 67卷 / 02期

基金：

新加坡国家研究基金会;

关键词：

Arabidopsis; Functional redundancy; Functional genomics; CAFRI-Arabidopsis; Web resource; GENETIC REDUNDANCY; STRESS; RNA; DUPLICATION; EXPRESSION; ALIGNMENT;

D O I：

10.1007/s12374-024-09421-z

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

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.

引用

页码：99 / 108

页数：10

共 74 条

[1] Genome-wide Insertional mutagenesis of Arabidopsis thaliana [J].

Alonso, JM ;

Stepanova, AN ;

Leisse, TJ ;

Kim, CJ ;

Chen, HM ;

Shinn, P ;

Stevenson, DK ;

Zimmerman, J ;

Barajas, P ;

Cheuk, R ;

Gadrinab, C ;

Heller, C ;

Jeske, A ;

Koesema, E ;

Meyers, CC ;

Parker, H ;

Prednis, L ;

Ansari, Y ;

Choy, N ;

Deen, H ;

Geralt, M ;

Hazari, N ;

Hom, E ;

Karnes, M ;

Mulholland, C ;

Ndubaku, R ;

Schmidt, I ;

Guzman, P ;

Aguilar-Henonin, L ;

Schmid, M ;

Weigel, D ;

Carter, DE ;

Marchand, T ;

Risseeuw, E ;

Brogden, D ;

Zeko, A ;

Crosby, WL ;

Berry, CC ;

Ecker, JR .

SCIENCE, 2003, 301 (5633) :653-657

[2] OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more [J].

Altenhoff, Adrian M. ;

Train, Clement-Marie ;

Gilbert, Kimberly J. ;

Mediratta, Ishita ;

de Farias, Tarcisio Mendes ;

Moi, David ;

Nevers, Yannis ;

Radoykova, Hale-Seda ;

Rossier, Victor ;

Vesztrocy, Alex Warwick ;

Glover, Natasha M. ;

Dessimoz, Christophe .

NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D373-D379

[3] Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].

Kaul, S ;

Koo, HL ;

Jenkins, J ;

Rizzo, M ;

Rooney, T ;

Tallon, LJ ;

Feldblyum, T ;

Nierman, W ;

Benito, MI ;

Lin, XY ;

Town, CD ;

Venter, JC ;

Fraser, CM ;

Tabata, S ;

Nakamura, Y ;

Kaneko, T ;

Sato, S ;

Asamizu, E ;

Kato, T ;

Kotani, H ;

Sasamoto, S ;

Ecker, JR ;

Theologis, A ;

Federspiel, NA ;

Palm, CJ ;

Osborne, BI ;

Shinn, P ;

Conway, AB ;

Vysotskaia, VS ;

Dewar, K ;

Conn, L ;

Lenz, CA ;

Kim, CJ ;

Hansen, NF ;

Liu, SX ;

Buehler, E ;

Altafi, H ;

Sakano, H ;

Dunn, P ;

Lam, B ;

Pham, PK ;

Chao, Q ;

Nguyen, M ;

Yu, GX ;

Chen, HM ;

Southwick, A ;

Lee, JM ;

Miranda, M ;

Toriumi, MJ ;

Davis, RW .

NATURE, 2000, 408 (6814) :796-815

[4] Transcriptional induction of cell wall remodelling genes is coupled to microtubule-driven growth isotropy at the shoot apex in Arabidopsis [J].

Armezzani, Alessia ;

Abad, Ursula ;

Ali, Olivier ;

Robin, Ameprimelie Andres ;

Vachez, Laetitia ;

Larrieu, Antoine ;

Mellerowicz, Ewa J. ;

Taconnat, Ludivine ;

Battu, Virginie ;

Stanislas, Thomas ;

Liu, Mengying ;

Vernoux, Teva ;

Traas, Jan ;

Sassi, Massimiliano .

DEVELOPMENT, 2018, 145 (11)

[5] The Plastid Lipase PLIP1 Is Critical for Seed Viability in diacylglycerol acyltransferase1 Mutant Seed [J].

Aulakh, Karanbir ;

Durrett, Timothy P. .

PLANT PHYSIOLOGY, 2019, 180 (04) :1962-1974

[6] Does functional redundancy affect ecological stability and resilience? A review and meta-analysis [J].

Biggs, Christopher R. ;

Yeager, Lauren A. ;

Bolser, Derek G. ;

Bonsell, Christina ;

Dichiera, Angelina M. ;

Hou, Zhenxin ;

Keyser, Spencer R. ;

Khursigara, Alexis J. ;

Lu, Kaijun ;

Muth, Arley F. ;

Negrete, Benjamin, Jr. ;

Erisman, Brad E. .

ECOSPHERE, 2020, 11 (07)

[7] Flowering time regulation in crops - what did we learn from Arabidopsis? [J].

Bluemel, Martina ;

Dally, Nadine ;

Jung, Christian .

CURRENT OPINION IN BIOTECHNOLOGY, 2015, 32 :121-129

[8] GABI-DUPLO: a collection of double mutants to overcome genetic redundancy in Arabidopsis thaliana [J].

Bolle, Cordelia ;

Huep, Gunnar ;

Kleinboelting, Nils ;

Haberer, Georg ;

Mayer, Klaus ;

Leister, Dario ;

Weisshaar, Bernd .

PLANT JOURNAL, 2013, 75 (01) :157-171

[9] Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin [J].

Borg, Michael ;

Jacob, Yannick ;

Susaki, Daichi ;

LeBlanc, Chantal ;

Buendia, Daniel ;

Axelsson, Elin ;

Kawashima, Tomokazu ;

Voigt, Philipp ;

Boavida, Leonor ;

Becker, Jorg ;

Higashiyama, Tetsuya ;

Martienssen, Robert ;

Berger, Frederic .

NATURE CELL BIOLOGY, 2020, 22 (06) :621-+

[10] A stress-free walk from Arabidopsis to crops [J].

Chew, Yin Hoon ;

Halliday, Karen J. .

CURRENT OPINION IN BIOTECHNOLOGY, 2011, 22 (02) :281-286

← 1 2 3 4 5 6 7 8 →