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For: Yi W, Luan A, Liu C, Wu J, Zhang W, Zhong Z, Wang Z, Yang M, Chen C, He Y. Genome-wide identification, phylogeny, and expression analysis of GRF transcription factors in pineapple (Ananas comosus). Front Plant Sci 2023;14:1159223. [PMID: 37123828 PMCID: PMC10140365 DOI: 10.3389/fpls.2023.1159223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]

For:	Yi W, Luan A, Liu C, Wu J, Zhang W, Zhong Z, Wang Z, Yang M, Chen C, He Y. Genome-wide identification, phylogeny, and expression analysis of GRF transcription factors in pineapple (Ananas comosus). Front Plant Sci 2023;14:1159223. [PMID: 37123828 PMCID: PMC10140365 DOI: 10.3389/fpls.2023.1159223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]

Number

Cited by Other Article(s)

Roy A, Chaurasia H, Kumar B, Kumari N, Jaiswal S, Srivastava M, Iquebal MA, Angadi UB, Kumar D. FEAtl: a comprehensive web-based expression atlas for functional genomics in tropical and subtropical fruit crops. BMC PLANT BIOLOGY 2024;24:890. [PMID: 39343895 PMCID: PMC11440752 DOI: 10.1186/s12870-024-05595-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 09/16/2024] [Indexed: 10/01/2024]

Abstract

BACKGROUND

Fruit crops, including tropical and subtropical fruits like Avocado (Persea americana), Fig (Ficus carica), Date Palm (Phoenix dactylifera), Mango (Mangifera indica), Guava (Psidium guajava), Papaya (Carica papaya), Pineapple (Ananas comosus), and Banana (Musa acuminata) are economically vital, contributing significantly to global agricultural output, as classified by the FAO's World Programme for the Census of Agriculture. Advancements in next-generation sequencing, have transformed fruit crop breeding by providing in-depth genomic and transcriptomic data. RNA sequencing enables high-throughput analysis of gene expression, and functional genomics, crucial for addressing horticultural challenges and enhancing fruit production. The genomic and expression data for key tropical and sub-tropical fruit crops is currently lacking a comprehensive expression atlas, revealing a significant gap in resources for horticulturists who require a unified platform with diverse datasets across various conditions and cultivars.

RESULTS

The Fruit Expression Atlas (FEAtl), available at http://backlin.cabgrid.res.in/FEAtl/ , is a first-ever extensive and unified expression atlas for tropical and subtropical fruit crops developed using 3-tier architecture. The expressivity of coding and non-coding genes, encompassing 2,060 RNA-Seq samples across 91 tissue types and 177 BioProjects, it provides a comprehensive view of gene expression patterns for different tissues under various conditions. FEAtl features multiple tabs that cater to different aspects of the dataset, namely, Home, About, Analyze, Statistics, and Team and contains seven central functional modules: Transcript Information,Sample Information, Expression Profiles in FPKM and TPM, Functional Analysis, Genes Based on Tau Score, and Search for Specific Gene. The expression of a transcript of interest can be easily queried by searching by tissue ID and transcript type. Expression data can be displayed as a heat map, along with functional descriptions as well as Gene Ontology and Kyoto Encyclopedia of Genes and Genomes.

CONCLUSIONS

This atlas represents a groundbreaking compilation of a wide array of information pertaining to eight distinct fruit crops and serves as a fundamental resource for comparative analysis among different fruit species and is a catalyst for functional genomic studies. Database availability: http://backlin.cabgrid.res.in/FEAtl/ .

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Lu J, Wang Z, Li J, Zhao Q, Qi F, Wang F, Xiaoyang C, Tan G, Wu H, Deyholos MK, Wang N, Liu Y, Zhang J. Genome-Wide Analysis of Flax (Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors. Int J Mol Sci 2023;24:17107. [PMID: 38069430 PMCID: PMC10707037 DOI: 10.3390/ijms242317107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open

Affiliation(s)

Jianyu Lu Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
Zhenhui Wang Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
Jinxi Li Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
Qian Zhao Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
Fan Qi Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
Fu Wang Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
Chunxiao Xiaoyang Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
Guofei Tan Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
Hanlu Wu Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
Michael K. Deyholos Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V5K1K5, Canada;
Ningning Wang Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
Yingnan Liu Institute of Natural Resources and Ecology, Heilongjiang Academy of Science, Harbin 150040, China
Jian Zhang Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.) Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V5K1K5, Canada;

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