Transcriptional profiling of the CAM plant Agave salmiana reveals conservation of a genetic program for regeneration

Developmental biology

Araceli Oropeza-Aburto^1¹  Juan Caballero-Pérez^2²  Sergio Alan Cervantes-Pérez^1³  Annie Espinal-Centeno^2,1⁴ 

[1] Departamento de Ingeniería Genética, Unidad Irapuato, CINVESTAV-Irapuato, Gto, Mexico^3;Escuela de Agronomía, Universidad de La Salle Bajío, León, Gto, Mexico^4;Metabolic Engineering Group, Unidad de Genómica Avanzada-LANGEBIO, CINVESTAV-Irapuato, Gto, Mexico^1;Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada-LANGEBIO, CINVESTAV-Irapuato, Gto, Mexico^2

关键词: CAM;    Crassulacean Acid Metabolism;    ORF;    Opening Reading Frame;    NGS;    Next-Generation Sequencing;    CO2;    Carbone Dioxide;    PEG;    Preferentially Expressed Genes;    BAP;    6-benzylaminopurine;    CIM;    Callus Induction Media;    RIN;    RNA Integrity Number;    FAE;    Formaldehyde/acetic Acid/Ethanol;    DAPI;    4';    , 6-Diamino-2-phenylindole;    SEM;    Scanning Electron Microscopy;    VP-SEM;    Variable Pressure Scanning Electron Microscopy;    SRA;    Short Read Archive;    NCBI;    National Center of Biotechnology Information;    GO;    Gene Ontology;    CPM;    Counts per Million;    CPC;    Coding Potential Calculator;    NF;    Normalized Frequency;    TMM;    Trimmed mean of M Values;    RPKM;    Reads per Kilobase per Million;    FDR;    False Discovery Rate;    PET;    Preferentially Expressed Transcripts;    PCA;    Principal Component Analysis;    HC;    Hierarchical Clustering;    BBM;    BABY BOOM;    FC;    Functional Category;    PLT5;    PLETHORA 5;    PIN1;    PIN-FORMED;    CYCD4;    CYCLIN D4;    CDKB2;    CYCLIN DEPENDENT KINASE TYPE B-2;    LBD16;    LATERAL ORGAN BOUNDARIES DOMAIN 16;    LBD29;    LATERAL ORGAN BOUNDARIES DOMAIN 29;    LTP;    LIPID TRANSFER PROTEIN;    DEG;    Differentially Expressed Gene;    PLT1;    PLETHORA 1;    PIN2;    PIN-FORMED 2;    YUC10;    YUCCA 10;    TSD2;    TUMOROUS SHOOT DEVELOPMENT 2;    ARF7;    AUXIN RESPONSE FACTOR 7;    E2F;    ELONGATION FACTOR 2;    PIN7;    PIN-FORMED 7;    TSD1;    TUMOROUS SHOOT DEVELOPMENT 1;    SCR;    SCARECROW;    CUC2;    CUP SHAPED COTYLEDON 2;    RBR1;    RETINOBLASTOMA-RELATED 1;    PLT2;    PLETHORA 2;    PIN4;    PIN-FORMED 4;    AP2;    APETALA 2;    PLT3;    PLETHORA 3;    ESR1;    ENHANCER OF SHOOT REGENERATION 1;    ESR2;    ENHANCER OF SHOOT REGENERATION 2;    ARR1;    TYPE A RESPONSE REGULATOR 1;    CYCD3;    1;    Cyclin Dependent Type D3;    1;    PLT;    PLETHORA;    CDKB1;    1;    CYCLIN DEPENDENT KINASE TYPE B1-1;    MAI;    Months After Induction;    ARF11;    AUXIN RESPONSE FACTOR 11;    ARF19;    AUXIN RESPONSE FACTOR 19;    LBD;    LATERAL ORGAN BOUNDARIES DOMAIN;    CDKBs;    Type B Cyclin Dependent Kinases;    CYCD;    Cyclin D;    RBR;    RETINOBLASTOMA RELATED PROTEIN;    WOX5;    WUSCHEL RELATED HOMEOBOX 5;    DGE;    Differential Gene Expression;    Agave salmiana;    Callus;    Regeneration;    RNAseq-cell reprogramming;    Conservation-CAM;   

DOI  :  10.1016/j.ydbio.2018.04.018

学科分类：生物科学（综合）

来源: Academic Press

【 摘 要 】

In plants, the best characterized plant regeneration process is de novo organogenesis. This type of regeneration is characterized by the formation of a multicellular structure called callus. Calli are induced via phytohormone treatment of plant sections. The callus formation in plants like Agave species with Crassulacean Acid Metabolism (CAM) is poorly studied. In this study, we induced callus formation from Agave salmiana leaves and describe cell arrangement in this tissue. Moreover, we determined and analyzed the transcriptional program of calli, as well as those of differentiated root and leaf tissues, by using RNA-seq. We were able to reconstruct 170,844 transcripts of which 40,644 have a full Open Reading Frame (ORF). The global profile obtained by Next Generation Sequencing (NGS) reveals that several callus-enriched protein coding transcripts are orthologs of previously reported factors highly expressed in Arabidopsis calli. At least 62 genes were differentially expressed in Agave calli, 50 of which were up-regulated. Several of these are actively involved in the perception of, and response to, auxin and cytokinin. Not only are these the first results for the A. salmiana callus, but they provide novel data from roots and leaves of this Agave species, one of the largest non-tree plants in nature.

【 授权许可】

CC BY