Abstract
Main conclusion
Soybean possesses 19 CMF genes which mainly arose from duplication events. Their features and motifs are highly conserved but transcriptional data indicated functional diversity in metabolism and stress responses.
Abstract
CCT [for CONSTANS, CONSTANS-like (CO-like), and timing of CAB expression1 (TOC1)] domain-containing genes play important roles in regulating flowering, plant growth, and grain yield and are also involved in stress responses. The CMF (CCT motif family) genes, included in the CCT family, contain a single CCT domain as the only identifiable domain in their predicted protein sequence and are interesting targets for breeding programs. In this study, we identified 19 putative GmCMF genes, based on the latest soybean (Glycine max) genome annotation. The predicted GmCMF proteins were characterized based on conserved structural features, and a phylogenetic tree was constructed including all CMF proteins from rice and Arabidopsis as representative examples of the monocotyledonous (monocot) and dicotyledonous (dicot) plants, respectively. High similarities in the conserved motifs of the protein sequences and the gene structures were found. In addition, by analyzing the CMF gene family in soybean, we identified seven pairs of genes that originated from segmental chromosomal duplication events attributable to the most recent whole-genome duplication (WGD) event in the Glycine lineage. Expression analysis of GmCMF genes in various tissues and after specific treatments demonstrated tissue and stress-response specific differential expression. Gene expression analysis was complemented by the identification of putative cis-elements present in the promoter regions of the genes through a bioinformatics approach, using the existing soybean reference genome sequence and gene models. Co-functional networks inferred from distinct types of genomics data—including microarrays and RNA-seq samples from soybean—revealed that GmCMF genes might play crucial roles in metabolism and transport processes. The results of this study, the first systematic analysis of the soybean CCT gene family, can serve as a strong foundation for further elucidation of their physiological functions and biological roles.
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Availability of data and materials
The data generated or analyzed in this study are included in this article and its Additional materials. All sequence information regarding soybean is available at a public database, SoyBase (http://www.soybase.org/). AtCMF, OsCMF proteins and the expression data of GmCMFs were retrieved from Phytozome V12.1 database (https://www.phytozome.jgi.doe.gov/pz/portal.html). Duplication blocks were identified using the PGDD database (http://www.chibba.agtec.uga.edu/duplication/), and co-functional genes were retrieved from SoyNet database (http://www.inetbio.org/soynet/).
Abbreviations
- CCT:
-
CONSTANS, CONSTANS-like (CO-like), and timing of CAB expression1 (TOC1)
- CIA2:
-
CHLOROPLAST IMPORT APPARATUS 2
- CMF:
-
CCT motif family
- CO-like:
-
CONSTANS-LIKE
- Ka/Ks:
-
Non-synonymous/synonymous substitution
- MYA:
-
Millions of years ago
- PRR:
-
PSEUDORESPONSE REGULATOR
- WGD:
-
Whole-genome duplication
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Acknowledgements
D. A. M. is recipient of a fellowship of Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). M. I. Z. is a career member of CONICET.
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This work was supported by Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT, PICT2017-1301).
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Supplementary file1 Supplementary Fig. S1 Comparative analysis of CMF genes in several plant genomes. a Number of CCT, CMF, and total coding genes in each plant species retrieved from PLAZA4.0 (Van Bel et al. 2018). b Parameters of linear regression analysis for gene number pairs: total coding gene and CMF gene number, total coding gene and CCT gene number, and finally CCT and CMF gene number. Values were calculated with InfoStat software (Rienzo et al. 2017). Supplementary Fig. S2 A maximum likelihood (ML) unrooted phylogenetic tree was constructed using MEGA X with 1000 bootstrap replications and an optimal Jones-Taylor-Thornton (JTT) model using the CMF proteins from soybean, rice, Arabidopsis, Chlamydomonas reinhardtii and Physcomitrella patens subsp. patens. For Arabidopsis and rice the TAIR annotation release 10 of the A. thaliana genome release 9 (Lamesch et al. 2012) and the MSU Release 7.0 of the annotation of the genome of the Nipponbare/ japonica subspecies of O. sativa (Ouyang et al. 2007) were used. A release of the mapped CC-503 MT + genome assembly and version 5.5 annotation (Merchant et al. 2007) and for P. patens subsp. patens the v3.3 annotation of the v3.0 assembly (Lang et al. 2018) were used for C. reinhardtii and P. patens subsp. patens, respectively. Supplementary Fig. S3 Expression levels of GmCMF genes in five tissues: flower, pod, leaves, stem, and root by qRT-PCR (40-dCT). Results are presented as means ± SD of three biological replicates. Different letters indicate significant differences at P < 0.05 according to the LSD ANOVA test (PDF 1284 KB)
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Mengarelli, D.A., Zanor, M.I. Genome-wide characterization and analysis of the CCT motif family genes in soybean (Glycine max). Planta 253, 15 (2021). https://doi.org/10.1007/s00425-020-03537-5
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DOI: https://doi.org/10.1007/s00425-020-03537-5