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Genome-wide identification, classification, and expression of phytocyanins in Populus trichocarpa

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Abstract

Main conclusion

74 phytocyanin genes were identified in the Populus trichocarpa genome. Phylogenetic analysis grouped the PC proteins into four subfamilies (UCs, PLCs, SCs, and ENODLs). Closely related PC proteins share similar motifs, implying similar functions. Expression profiles of PtPC genes were analyzed in response to drought and salt-stress.

Phytocyanins (PCs) are blue copper proteins associated with electron carrier activity that have a large influence on plant growth and resistance. The majority of PCs are chimeric arabinogalactan proteins (AGPs). In this work, we identified 74 PC genes in Populus trichocarpa and analyzed them comprehensively. Based on the ligands composition of copper-binding sites, glycosylation state, the domain structure and spectral characteristics of PC genes, PCs were divided into four subfamilies [uclacyanins (UCs), plantacyanins (PLCs), stellacyanins (SCs) and early nodulin-like proteins (ENODLs)], and phylogenetic relationship analysis classified them into seven groups. All PtPCs are randomly distributed on 17 of the 19 poplar chromosomes, and they appear to have undergone expansion via segmental duplication. Eight PtPCs do not contain introns, and each group has a similar conserved motif structure. Promoter analysis revealed cis-elements related to growth, development and stress responses, and established orthology relationships of PCs between Arabidopsis and poplar by synteny analysis. Expression profile analysis and qRT-PCR analysis showed that PtPCs were expressed widely in various tissues. Quantitative real-time RT-PCR analysis of PC genes expression in response to salt and drought stress revealed their stress-responses profiles. This work provides a theoretical basis for a further study of stress resistance mechanisms and the function of PC genes in poplar growth and development.

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Abbreviations

AG:

Arabinogalactan

AGPs:

Arabinogalactan proteins

ENODLs:

Early nodulin-like proteins

PCs:

Phytocyanins

PCLD:

Plastocyanin-like domain

PLCs:

Plantacyanins

SCs:

Stellacyanins

SP:

Signal peptide

UCs:

Uclacyanins

K s :

Number of synonymous substitutions per synonymous site

K a :

Number of non-synonymous substitutions per non-synonymous site

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Acknowledgements

We thank the members of the Laboratory of Modern Biotechnology for their assistance in this study.

Funding

National Natural Science Foundation of China (31370561) and National Science and Technology Support Plan Corpus (2015BAD07B070104).

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Author notes

  1. Shuangshuang Luo and Wenfang Hu contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Crop Biology of Anhui Province, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China

    Shuangshuang Luo, Wenfang Hu, Yue Wang, Bin Liu, Hanwei Yan & Yan Xiang

  2. Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China

    Shuangshuang Luo, Wenfang Hu, Yue Wang, Bin Liu, Hanwei Yan & Yan Xiang

  3. National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China

    Hanwei Yan & Yan Xiang

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  1. Shuangshuang Luo
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Correspondence to Hanwei Yan or Yan Xiang.

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Fig. S1

Protein backbones of PCs in P. trichocarpa. The coloured sequences at the N and C terminus indicate predicted signal peptides (green) and GPI anchor addition sequences (purple) if present in the sequences. Putative AG sites (blue) are also indicated. Red font indicates N-glycosylation site. Extensins SP3, SP4 and SP5 repeats are indicated (light blue) if present. Note that the putative AG glycomodules are only checked in the proteins containing N-secretion signals (TIFF 32125 kb)

Fig. S2

Exon–intron structures and conserved domains of the predicted PtPC proteins. Exons, introns and untranslated regions (UTRs) are represented by yellow rectangles, grey lines and blue rectangles, respectively (TIFF 437 kb)

Fig. S3

Sliding window plots of Ka/Ks ratios of representative duplicated PtPC gene paralogs. The x-axis denotes the nucleotide position, and the y-axis denotes the Ka/Ks ratio (TIFF 68 kb)

Fig. S4

Extensive microsynteny of PC regions between Arabidopsis and poplar. Arabidopsis and Populus chromosomes are shown in different colours. Numbers along each chromosome box indicate sequence length in megabases. Whole chromosomes of the two species harbouring PC regions are encircled. Black lines represent syntenic relationships between PC regions (TIFF 3195 kb)

Fig. S5

Synteny analysis of PC genes in Populus. Black lines represent syntenic relationships (TIFF 2627 kb)

Fig. S6

Hierarchical clustering of poplar PC gene expression. The heatmap shows hierarchical clustering of PtPC genes across various tissues/organs. Affymetrix microarray data under accession number GSE13990 encompassing results from six organ/tissue types including young leaves (YL), roots (R), xylem (XY), female catkin (FC), male catkin (MC) and mature leaves (ML) were re-analysed (TIFF 621 kb)

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Luo, S., Hu, W., Wang, Y. et al. Genome-wide identification, classification, and expression of phytocyanins in Populus trichocarpa. Planta 247, 1133–1148 (2018). https://doi.org/10.1007/s00425-018-2849-2

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