Molecular evolution and diversification of phytoene synthase (PSY) gene family

Lisboa, Marcia Pagno; Canal, Drielli; Filgueiras, João Pedro Carmo; Turchetto-Zolet, Andreia Carina

doi:10.1590/1678-4685-GMB-2021-0411

person Marcia Pagno Lisboa

schoolUniversidade Federal do Rio Grande do Sul (UFRGS), Departamento de Genética, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.

person Drielli Canal

schoolUniversidade Federal do Rio Grande do Sul (UFRGS), Departamento de Genética, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.

person João Pedro Carmo Filgueiras

schoolUniversidade Federal do Rio Grande do Sul (UFRGS), Departamento de Genética, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.

person Andreia Carina Turchetto-Zolet

schoolUniversidade Federal do Rio Grande do Sul (UFRGS), Departamento de Genética, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.

0000-0002-7365-1360

personSend correspondence to Andreia Carina Turchetto-Zolet. Universidade Federal do Rio Grande do Sul (UFRGS), Departamento de Genética, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil. E-mail:
aturchetto@gmail.com

Associate Editor

Louis Bernard Klaczko

Conflict of Interest

The authors declare no conflict of interest.

groupsAuthor Contributions

ACTZ and MPL performed the experiments; ACTZ, MPL, DC, and JPCF performed the analysis; ACTZ, MPL, and JPCF analyzed the data; MPL wrote the manuscript; all authors read and approved the final version.

Figures (3)
Tables (1)

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Figure 1 - Phylogenetic tree for PSY genes in representative Viridiplantae, fungi, arthropods, brown algae, red algae, cyanobacteria, and prokaryote lineages, providing insight into PSY origin and diversification among terrestrial plants. Figures show the resulting tree of the Bayesian inference analysis and present both posterior probabilities (numbers in red) with a cut-off point of 0, 8 and bootstrap values (numbers in blue) with a cut-off point of 70. The tree was rooted with prokaryotes as a sister group of the other organisms (root selected manually in FigTree v.1.4.4). Bayesian and maximum likelihood analyses were performed using PSY amino acid sequences from 166 selected representative species. Five main nodes that potentially mark taxonomic divergence during plant evolution (Nodes 1, 2, 3, 4 and 5) are marked with green circles. Inside the square in the upper right corner of the figure is the original unrooted tree.

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Figure 2 - Exon-intron organization of PSY genes in terrestrial plants. PSY sequences from 13 representative species (Physcomitrella patens, Selaginella moellendorffii, Brachypodium distachyon, Setaria italica, Oryza sativa, Sorghum bicolor, Solanum lycopersicum, Solanum tuberosum, Eucalyptus grandis, Citrus sinensis, Arabidopsis thaliana, Brassica rapa, Glycine max) are presented. Gene features are displayed on a Bayesian phylogenetic tree.

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Figure 3- Amino acid sequence logo of PSY alignments from angiosperm species, highlighting the high gene conservation. The vertical axis indicates information content of a sequence position, in bits (log2 4 = 2 bits for DNA/RNA, log2 20 = 4.3 bits for protein). The height of the y-axis is the maximum entropy for a given sequence type. The horizontal axis indicates the residue number. The blue line indicates the SQS_PSY domain.

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Table 1 - Gene expression analysis from Genevestigator showing expression pattern of PSY in anatomical parts and developmental stages of Arabidopsis thaliana, Glycine max, Oryza sativa and Sorghum bicolor.

Species	Accesion number	Location on phylogeny	Expression data		Source
Species	Accesion number	Location on phylogeny	Development stadios	Anatomical parts	Source
Arabidopsis thaliana	AT5G17230.1	Subgroup E2	The expression was high in all stages, except in final ripening	The expression detected in almost all anatomical parts, with high expression level detected in sperm cell, mesophyll cell protoplast, root culture, seedling culture, shoot cell and tissues, leaf cell and tissues, inflorescence parts	Figure S8 and S9
Glycine max	Glyma.14G209700	Subgroup E2	The expression was detected in all stages, with higher expression level in main shoot growth, stem elongation, inflorescence formation and flowering	Higher expression was detected in cotyledon, shoot apex, hypocotyl, flower, pod, pericarp (pod wall), shoot, stem internode, leaf, unifoliolate leaf, trifoliolate leaf, shoot apex, shoot apical meristem	Figure S10 and S11
	Glyma.02G240200	Subgroup E2	The expression was detected in all stages, with higher expression level in main shoot growth, stem elongation, inflorescence formation and flowering	Higher expression was detected in cotyledon, shoot apex, hypocotyl, flower, pod, pericarp (pod wall), shoot, stem internode, leaf, unifoliolate leaf, trifoliolate leaf, shoot apex, shoot apical meristem	Figure S10 and S11
	Glyma.14G031200	Subgroup E1	The expression was detected in all stages, with higher expression level in main shoot growth and inflorescence formation	Higher expression was detected in shoot apex, flower, pod, shoot, leaf, unifoliolate leaf, trifoliolate leaf shoot apex, shoot apical meristem	Figure S10 and S11
	Glyma.02G283400	Subgroup E1	The expression was detected in all stages, with higher expression level in main shoot growth and inflorescence formation	Higher expression was detected in shoot apex, flower, pod, shoot, leaf, unifoliolate leaf, trifoliolate leaf shoot apex, shoot apical meristem	Figure S10 and S11
	Glyma.18G111900	Subgroup E1	The expression was detected in all stages, with higher expression level in main shoot growth, inflorescence formation and flowering	Higher expression was detected in cotyledon, shoot apex, flower, pod, shoot, leaf, unifoliolate leaf, trifoliolate leaf, shoot apex, shoot apical meristem	Figure S10 and S11
	Glyma.08G306200	Subgroup E1	The expression was detected in all stages, with higher expression level in main shoot growth, inflorescence formation and flowering	Higher expression was detected in cotyledon, shoot apex, flower, pod, shoot, leaf, unifoliolate leaf, trifoliolate leaf, shoot apex, shoot apical meristem	Figure S10 and S11
	Glyma.18G000600	Subgroup E3	Low level of expression in all stages	Low expression was detected in root	Figure S10 and S11
Oryza sativa	LOC_Os09g38320	Subgroup M2	High level of expression in all stages	Higher expression was detected in seedling, coleoptile, leaf, root, radicle, panicle, spikelet, floret, stigma, ovary, panicle branch, peduncle, leaf, blade (lamina), central vein, collar	Figure S12 and S13
	LOC_Os06g51290	Subgroup M2	High level of expression in all stages	Higher expression was detected in seedling, leaf, panicle, spikelet, floret, ovary, panicle branch, shoot, leaf, blade (lamina), central vein	Figure S12 and S13
	LOC_Os12g43130	Subgroup M1	High level of expression in all stages	Higher expression was detected in shoot, leaf, blade (lamina), central vein, flag leaf	Figure S12 and S13
Sorghum bicolor	Sobic.002G292600	Subgroup M2	The expression was detected in all stages, with higher expression level in flowering stage	Medium expression was detected in all 9 anatomical parts with higher expression in leaf	Figure S14 and S15
Sorghum bicolor	Sobic.008G180800	Subgroup M1	The expression was detected in all stages, with higher expression level in stem elongation stage	Medium expression was detected in all 9 anatomical parts	Figure S14 and S15