Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions
Abstract
:1. Introduction
2. Results and Discussions
2.1. Identification of the FLA Family in Plants
2.2. Phylogenetic Analysis and Classification of FLAs
2.3. Structural and Evolutionary Analysis of FLAs
2.4. Analysis of FLA Duplication Patterns during the Process of Evolution
3. Materials and Methods
3.1. Bioinformatics Identification of FLAs
3.2. Multiple Sequence Alignment and Phylogenetic Analysis
3.3. Motif Prediction
3.4. Gene Duplication and Molecular Evolution
4. Conclusions
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
Abbreviations
FLA | Fasciclin-like arabinogalactan protein |
AGP | Arabinogalactan protein |
GPI | Glycosylphosphatidylinositol |
PAST% | The percentage of Pro, Ala, Ser, and Thr residues in a protein amino-acid sequence |
Ccr | Chondrus crispus |
Cre | Chlamydomonas reinhardtii |
Mpo | Marchantia polymorpha |
Smo | Selaginella moellendorffii |
Pab | Picea abies |
Atr | Amborella trichopoda |
Egr | Eucalyptus grandis |
Pt | Populus trichocarpa |
Bdi | Brachypodium distachyon |
Os | Oryza sativa |
Ka | Nonsynonymous substitution rate |
Ks | Synonymous substitution rate |
PGDD | Plant Genome Duplication Database |
NCBI | National Center for Biotechnology Information |
ConGenIE | Conifer Genome Integrative Explorer |
HMM | Hidden Markov Model |
BLASTP | Protein Basic Local Alignment Search Tool |
MYN | Modified Yang-Nielsen Algorithm |
MCSCAN | Multiple Collinearity Scan |
MEME | Multiple Expectation maximization for Motif Elicitation |
LG | Le_Gascuel_2008 model |
G | Gamma distribution |
I | Evolutionarily invariable |
GSDS | Gene Structure Display Server |
OrcAE | Online Resource for Community Annotation of Eukaryotes |
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Lineage | Organism | Genome Size (Mb) | No. of Predicted Genes | No. of FLA Genes | Reference |
---|---|---|---|---|---|
Red algae | Chondrus crispus | 104.98 | 9843 | 1 | This study |
Green algae | Chlamydomonas reinhardtii | 120.405 | 14,488 | 11 | This study |
Chara braunii | 1751.21 | 35,424 | 24 | This study | |
Liverworts | Marchantia polymorpha | 215.739 | 19,287 | 14 | This study |
Mosses | Physcomitrella patens | 472.081 | 23,733 | 12 | This study |
Lycophytes | Selaginella moellendorffii | 212.315 | 34,782 | 9 | This study |
Gymnosperm | Picea abies | 19,600 | 28,354 | 24 | This study |
Amborellales | Amborella trichopoda | 706.495 | 19,354 | 12 | This study |
Eudicots | Arabidopsis thaliana | 119.148 | 38,093 | 22 | Schultz et al. [21] |
Eucalyptus grandis | 691.43 | 45,226 | 19 | MacMillan et al. [13] | |
Populus trichocarpa | 434.29 | 37,197 | 49 | Showalter et al. [24] | |
Monocots | Brachypodium distachyon | 218.345 | 34,310 | 23 | This study |
Oryza sativa | 374.423 | 33,185 | 26 | Ma and Zhao [12] |
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He, J.; Zhao, H.; Cheng, Z.; Ke, Y.; Liu, J.; Ma, H. Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions. Int. J. Mol. Sci. 2019, 20, 1945. https://doi.org/10.3390/ijms20081945
He J, Zhao H, Cheng Z, Ke Y, Liu J, Ma H. Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions. International Journal of Molecular Sciences. 2019; 20(8):1945. https://doi.org/10.3390/ijms20081945
Chicago/Turabian StyleHe, Jiadai, Hua Zhao, Zhilu Cheng, Yuwei Ke, Jiaxi Liu, and Haoli Ma. 2019. "Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions" International Journal of Molecular Sciences 20, no. 8: 1945. https://doi.org/10.3390/ijms20081945