Adaptive and degenerative evolution of the S-Phase Kinase-Associated Protein 1-Like family in Arabidopsis thaliana

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Plant Biology

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Introduction

Materials and Methods

Identification of Skp1 genes in A. lyrata and A. halleri

Sequence alignment and phylogenetic analysis

Birth and death of the Skp1 genes in the Arabidopsis genus

Gene structure analysis and reference sequence retrieval

Sequence assembly for polymorphism analysis

Determination of tandemly duplicated Skp1 genes

Clustering analysis

Expression data resources

Cross species test of neutral evolution

Molecular cloning and yeast two-hybrid analysis

Results

Identification of Skp1 genes in three closely related Arabidopsis species

Phylogenetic analysis of the Skp1 genes in a short evolutionary history

Low evolutionary constraints of intronless ASK genes

Expression variation of the ASK genes

Differential sequence polymorphism of the ASK genes

Variation association of ASK1 expression and polymorphism

Variance of biochemical interactions of ASK1 and ASK2 with known F-box proteins

Discussion

Retroposed ASK genes originated from one single ancestor locus

Degenerative processes of ASK genes

The large expression variance of ASK1 may indicate diverse functions of SCF complexes

Conclusions

Supplemental Information

OrthoMCL groups of Skp1 proteins in Ath, Aly, and Aha species.

DOI: 10.7717/peerj.6740/supp-1

Gene identifications of 15 known F-box proteins selected for testing the differential interactions with ASK1 and ASK2.

DOI: 10.7717/peerj.6740/supp-2

Raw data for β-galactosidase activity assay.

β-galactosidase.

DOI: 10.7717/peerj.6740/supp-3

An improved amino acid sequence alignment of 45 Arabidopsis Skp1 protein sequences.

DOI: 10.7717/peerj.6740/supp-4

A GeneWise reannotation uncovers a frame-shift mutation in ASK6.

DOI: 10.7717/peerj.6740/supp-5

A GeneWise reannotation uncovers a frame-shift mutation in AlySkp02.

DOI: 10.7717/peerj.6740/supp-6

A GeneWise reannotation uncovers a frame-shift mutation in AhaSkp11.

DOI: 10.7717/peerj.6740/supp-7

Amino acid sequences of the Skp1 proteins annotated in A. thaliana, A. lyrata, and A. halleri.

DOI: 10.7717/peerj.6740/supp-8

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Zhihua Hua conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Zhenyu Gao performed the experiments, revised the manuscript.

Data Availability

The following information was supplied regarding data availability:

The raw data are available in File S1 and Table S3.

Funding

This work was supported by a National Science Foundation CAREER award (MCB-1750361 to Zhihua Hua) and a Baker Award from Ohio University (IA1017002 to Zhihua Hua). Zhenyu Gao was a senior visiting scholar in the Hua lab, in part supported by 151 Talents Project from the province of Zhejiang, China. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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