Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner

Zhenquan Duan,Tian Zhang,Yongli Zhang,Hui Song,Mingwei Chen

doi:10.1186/s13007-022-00840-y

Abstract

BackgroundCultivated peanut (Arachis hypogaea, AABB genome), an allotetraploid from a cross between A. duranensis (AA genome) and A. ipaensis (BB genome), is an important oil and protein crop with released genome and RNA-seq sequence datasets. These datasets provide the molecular foundation for studying gene expression and evolutionary patterns. However, there are no reports on the proteomic data of A. hypogaea cv. Tifrunner, which limits understanding of its gene function and protein level evolution.ResultsThis study sequenced the A. hypogaea cv. Tifrunner leaf and root proteome using the tandem mass tag technology. A total of 4803 abundant proteins were identified. The 364 differentially abundant proteins were estimated by comparing protein abundances between leaf and root proteomes. The differentially abundant proteins enriched the photosystem process. The number of biased abundant homeologs between the two sub-genomes A (87 homeologs in leaf and root) and B (69 and 68 homeologs in leaf and root, respectively) was not significantly different. However, homeologous proteins with biased abundances in different sub-genomes enriched different biological processes. In the leaf, homeologs biased to sub-genome A enriched biosynthetic and metabolic process, while homeologs biased to sub-genome B enriched iron ion homeostasis process. In the root, homeologs with biased abundance in sub-genome A enriched inorganic biosynthesis and metabolism process, while homeologs with biased abundance in sub-genome B enriched organic biosynthesis and metabolism process. Purifying selection mainly acted on paralogs and homeologs. The selective pressure values were negatively correlated with paralogous protein abundance. About 77.42% (24/31) homeologous and 80% (48/60) paralogous protein pairs had asymmetric abundance, and several protein pairs had conserved abundances in the leaf and root tissues.ConclusionsThis study sequenced the proteome of A. hypogaea cv. Tifrunner using the leaf and root tissues. Differentially abundant proteins were identified, and revealed functions. Paralog abundance divergence and homeolog bias abundance was elucidated. These results indicate that divergent abundance caused retention of homologs in A. hypogaea cv. Tifrunner.

Highlights

Cultivated peanut (Arachis hypogaea), an important oil and protein crop, is an allotetraploid from a cross between A. duranensis and A. ipaensis [1,2,3]
Tifrunner were sequenced under normal growth conditions, and the cleaned raw data was released on PeanutBase [9, 10]
Several proteins lacking during the proteome sequencing of leaf and root tissues could not be quantified (Additional file 1: Fig. S1e)

Summary

Introduction

Cultivated peanut (Arachis hypogaea), an important oil and protein crop, is an allotetraploid from a cross between A. duranensis and A. ipaensis [1,2,3]. Tifrunner, which limits the understanding of its gene functions. Cultivated peanut (Arachis hypogaea, AABB genome), an allotetraploid from a cross between A. duranensis (AA genome) and A. ipaensis (BB genome), is an important oil and protein crop with released genome and RNA-seq sequence datasets. These datasets provide the molecular foundation for studying gene expression and evolutionary patterns. Tifrunner, which limits understanding of its gene function and protein level evolution

Methods

Results

Discussion

Conclusion