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

Abstract

Background 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. 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. Results This 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. Conclusions This 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.

Deciphering peanut complex genomes paves a way to understand its origin and domestication

“…In the leaf, homeologs enriched biosynthetic and metabolic process in At subgenome, while iron ion homeostasis process in Bt subgenome. In the root, homeologs enriched inorganic biosynthesis and metabolism process in At subgenome, while organic biosynthesis and metabolism process in Bt subgenome (Duan et al ., 2022 ). Nevertheless, peanut genome complexity combines allotetraploidy with other gene duplication mechanisms.…”

Crop Proteomics under Abiotic Stress: From Data to Insights

“…In maize seedlings, substantial differences in post-transcriptional and translational changes between salt-treated embryo and endosperm were noticed using SWATH-MS, which indicated that the elevation of ABA level was an endosperm-dependent process [ 34 ]. In peanuts, differentially abundant proteins were identified using LC-MS coupled with tandem mass tag (TMT), and it was found that homologous proteins enriched different biological processes between the two subgenomes A and B [ 35 ]. SWATH-MS represents a valuable tool for quantitative proteomics based on its ability to generate reproducible data with the added benefit of allowing reinterrogation of data to improve analytical performance.…”