The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

Abstract

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.

Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

“…Regarding the distribution of introns in common bean PKs, the maximum intron number observed was 28 – the same number found for soybean (Liu et al, 2015) and cowpea (Ferreira-Neto et al, 2021). Among available kinomes, the highest numbers of introns were found in grapevine (49) (Zhu et al, 2018b), sugarcane (52) (Aono et al, 2021), and pineapple (67) (Zhu et al, 2018a). The mean introns number found for common bean PKs (5.74) is lower than those found for strawberry (Liu et al, 2020) and pineapple (Zhu et al, 2018a), which were 6.45 and 6.59, respectively.…”

“…Additionally, in sorghum, sugarcane (Aono et al, 2021), grapevine (Zhu et al, 2018b), pineapple (Zhu et al, 2018a), and wheat (Yan et al, 2017), the AGC RSK-2 subfamily was also the most numerous. The second most numerous families were found to be RLK-Pelle WAK in sorghum (Aono et al, 2021), AGC NDR in wheat (Yan et al, 2017), and RLK-Pelle DLSV in sugarcane (Aono et al, 2021), grapevine (Zhu et al, 2018b) and pineapple (Zhu et al, 2018a). Only 36 (3%) of common bean PKs presented more than one kinase domain, which were distributed into 16 families.…”

Incidence and Distribution of Four Viruses Causing Diverse Mosaic Diseases of Sugarcane in China

“…Sugarcane (Saccharum spp. hybrid) is an important sugar crop that accounts for 80% of sugar production and is also a renewable energy crop that provides 40% of fuel ethanol worldwide [1]. Sugarcane production in China mainly occurs in the southern and southwestern regions, including three main sugar-producing provinces Guangxi, Yunnan, and Guangdong, which combined produce 88% of sugar in China.…”

Recent Advances in Sugarcane Genomics, Physiology, and Phenomics for Superior Agronomic Traits

“…Sorghum is considered to be the reference model for comparative studies due to it being closest in synteny with sugarcane ( Le Cunff et al, 2008 ; de Setta et al, 2014 ; Aono et al, 2021 ). Next-generation sequencing (NGS)-based genotyping is now popularly used in many crop species that lack reference genomes and has become the primary choice for many breeders due to its cost-effectiveness and speed ( Chung et al, 2017 ).…”