Genome-Wide Characterization of Lectin Receptor Kinases in Saccharum spontaneum L. and Their Responses to Stagonospora tainanensis Infection

Abstract

Sugarcane is an important sugar and bioenergy ethanol crop, and the hyperploidy has led to stagnant progress in sugarcane genome decipherment, which also hindered the genome-wide analyses of versatile lectin receptor kinases (LecRKs). The published genome of Saccharum spontaneum, one of the two sugarcane ancestor species, enables us to study the characterization of LecRKs and their responses to sugarcane leaf blight (SLB) triggered by Stagonospora tainanensis. A total of 429 allelic and non-allelic LecRKs, which were classified into evolved independently three types according to signal domains and phylogeny, were identified based on the genome. Regarding those closely related LecRKs in the phylogenetic tree, their motifs and exon architectures of representative L- and G-types were similar or identical. LecRKs showed an unequal distribution on chromosomes and more G-type tandem repeats may come from the gene expansion. Comparing the differentially expressed LecRKs (DELs) in response to SLB in sugarcane hybrid and ancestor species S. spontaneum, we found that the DEL number in the shared gene sets was highly variable among each sugarcane accession, which indicated that the expression dynamics of LecRKs in response to SLB were quite different between hybrids and particularly between sugarcane hybrid and S. spontaneum. In addition, C-type LecRKs may participate in metabolic processes of plant–pathogen interaction, mainly including pathogenicity and plant resistance, indicating their putative roles in sugarcane responses to SLB infection. The present study provides a basic reference and global insight into the further study and utilization of LecRKs in plants.

Genome-Wide Identification of LRR-RLK Family in Saccharum and Expression Analysis in Response to Biotic and Abiotic Stress

“…Previous studies identified 225, 234 and 467 LRR-RLK genes in soybean [11], tomato [13] and Arabidopsis [14], respectively. Sugarcane is subjected to various abiotic and biotic stresses during growth and development [54,58]. It is worth noting that the members of LRR-RLK genes in all of these species mentioned are larger than those in Arabidopsis, which might be due to their small genome.…”

“…The field was watched throughout the plant life cycle, especially after appearance of sugarcane leaf blight disease (SLB) symptoms, and five different disease development stages were defined according to the previous report [54]. The leaf samples that had no visible sign of the SLB symptom and without pathogenic spores or hyphae observed under the microscope were represented as control [54]; Supplementary Material S5 shows the details. Three biological replicates were performed for each infection stage and for control (healthy), and a total of 18 samples were obtained.…”

“…Three biological replicates were performed for each infection stage and for control (healthy), and a total of 18 samples were obtained. For each sugarcane accession, three plants with similar growth vigor and disease severity were selected for sampling, and the leaf located at the same leaf position was collected [54]. The collected samples were immediately put into liquid nitrogen and stored at −80 • C for later use.…”

“…These qRT-PCR primers designed by Primer Premier 6 are listed in Supplementary Material Table S1. Furthermore, as an internal control primer, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) is unanimously recognized for its stability in academic research, such as in different sugarcane tissues and various adversity stress, and the primer sequence of GAPDH is universal [54]. Therefore, this housekeeping gene was used as the only internal control gene.…”

“…The qRT-PCR amplification was performed using SYBR Green Master Mix Reagent (TaKaRa, Shimogyo-ku, Kyoto, Japan), according to the manufacturer's instructions on an Applied Biosystems 7500 Real-Time PCR system. The standard qRT-PCR program refers to reports by Wang et al [54]. Three technical replicates for each sample were performed and the relative expression level of each gene was calculated from the 2 −∆∆Ct value [55].…”