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We report here the genome assembly and analysis of Microbacterium strain sp. LKL04, a Gram-positive bacterial endophyte isolated from switchgrass plants (Panicum virgatum) grown on a reclaimed coal-mining site. The 2.9-Mbp genome of this bacterium was assembled into a single contig encoding 2,806 protein coding genes.

This study sought to better understand how time of day (ToD) or turgor pressure might affect the flexural stiffness of sweet sorghum stalks and potentially regulate stalk lodging resistance. Stalk flexural stiffness measured across a 48 h period in 2019 showed a significant diurnal association with leaf water potential and stalk flexural stiffness. While the correlation between stalk flexural stiffness and this proxy for internal turgor status was statistically significant, it only accounted for roughly 2% of the overall variance in stiffness. Given that turgor status is a dynamic rather than fixed physiological variable like the cellular structure, these data suggest that internal turgor plays a small yet significant role in influencing the flexural stiffness of fully mature stalks prior to a stalk lodging event. The association was assessed at earlier developmental stages across three distinct cultivars and found not to be significant. Panicle weight and stalk basal weight, but not stalk Brix or water content, were found to be better predictors of stalk flexural stiffness than either ToD or turgor status. Observation across three cultivars and four distinct developmental stages ranging from the vegetative to the hard-dough stages suggests that stalk flexural stiffness changes significantly as a function of time. However, neither ToD nor turgor status appear to meaningfully contribute to observed variations in stalk flexural stiffness in either individual stalks or across larger populations. As turgor status was not found to meaningfully influence stalk strength or flexural stiffness at any developmental time point examined in any of the three sweet sorghum cultivars under study, turgor pressure likely offers only inconsequential contributions to the biomechanics underlying sweet sorghum stalk lodging resistance. [ABSTRACT FROM AUTHOR]

Stalk lodging contributes to significant crop yield losses. Therefore, understanding the biomechanical strength and structural rigidity of grain stalks can contribute to improving stalk lodging resistance in crops. From the structural constituents of the stalk, the rind provides the principal structure, supporting cells against tension and bending loads. In this work, the biomechanical and viscoelastic behavior of the rind from the internodes of two sweet sorghum varieties (Della and REDforGREEN (RG)), grown in two different growing seasons, were evaluated by three-point micro-bending tests using a dynamic mechanical analyzer (DMA). In addition, the chemical composition of rinds and the microfibril angle (MFA) of the cell wall were determined using XRD. The results revealed that the biomechanical behavior of Della varieties was stiffer and more resistant to loads than that of RG varieties. Two features of the rind biomechanical properties, flexural modulus (FM) and flexural strength (FS), showed a significant reduction for RG. Particularly, a reduction in FS of 16–37% and in FM of 22–41% were detected for RG1. Changes in the stalks' rind biomechanical properties were attributed to cell wall components. Total lignin and glucan/cellulose contents were positively correlated with the FM and FS of the rind. Subsequently, an increase in the two cell wall components drove an increase in stiffness. Furthermore, the MFA of the rind was also found to influence the rind strength. [ABSTRACT FROM AUTHOR]

The complexity in chemical composition alongside the genomic complexity of crop plants poses significant challenges for the characterization of their proteomes. This chapter provides specific methods that can be used for the extraction and identification of proteins from sweet potato, and a proteogenomic method for the subsequent peptide mapping on the haplotype-derived sweet potato genome assembly. We outline two basic methods for extracting proteins expressed in root and leaf tissues for the label-free quantitative proteomics-one phenol-based procedure and one polyethylene glycol (PEG) 4000-based fractionation method-and discuss strategies for the organ-specific protein extraction and increased recovery of low-abundance proteins. Next, we describe computational methods for improved proteome annotation of sweet potato based on aggregated genomics and transcriptomics resources available in our and public databases. Lastly, we describe an easily customizable proteogenomics approach for mapping sweet potato peptides back to their genome location and exemplify its use in improving genome annotations using a mass spectrometry data set.