The VQ motif-containing proteins play a vital role in various processes such as growth, resistance to biotic and abiotic stresses and development. However, there is currently no report on the VQ genes in sugarcane (Saccharum spp.). Herein, 78 VQ genes in Saccharum spontaneum were identified and classified into nine subgroups (I-IX) by comparative genomic analyses. Each subgroup had a similar structural and conservative motif. These VQ genes expanded mainly through whole-genome segmental duplication. The cis-regulatory elements (CREs) of the VQ genes were widely involved in stress responses, phytohormone responses and physiological regulation. The RNA-seq data showed that SsVQ gene expression patterns in 10 different samples, including different developmental stages, revealed distinct temporal and spatial patterns. A total of 23 SsVQ genes were expressed in all tissues, whereas 13 SsVQ genes were not expressed in any tissues. Sequence Read Archive (SRA) data showed that the majority of SsVQs responded to cold and drought stress. In addition, quantitative real-time PCR analysis showed that the SsVQs were variously expressed under salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA) and cold treatment. This study conducted a full-scale analysis of the VQ gene family in sugarcane, which could be beneficial for the functional characterization of sugarcane VQ genes and provide candidate genes for molecular resistance breeding in cultivated sugarcane in the future.

Modern sugarcane cultivars are highly polyploid with complex nuclear genomic genetic background, while their mitochondrion (mt) genomes are much simpler, smaller and more manageable and could provide useful phylogenetic information. In this study, the mt genome of a modern commercial cultivar A1 was sequenced via Illumina Hiseq XTen and PacBio Sequel platform. The assembled and annotated mitochondrial genomes of A1 were composed of two circular DNA molecules, one large and one small, which were named Chromosome 1 and Chromosome 2. The two distinct circular chromosomes of mitogenome construct is consisted with other sugarcane cultivars i.e., Saccharum officinarum Khon Kaen 3 and Saccharum spp. hybrids ROC22 and FN15. The Chromosome 1 of A1 mitogenome is 300,822 bp in length with the GC content of 43.94%, and 7.14% of Chromosome 1 sequences (21,468 nucleotides) are protein coding genes (PCGs) while 92.86% (279,354 nucleotides) are intergenic region. The length of Chromosome 2 is 144,744 bp with the GC content of 43.57%, and 8.20% of Chromosome 2 sequences (11,865 nucleotides) are PCGs while 91.80% (132,879 nucleotides) are intergenic region. A total of 43 genes are located on Chromosome 1, which contains 22 PCGs (six nad genes, four rps genes, four atp genes, three ccm genes, three cox genes, one mat gene and one mtt gene) and 21 non-coding genes including 15 tRNAs and 6 rRNAs. Chromosome 2 includes 18 genes in total, which contains 13 PCGs (four nad genes, three rps genes, two atp genes, one ccm gene, one cob gene, one cox gene and one rpl gene) and five non-coding genes (tRNA genes). Analysis of codon usage of 35 PCGs showed that codon ending in A/U was preferred. Investigation of gene composition indicated that the types and copy numbers of CDS genes, tRNAs and rRNAs of A1 and FN15 were identical. The cox1 gene has two copies and the trnP gene has one copy in A1, FN15 and ROC22 three lines, while there is only one copy of cox1 and two copies of trnP in S. officinarum Khon Kaen 3. In addition, S. officinarum Khon Kaen 3 have no nad1 gene and rps7 gene. 100 sequence repeats, 38 SSRs and 444 RNA editing sites in A1 mt genome were detected. Moreover, the maximum likelihood phylogenetic analysis found that A1 were more closely related to S. spp. hybrid (ROC22 and FN15) and S. officinarum (Khon Kaen 3). Herein, the complete mt genome of A1 will provide essential DNA molecular information for further phylogenetic and evolutionary analysis for Saccharum and Poaceae.

In plants, the multi-gene family of dual-function hexokinases (HXKs) plays an important role in sugar metabolism and sensing, that affects growth and stress adaptation. Sugarcane is an important sucrose crop and biofuel crop. However, little is known about the HXK gene family in sugarcane. A comprehensive survey of sugarcane HXKs, including physicochemical properties, chromosomal distribution, conserved motifs, and gene structure was conducted, identifying 20 members of the SsHXK gene family that were located on seven of the 32 Saccharum spontaneum L. chromosomes. Phylogenetic analysis showed that the SsHXK family could be divided into three subfamilies (group I, II and III). Motifs and gene structure were related to the classification of SsHXKs. Most SsHXKs contained 8–11 introns which was consistent with other monocots. Duplication event analysis indicated that HXKs in S. spontaneum L. primarily originated from segmental duplication. We also identified putative cis-elements in the SsHXK promoter regions which were involved in phytohormone, light and abiotic stress responses (drought, cold et al.). During normal growth and development, 17 SsHXKs were constitutively expressed in all ten tissues. Among them, SsHXK2, SsHXK12 and SsHXK14 had similar expression patterns and were more highly expressed than other genes at all times. The RNA-seq analysis showed that 14/20 SsHXKs had the highest expression level after cold stress for 6 h, especially SsHXK15, SsHXK16 and SsHXK18. As for drought treatment, 7/20 SsHXKs had the highest expression level after drought stress for 10 days, 3/20 (SsHKX1, SsHKX10 and SsHKX11) had the highest expression level after 10 days of recovery. Overall, our results revealed the potential biological function of SsHXKs, which may provide information for in-depth functional verification.