The complete mitochondrial genome of sugarcane (Saccharum spp.) variety FN15

Graph-based mitochondrial genomes of three foundation species in the Saccharum genus

KEY MESSAGE

We reported the graph-based mitochondrial genomes of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) for the first time. The results revealed pan-structural variation and evolutionary processes in the mitochondrial genomes within Saccharum. Saccharum belongs to the Andropogoneae, and cultivars species in Saccharum contribute nearly 80% of sugar production in the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes, including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short-repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenomes of three Saccharum species, and a systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitogenomes revealed the differential features of the Saccharum mitogenomes.

Developing new sugarcane varieties suitable for mechanized production in China: principles, strategies and prospects

The sugar industry, which relates to people's livelihood, is strategic and fundamental in the development of agricultural economy. In China, sugar derived from sugarcane accounts for approximately 85% of total sugar production. Mechanization is the "flower" of sugarcane industry. As the saying goes "when there are blooming flowers, there will be sweet honey." However, due to limitations in land resources, technology, equipment, organization, and management, mechanization throughout the sugarcane production process has not yet brought about the economic benefits that a mechanized system should provide and has not reached an ideal yield through the integration of agricultural machinery and agronomic practice. This paper briefly describes how to initiate the mechanization of Chinese sugarcane production to promote the sound, healthy, and rapid development of the sugarcane industry, and how to ultimately achieve the transformation of sugarcane breeding in China and the modernization of the sugarcane industry from three perspectives, namely, requirements of mechanized production for sugarcane varieties, breeding strategies for selecting new sugarcane varieties suitable for mechanized production, and screening for sugarcane varieties that are suitable for mechanization and diversification in variety distribution or arrangement in China. We also highlight the current challenges surrounding this topic and look forward to its bright prospects.

A Comprehensive Identification and Expression Analysis of VQ Motif-Containing Proteins in Sugarcane (Saccharum spontaneum L.) under Phytohormone Treatment and Cold Stress

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.

Characterization and Phylogenetic Analyses of the Complete Mitochondrial Genome of Sugarcane (Saccharum spp. Hybrids) Line A1

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.

The complete mitochondrial genome and phylogenetic analysis of sugarcane (Saccharum spp. hybrids) line 15a-53

The complete mitogenome of Saccharum spp. hybrid 15a-53 was determined in this study, which contains two distinct circular chromosomes, Chromosome 1 and 2. The length of Chromosome 1 is 300,848 bp with the GC content of 43.93%, while Chromosome 2 is 144,713 bp in length with the GC content of 43.57%. In Chromosome 1, 7.14% of the genome (21,468 nucleotides) is coding DNA and 92.86% (279,380 nucleotides) are intergenic region, while in Chromosome 2, 8.20% of genome (11,865 nucleotides) are coding DNA and 91.80% (132,848 nucleotides) are intergenic region. Chromosome 1 contains 20 protein-coding genes (three atp genes, three ccm genes, two cox genes, one mat gene, one mtt gene, six nad genes, and four rps genes), and 21 non-coding genes (15 tRNA and six rRNAs), while in Chromosome 2, there are 13 protein-coding genes (four nad genes, three rps genes, two atp genes, one ccm gene, one cob gene, one cox gene, and one rpl gene) and five tRNA genes. Maximum Likelihood phylogenetic analysis indicated that 15a-53 is close to S. spp. hybrid ROC22, S. spp. hybrid FN15 and S. officinarum Khon Kaen 3. The complete mitochondrial genome herein will provide useful sequence information for phylogenetic and evolutionary studies for Saccharum and Poaceae.