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Background Bougainvillea is a popular ornamental plant with brilliant color and long flowering periods. It is widely distributed in the tropics and subtropics. The primary ornamental part of the plant is its colorful and unusual bracts, rich in the stable pigment betalain. The developmental mechanism of the bracts is not clear, and the pathway of betalain biosynthesis is well characterized in Bougainvillea. Results At the whole-genome level, we found 23,469 protein-coding genes by assembling the RNA-Seq and Iso-Seq data of floral and leaf tissues. Genome evolution analysis revealed that Bougainvillea is related to spinach; the two diverged approximately 52.7 million years ago (MYA). Transcriptome analysis of floral organs revealed that flower development of Bougainvillea was regulated by the ABCE flower development genes; A-class, B-class, and E-class genes exhibited high expression levels in bracts. Eight key genes of the betalain biosynthetic pathway were identified by homologous alignment, all of which were upregulated concurrently with bract development and betalain accumulation during the bract initiation stage of development. We found 47 genes specifically expressed in stamens, including seven highly expressed genes belonging to the pentose and glucuronate interconversion pathways. BgSEP2b, BgSWEET11, and BgRD22 are hub genes and interacted with many transcription factors and genes in the carpel co-expression network. Conclusions We assembled protein-coding genes of Bougainvilea, identified the floral development genes, and constructed the gene co-expression network of petal, stamens, and carpel. Our results provide fundamental information about the mechanism of flower development and pigment accumulation in Bougainvillea, and will facilitate breeding of cultivars with high ornamental value.

Laccases play crucial roles in catalyzing lignin and flavonoid biosynthesis in plants, and are predominantly involved in lignin breakdown of bacteria and fungi. Lignin distributes in all parts of plant and is a key component in plant morphogenesis. The complex sugarcane genome limited the study of laccase genes, but our completed reference genome of tetraploid S. spontaneum AP85–441 makes it possible to study this gene family. We identified 29 laccase genes, and 10 genes with 4 alleles, 9 genes with 3 alleles, 5 genes with 2 alleles, 5 genes with 1 allele in sugarcane. Among them 4 genes have tandemly dupicated paralogs; and 12 genes have dispersely distributed paralogs. They distributed unevenly among 27 of 32 chromosomes, and 9 (31.03%) genes located in Chromosome 3. Phylogeny and conserved domain suggested sugarcane laccase genes had the highest similarity with sorghum, and laccase10 was the most conserved gene in monocots and dicotyledons. We found sugarcane laccase genes were regulated by light signal, phytohormones, abiotic stress and some tissue-specific transcription factors by predicted cis-elements in the promoters. Nine laccase genes had miR397 and miR528 target sites, which have been reported as post-transcriptionally regulated laccase genes. Four laccase genes had 4 new miRNA target sites, including stem specific miRNA. Analysis of RNA-seq data of different developmental stages of leaves and stems showed that 27 genes had expression of those tissues, and most of them mainly express in stems. Among them laccase 4 and laccase10 showed the highest expression level in mature stems, while laccase27 showed the highest expression in seedling leaves. Our results show the potential function of sugarcane laccase genes in catalyzing lignin biosynthesis, stress resistance, and morphogenesis. These findings and genomic resources will facilitate research on improving stress tolerance, lignin content, and biomass yield in sugarcane.

The TCP family genes have been under selection during domestication in maize and related andropogoneae crops. They encode plant-specific transcription factors involved in growth and development, especially in shaping the plant morphology and architecture. Sugarcane (Saccharum spp.) is the most productive in harvesting tonnage and 5th economically valuable crops worldwide for supporting world’s sugar and fuel ethanol production. Based on recently published sugarcane genome, we performed a genome-wide analysis of this gene family in the sugarcane genome and identified 22 TCP genes (SsTCPs), with 1–4 alleles each. They distributed across 28 chromosomes of S. spontaneum. Phylogenetic analysis showed that all 22 SsTCP genes can be classifed into two major groups: class I and class II. All 22 groups of SsTCPs showed species-specific clustering with TCPs of sorghum which indicate close relationship between sorghum and Saccharum. Structural organization of SsTCP genes showed that 37 SsTCPs are intronless and of the 22 SsTCPs with introns exist in coding region, which are different with TCPs of sorghum and wheat that located in UTR region. Expression study showed that transcripts of class I SsTCPs were more abundant than transcripts of class II SsTCPs. Moreover, the expression of SsTCP5–4, SsTCP6–2, SsTCP8–1, SsTCP12, SsTCP13, SsTCP15–1, SsTCP17–1 and SsTCP17–6 displayed significant change after plant hormones treatments, which suggest their function related to plant hormones. Cis-element analysis of SsTCPs’s promoter suggests that subfunctionalization may have occurred for homoeologous genes. Taken together, our analysis of TCPs in S. spontaneum provide a good starting for further studies to elucidate their specific function in sugarcane.

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.

In the version of this article originally published, the accession codes listed in the data availability section were incorrect and the section was incomplete. The text for this section should have read "The genome assembly and gene annotation have been deposited in the NCBI database under accession number QVOL00000000, BioProject number PRJNA483885 and BioSample number SAMN09753102. The data can also be downloaded from the following link: http://www.life.illinois.edu/ming/downloads/Spontaneum_genome/ ." The errors have been corrected in the HTML and PDF versions of the article.