Search

Background Sugarcane is a competitive candidate to serve as feedstock for biofuel production worldwide. Plant hormones play an important role in growth and development and regulate biomass yield. Understanding hormonal dynamics and their regulation is critical for increasing sugarcane biomass. To enhance our understanding of biological pathways involved in biomass accumulation, transcriptome analysis of highly segregating F2 introgression hybrids derived from the cross of Saccharum officinarum'LA Purple' and wild S. robustum 'MOL5829' was performed in this study. Recently sequenced information rich allele-specific genome of S. officinarumserved as a reference to identify differentially regulated genes in two groups of extreme segregants of biomass. Results Overall, 8059 differentially expressed genes (log2FC > 2) were grouped into distinct categories viz. Gene Models (21.5%) (GMs), alleles (68%), paralogs (10%) and tandemly duplicated genes (0.14%). KEGG analysis showed enrichment of auxin (IAA), jasmonic acid (JA) and abscisic acid (ABA) related pathways and interesting regulatory roles of three hormone repressor gene families (Aux/IAA, PP2C, and JAZ) of IAA, ABA and JA, respectively. Signaling pathways of these hormones indicated down-regulation of AUX/IAA and PP2C and up-regulation of JAZ repressor genes in high biomass group controlling the expression of downstream growth and development genes. Endogenous hormone levels show higher IAA and ABA contents in high biomass and vice versa for JA. Weighted co-expression network analysis (WGCNA) demonstrated high connectivity between identified hormones related key genes and cell wall structural genes in high biomass genotypes. FPKM and RT-PCR based expression analysis showed the up-regulation of carbohydrate structural genes and down regulation of inflorescence and senescence related genes, which indicated an extended vegetative growth phase in high biomass genotypes. Furthermore, high biomass group displayed modulated regulation of hormones which was achieved by the cumulative expression of Gene Models (GMs), dominant alleles, paralogs, and tandemly duplicated genes. Conclusion Our data revealed that activators and repressors of disparate hormone (IAA, JA, and ABA) signaling pathways are the points of hormone crosstalk in contrasting biomass F2 segregants and could be applied for engineering high biomass acquiring varieties.

Recent studies have shown that global metabolic reprogramming is a common event in plant innate immunity; however, the relevant molecular mechanisms remain largely unknown. Here, we identified a pathogen-induced glycosyltransferase, UGT73C7, that plays a critical role in Arabidopsis disease resistance through mediating redirection of the phenylpropanoid pathway. Loss of UGT73C7 function resulted in significantly decreased resistance to Pseudomonas syringae pv. tomato DC3000, whereas constitutive overexpression of UGT73C7 led to an enhanced defense response. UGT73C7-activated immunity was demonstrated to be dependent on the upregulated expression of SNC1, a Toll/interleukin 1 receptor-type NLR gene. Furthermore, in vitro and in vivo assays indicated that UGT73C7 could glycosylate p-coumaric acid and ferulic acid, the upstream metabolites in the phenylpropanoid pathway. Mutations that lead to the loss of UGT73C7 enzyme activities resulted in the failure to induce SNC1 expression. Moreover, glycosylation activity of UGT73C7 resulted in the redirection of phenylpropanoid metabolic flux to biosynthesis of hydroxycinnamic acids and coumarins. The disruption of the phenylpropanoid pathway suppressed UGT73C7-promoted SNC1 expression and the immune response. This study not only identified UGT73C7 as an important regulator that adjusts phenylpropanoid metabolism upon pathogen challenge, but also provided a link between phenylpropanoid metabolism and an NLR gene.

Nelumbo lutea (American lotus), which differs from Nelumbo nucifera (Asian lotus) morphologically, is one of the two remaining species in the basal eudicot family Nelumbonaceae. Here, we assembled the 843-Mb genome of American lotus into eight pseudochromosomes containing 31 382 protein-coding genes. Comparative analyses revealed conserved synteny without large chromosomal rearrangements between the genomes of American and Asian lotus and identified 29 533 structural variants (SVs). Carotenoid and anthocyanin pigments determine the yellow and red petal colors of American and Asian lotus, respectively. The structural genes encoding enzymes of the carotenoid and anthocyanin biosynthesis pathways were conserved between two species but differed in expression. We detected SVs caused by repetitive sequence expansion or contraction among the anthocyanin biosynthesis regulatory MYB genes. Further transient overexpression of candidate NnMYB5 induced anthocyanin accumulation in lotus petals. Alternative oxidase (AOX), uncoupling proteins (UCPs), and sugar metabolism and transportation contributed to carpel thermogenesis. Carpels produce heat with sugars transported from leaves as the main substrates, because there was weak tonoplast sugar transporter (TST) activity, and with SWEETs were highly expressed during thermogenesis. Cell proliferation-related activities were particularly enhanced in the warmer carpels compared with stamens during the cold night before blooming, which suggested that thermogenesis plays an important role in flower protogyny. Population genomic analyses revealed deep divergence between American and Asian lotus, and independent domestication affecting seed, rhizome, and flower traits. Our findings provide a high-quality reference genome of American lotus for exploring the genetic divergence and variation between two species and revealed possible genomic bases for petal color, carpel thermogenesis and domestication in lotus.

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.

Rambutan is a popular tropical fruit known for its exotic appearance, has long flexible spines on shells, extraordinary aril growth, desirable nutrition, and a favorable taste. The genome of an elite rambutan cultivar Baoyan 7 was assembled into 328 Mb in 16 pseudo-chromosomes. Comparative genomics analysis between rambutan and lychee revealed that rambutan chromosomes 8 and 12 are collinear with lychee chromosome 1, which resulted in a chromosome fission event in rambutan (n = 16) or a fusion event in lychee (n = 15) after their divergence from a common ancestor 15.7 million years ago. Root development genes played a crucial role in spine development, such as endoplasmic reticulum pathway genes, jasmonic acid response genes, vascular bundle development genes, and K+ transport genes. Aril development was regulated by D-class genes (STK and SHP1), plant hormone and phenylpropanoid biosynthesis genes, and sugar metabolism genes. The lower rate of male sterility of hermaphroditic flowers appears to be regulated by MYB24. Population genomic analyses revealed genes in selective sweeps during domestication that are related to fruit morphology and environment stress response. These findings enhance our understanding of spine and aril development and provide genomic resources for rambutan improvement.

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.

Summary Banyan trees are distinguished by their extraordinary aerial roots. The Ficus genus includes species that have evolved a species-specific mutualism system with wasp pollinators. We sequenced genomes of the Chinese banyan tree, F. microcarpa, and a species lacking aerial roots, F. hispida, and one wasp genome coevolving with F. microcarpa, Eupristina verticillata. Comparative analysis of the two Ficus genomes revealed dynamic karyotype variation associated with adaptive evolution. Copy number expansion of auxin-related genes from duplications and elevated auxin production are associated with aerial root development in F. microcarpa. A male-specific AGAMOUS paralog, FhAG2, was identified as a candidate gene for sex determination in F. hispida. Population genomic analyses of Ficus species revealed genomic signatures of morphological and physiological coadaptation with their pollinators involving terpenoid- and benzenoid-derived compounds. These three genomes offer insights into and genomic resources for investigating the geneses of aerial roots, monoecy and dioecy, and codiversification in a symbiotic system.

Pineapple (Ananas comosus L.) is an important tropical fruit crop, not only because of its economic value but also due to its CAM photosynthesis that exhibits the highest water-use efficiency comparing to plants with C3 and C4 photosynthesis. The genome of pineapple variety F153 was sequenced using a combination of DNA sequencing technologies, including Illumina, Moleculo, 454, and PacBio single-molecule long reads. Pooled bacterial artificial chromosome (BAC) sequences were used to assist the genome assembly, and the final assembly reached 382 Mb, 72.6% of the estimated 526 Mb. An ultrahigh-density genetic map with 25 linkage groups was used to correct chimeric scaffolds and anchored 564 scaffolds, covering 316 Mb, or 82.7%, of the assembled genome. The pineapple genome was annotated by MAKER and 27,024 genes, and 10,151 alternative splicing events were identified. Transposable elements (TEs) accounted for 44% of the assembly. The 27.4% unassembled sequences are all highly repetitive centromere, telomere, and rDNA clusters (2.4%) and TEs (25%), indicating that TEs accounted for 69% of the pineapple genome. LTR retrotransposons were the most abundant of TEs, representing 33% of the assembly. Intragenomic syntenic analysis of pineapple genome traced karyotype evolution from seven monocot ancestral chromosomes to current 25 chromosomes, and two ancient whole-genome duplication (WGD) events (σ and τ) in pineapple genome were detected, but not the more recent ρ WGD. Candidate genes involved in the carbon fixation module of CAM were identified in the pineapple genome, and nine genes were found to have a diurnal expression pattern in the green leaf tissue. CAM-related genes were enriched with circadian clock cis-regulatory elements. The pineapple genome will accelerate the progress relevant to fundamental biology and/or pineapple production, including drought tolerance.

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.