Genome-wide analysis of the GRAS gene family in Liriodendron chinense reveals the putative function in abiotic stress and plant development

Introduction

GRAS genes encode plant-specific transcription factors that play essential roles in plant growth and development. However, the members and the function of the GRAS gene family have not been reported in Liriodendron chinense. L. chinense, a tree species in the Magnolia family that produces excellent timber for daily life and industry. In addition, it is a good relict species for plant evolution research.

Methods

Therefore, we conducted a genome-wide study of the LcGRAS gene family and identified 49 LcGRAS genes in L. chinense.

Results

We found that LcGRAS could be divided into 13 sub-groups, among which there is a unique branch named HAM-t. We carried out RNA sequencing analysis of the somatic embryos from L. chinense and found that LcGRAS genes are mainly expressed after heart-stage embryo development, suggesting that LcGRAS may have a function during somatic embryogenesis. We also investigated whether GRAS genes are responsive to stress by carrying out RNA sequencing (RNA-seq) analysis, and we found that the genes in the PAT subfamily were activated upon stress treatment, suggesting that these genes may help plants survive stressful environments. We found that PIF was downregulated and COR was upregulated after the transient overexpression of PATs, suggesting that PAT may be upstream regulators of cold stress.

Discussion

Collectively, LcGRAS genes are conserved and play essential roles in plant development and adaptation to abiotic stress.

Transcriptomic profiling of the floral fragrance biosynthesis pathway of Liriodendron and functional characterization of the LtuDXR gene

Floral fragrance, which has the function of attracting pollinators, is a class of volatile secondary metabolites mainly released by the secretory tissue of petals. Terpenoids are key components of floral volatile substances. Previous studies have shown that there are significant differences in the concentration and composition of volatile floral fragrances, especially terpenoids, between Liriodendron chinense and L. tulipifera. At present, the mechanism by which the synthesis of floral fragrance is regulated in Liriodendron remains unexplored. In this study, we analyzed the differentially expressed genes (DEGs) of L. chinense and L. tulipifera, and identified 130 DEGs related to terpenoid synthesis. A KEGG enrichment analysis of DEGs related to terpenoid biosynthesis revealed that the monoterpenoid biosynthesis pathway was the most significant. We cloned the LtuDXR gene from L. tulipifera using RACE technology. RT-qPCR results showed that the expression of the LtuDXR gene was the highest in the early florescence petals, indicating that the LtuDXR gene may play a role in the synthesis of volatile terpenoids. Subcellular localization showed that the LtuDXR protein is mainly localized in the chloroplast. Overexpression of LtuDXR in Arabidopsis thaliana significantly increased the plant height, DXR enzyme activity, and carotenoid content. In this study, we identified and functionally characterized LtuDXR, which is involved in terpenoid synthesis in Liriodendron. Our work lays the foundation for further exploration of the molecular mechanism by which terpenoid biosynthesis is regulated in Liriodendron.

Genome-Wide Identification and Expression Analysis of R2R3-MYB Family Genes Associated with Petal Pigment Synthesis in Liriodendron

The MYB transcription factor family is one of the largest families in plants, and its members have various biological functions. R2R3-MYB genes are involved in the synthesis of pigments that yield petal colors. Liriodendron plants are widely cultivated as ornamental trees owing to their peculiar leaves, tulip-like flowers, and colorful petals. However, the mechanism underlying petal coloring in this species is unknown, and minimal information about MYB genes in Liriodendron is available. Herein, this study aimed to discern gene(s) involved in petal coloration in Liriodendron via genome-wide identification, HPLC, and RT-qPCR assays. In total, 204 LcMYB superfamily genes were identified in the Liriodendron chinense genome, and 85 R2R3-MYB genes were mapped onto 19 chromosomes. Chromosome 4 contained the most (10) R2R3-MYB genes, and chromosomes 14 and 16 contained the fewest (only one). MEME analysis showed that R2R3-MYB proteins in L. chinense were highly conserved and that their exon-intron structures varied. The HPLC results showed that three major carotenoids were uniformly distributed in the petals of L. chinense, while lycopene and β-carotene were concentrated in the orange band region in the petals of Liriodendron tulipifera. Furthermore, the expression profiles via RT-qPCR assays revealed that four R2R3-MYB genes were expressed at the highest levels at the S3P/S4P stage in L. tulipifera. This result combined with the HPLC results showed that these four R2R3-MYB genes might participate in carotenoid synthesis in the petals of L. tulipifera. This work laid a cornerstone for further functional characterization of R2R3-MYB genes in Liriodendron plants.

Genome Sequence and Comparative Analysis of Colletotrichum gloeosporioides Isolated from Liriodendron Leaves

Colletotrichum gloeosporioides is a hemibiotrophic pathogen causing significant losses to economically important crops and forest trees, including Liriodendron. To explore the interaction between C. gloeosporioides and Liriodendron and to identify the candidate genes determining the pathogenesis, we sequenced and assembled the whole genome of C. gloeosporioides Lc1 (CgLc1) using PacBio and Illumina next generation sequencing and performed a comparative genomic analysis between CgLc1 and Cg01, the latter being a described endophytic species of the C. gloeosporioides complex. Gene structure prediction identified 15,744 protein-coding genes and 837 noncoding RNAs. Species-specific genes were characterized using an ortholog analysis followed by a pathway enrichment analysis, which showed that genes specific to CgLc1 were enriched for the arginine biosynthetic process. Furthermore, genome synteny analysis revealed that most of the protein-coding genes fell into collinear blocks. However, two clusters of polyketide synthase genes were identified to be specific for CgLc1, suggesting that they might have an important role in virulence control. Transcriptional regulators coexpressed with polyketide synthase genes were detected through a Weighted Correlation Network Analysis. Taken together, this work provides new insight into the virulence- and pathogenesis-associated genes present in C. gloeosporioides and its possible lifestyle.

reveal candidate genes involved in nectary development and nectar secretion

BACKGROUND

Nectar is a major floral attractant and reward for insects that ensures pollination. Liriodendron, a genus of the Magnoliaceae family, includes only two relict species, L. chinense and L. tulipifera, which are considered "basal angiosperms" according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of nectaries, the mechanism of nectar secretion and the molecular mechanism of nectary development in Liriodendron remain poorly understood.

METHODS

In this study, we examined the nectary surface cells and change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select appropriate samples for subsequent research. Transcriptome sequencing was of the top and middle parts of immature nectaries and the middle part of mature and postsecretory nectaries in L. tulipifera was performed. We evaluated the expression profiles of 21 DEGs that are closely related to nectary development and nectar secretion for real-time quantitative PCR analysis.

RESULTS

L. tulipifera nectaries are starch-storing nectaries and are located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb of clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02-79.77% efficiency. In total, 26,955 DEGs were identified by performing six pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 21 candidate genes.

CONCLUSIONS

We evaluated the nectary development and secretion processes comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that nectaries play important roles in flavonoid synthesis and petal color presentation.

(Magnoliaceae): investigation of intra-species chloroplast variations

Liriodendron tulifipera L. belongs to Magnoliaceae which is one of the basal angiosperm families. To understand intra-species variations on chloroplast genome in Liriodendron genus, we presented complete chloroplast genome of L. tulifipera, which is 156,387 bp long and has four subregions: 85,606 bp of large single copy (LSC) and 18,778 bp of small single copy (SSC) regions are separated by 26,002 bp of inverted repeat (IR) regions including 129 genes (84 coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.0% and those in the LSC, SSC, and IR regions are 34.9%, 30.5%, and 42.8%, respectively. Twelve single nucleotide polymorphisms (SNPs) located in one region and one insertion and deletion are found between two L. tulifipera genomes. INDEL Phylogenetic trees show that two L. tulifipera chloroplasts are clustered together and are sister to Magnolia species.

Interspecies evolutionary divergence in Liriodendron, evidence from the nucleotide variations of LcDHN-like gene

Background

Liriodendron is a genus of Magnoliaceae, which consists of two relict species, Liriodendron chinense and L. tulipifera. Although the morphologies are highly similar, the two species exhibit different adaptive capacity. Dehydrins (DHNs) are abiotic stresses resistant proteins in planta, which are associated with adaptive evolution. To better understand the evolution divergence between L. chinense and L. tulipifera and how DHN genes are associated with adaptation evolution, we firstly investigated the DNA polymorphisms of the LcDHN-like gene in 21 L. chinense and 6 L. tulipifera populations.

Results

A 707 bp LcDHN-like gene was cloned, which included a 477 bp open reading frame (ORF) and coding 158 amino acids. 311 LcDHN-like gDNA sequences were obtained from 70 L. chinense and 35 L. tulipifera individuals. The AMOVA and phylogenetic relationship analysis showed significant differences between the two species. A higher genetic diversity was observed in L. tulipifera compared to L. chinense, in consistent with the higher adaptive capacity of L. tulipifera. Our data also suggested that the LcDHN-like genes’ polymorphisms were under neutral mutation and purifying selection model in the L. chinense and L. tulipifera populations, respectively. The distinct expanding range and rate between the two species, haplotypes shared only in L.chinense’s nearby populations, and wide dispersals in L. tulipifera could contribute to the obscure east-west separation in L. chinense and entirely unordered phylogeny in L. tulipifera. The completely separated nonsynonymous substitution at position 875 and the higher range scope of aliphatic index in L. tulipifera populations may be related with its higher adaptive capacity. Taken together, our study suggests LcDHN-like gene is a potential mark gene responsible for adaptive evolution divergence in Liriodendron.

Conclusions

Significant differences and completely distinct haplogroups between L. chinense and L. tulipifera showed that the two species have evolved into different directions. The more widely distribution, earlier haplogroups divergence events, and richer SNPs variations in L. tulipifera could imply its stronger adaptation in this species. And potential effect of the allelic variations in LcDHN-like gene may reflect the difference of water stress and chill tolerance between L. chinense and L. tulipifera, which could provide some information for further adaption evolution studies of Liriodendron.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1318-7) contains supplementary material, which is available to authorized users.

Phenylethanoid glycosides in tepals of Magnolia salicifolia and their occurrence in flowers of Magnoliaceae

Phenylethanoid glycosides were among the major UV-absorbing components in 80% aq. CH3OH extracts of the tepals of Magnolia salicifolia (Siebold & Zucc.) Maxim. (Magnoliaceae; Magnolia subgenus Yulania). Structural characterisation of isolated compounds by spectroscopic and chemical methods revealed three previously unrecorded examples, yulanoside A, yulanoside B and 2'-rhamnoechinacoside, and the known compounds echinacoside and crassifolioside; chromatographic methods also identified verbascoside in the tepal extract. Yulanoside A is the first reported example of a phenylethanoid pentaglycoside, namely hydroxytyrosol 1-O-{β-D-glucopyranosyl-(1→4)-β-D-glucopyranosyl-(1→6)-[3,4-dihydroxycinnamoyl-(→4)][α-L-rhamnopyranosyl-(1→3)][α-L-rhamnopyranosyl-(1→2)]-β-D-glucopyranoside}. A survey of Magnolia sensu lato and Liriodendron (the two genera of Magnoliaceae) suggested that yulanoside A and its deglucosyl derivative (yulanoside B) were a feature of the tepal chemistry of Magnolia subgenus Yulania (except Magnolia acuminata, the sole member of section Tulipastrum, which did not accumulate phenylethanoid glycosides). The two species of Liriodendron and examined examples of Magnolia subgenus Magnolia sections Magnolia and Rytidospermum (subsection Oyama) also accumulated phenylethanoid glycosides in their tepals and in these species, and in subgenus Yulania, the major compounds were one or more of echinacoside, 2'-rhamnoechinacoside, crassifolioside and verbascoside. Levels of phenylethanoid glycosides were found to be much lower in species studied from Magnolia sections Gwillimia, Macrophylla and Rytidospermum (subsection Rytidospermum), although yulanoside A was detectable in M. macrophylla and this may have some bearing on the placement of section Macrophylla, which is currently uncertain. In the isolates of yulanoside B and echinacoside, minor phenylethanoid glycosides were determined to be analogues of these compounds with β-D-xylose at C-3' of the primary glucose rather than α-L-rhamnose.

Fruit structure in Magnoliaceae s.l. and Archaeanthus and their relationships

PREMISE OF THE STUDY

The family Magnoliaceae s.l. is a basal angiosperm family with two subfamilies-Magnolioideae and Liriodendroideae, which differ by the types and structure of their fruits and seeds. The late Albian genus Archaeanthus shares many features of its reproductive organs with Magnoliaceae s.l., but its pericarp anatomy was never studied in detail. A broad-scale carpological investigation of Archaeanthus and Magnoliaceae s.l. was undertaken to reveal the nature of the similarities in fruit structure and to reconstruct Archaeanthus pericarp anatomy. These data are important to determine the early stages of fruit morphogenesis and thus to clarify relationships of Archaeanthus to the taxa of Magnoliaceae s.l.

METHODS

The pericarp anatomy was studied with light microscopy, SEM, and polarizing microscopy.

KEY RESULTS

The dehiscent, polyspermous follicles shed from the receptacle of Archaeanthus share similarities with dehiscent follicles of Magnoliaceae s.s. and shedding nutlets of Liriodendron. The seeds of Archaeanthus are dorsiventrally flattened, ovoid, and encircled with a single circular wing. The pericarps of all the taxa studied are differentiated into exocarp (epidermis), multilayered mesocarp, and endocarp (fiber-like sclereids). The mesocarp consists of parenchyma with scattered secretory cells and sclereid clusters (Magnoliaceae s.s., Archaeanthus) or composed by sclerenchyma (Liriodendron).

CONCLUSIONS

The specializations of dehiscent multifollicles of unknown Cretaceous ancestors for different modes of seed and fruitlet dispersal formed the basis for the differentiation of two evolutionary lines with their divergence occurring more than 100 million years ago: Magnoliaceae s.s. and the Archaeanthus-Liriodendroidea-Liriodendron line (Liriodendraceae s.l.) within the order Magnoliales.