The Analysis of Genes and Phytohormone Metabolic Pathways Associated with Leaf Shape Development in Liriodendron chinense via De Novo Transcriptome Sequencing

Abstract

The leaf, a photosynthetic organ that plays an indispensable role in plant development and growth, has a certain ability to adapt to the environment and exhibits tremendous diversity among angiosperms. Liriodendron chinense, an ancestral angiosperm species, is very popular in landscaping. The leaf of this species has two lobes and resembles a Qing Dynasty Chinese robe; thus, leaf shape is the most valuable ornamental trait of the tree. In this work, to determine the candidate genes associated with leaf development in L. chinense, scanning electron microscopy (SEM) was employed to distinguish the developmental stages of tender leaves. Four stages were clearly separated, and transcriptome sequencing was performed for two special leaf stages. Altogether, there were 48.23 G clean reads in the libraries of the two leaf developmental stages, and 48,107 assembled unigenes were annotated with five databases. Among four libraries, 3118 differentially expressed genes (DEGs) were enriched in expression profiles. We selected ten DEGs associated with leaf development and validated their expression patterns via quantitative real-time PCR (qRT-PCR) assays. Most validation results were closely correlated with the RNA-sequencing data. Taken together, we examined the dynamic process of leaf development and indicated that several transcription factors and phytohormone metabolism genes may participate in leaf shape development. The transcriptome data analysis presented in this work aims to provide basic insights into the mechanisms mediating leaf development, and the results serve as a reference for the genetic breeding of ornamental traits in L. chinense.

Overexpression of a Novel LcKNOX Transcription Factor from Liriodendron chinense Induces Lobed Leaves in Arabidopsis thaliana

“…To identify the candidate gene sequences that encode KNOX proteins in L. chinense, their unigenes were selected from the DEGs (differentially expressed genes) in L. chinense leaves at different stages in a transcriptome database [22]. Then, the 3 and 5 RACE (rapid-amplification of cDNA ends) primers were designed according to the transcriptomic annotated KNOX1 and KNOX6 sequences, respectively.…”

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

“…L. chinense is distributed throughout southern China and northern Vietnam, and it plays increasingly important economic and ecological roles because of its high value for greening, furniture manufacturing and pharmaceutical manufacturing [1][2][3]. In addition, owing to its crucial phylogenetic position that enables the study of the evolution of extant owering plants, L. chinense has been the topic of an increasing amount of scienti c research, such as research on gene ow among natural populations of L. chinense [4], transcriptomic analyses of L. chinense petals and leaves [5], the study of genes associated with L. chinense leaf shape development [6], and the wholegenome sequencing of L. chinense (the complete sequence of which was completed in 2018) [7]. However, a reference transcriptome of L. chinense has not been reported.…”

“…Next-generation sequencing (NGS) technology has been widely applied to studies of metabolic pathways, differential gene expression, and regulatory mechanisms in model or non-model species, such as maize (Zea mays) [18], rice (Oryza sativa) [19], Cucumis sativus L. [20], Cinnamomum camphora [21], and L. chinense [6] because of their high throughput, high accuracy and low cost. However, NGS also has some weaknesses, such as the di culty of sequence assembly, the possibility of producing low-quality transcripts, and the inability to capture full-length transcripts effectively [22][23][24][25][26][27][28].…”

“…In pineapple (Ananas comosus), researchers detected 273 tissue-speci c genes, which provided a basis for the study of the genetic mechanisms that regulate fruit phenotypes [43]. Although studies of L. chinense tissues (leaves and petals) have been reported, tissue-speci c genes in L. chinense remain unknown, and this lack of knowledge impedes our understanding of tissue traits of this species [5,6].…”

“…Researchers have studied the transcriptome of L. chinense but have focused on only one or two tissues [5,6]; a high-quality reference transcriptome of L. chinense is still needed. More importantly, research on MIKC-type MADS-box genes in L. chinense has not been reported.…”