Global Transcriptome Analyses Reveal Differentially Expressed Genes of Six Organs and Putative Genes Involved in (Iso)flavonoid Biosynthesis in Belamcanda chinensis

Abstract

Belamcanda chinensis (L.) DC., a perennial herb of the family Iridaceae, is rich in a variety of (iso)flavonoids with significant organ-specific distribution and has a swollen rhizome that is widely used in East Asia as a traditional medicine. In the present study, comprehensive transcriptomes of six organs (root, rhizome, aerial stem, leaf, flower, and young fruit) of B. chinensis were obtained by high-throughput RNA-sequencing and de novo assembly. A total of 423,661 unigenes (mean length = 618 bp, median length = 391 bp) were assembled and annotated in seven databases: Non-redundant protein sequences, Nucleotide sequences, Swiss-Prot, Protein family database, euKaryotic Ortholog Groups, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO). A total of 4995 transcription factors were identified, including 408 MYB, 182 bHLH, 277 AP2/ERF, and 228 WRKY genes. A total of 129 cytochrome P450 unigenes belonging to 10 divergent clans were identified and grouped into clades in a phylogenetic tree that showed their inferred evolutionary relationship. Differentially expressed unigenes among the six organs were subjected to GO and KEGG enrichment analysis to profile the functions of each organ. Unigenes associated with (iso)flavonoid biosynthesis were then profiled by expression level analysis. Additionally, the complete coding sequences of six predicted enzymes essential to the (iso)flavonoid pathway were obtained, based on the annotated unigenes. This work reveals clear differences in expression patterns of genes among the six organs and will provide a sound platform to understand the (iso)flavonoid pathways in B. chinensis.

Genome-wide analysis of the bHLH gene family in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube

“…Furthermore, the functions of many bHLH proteins in plants have been studied in detail. bHLHs play various roles in plant development [16–18], signal transduction [8], tolerance [19–21] and secondary metabolite production [22]. Identification of bHLHs at a genome-wide level is the first step toward further studies into their biological functions.…”

“…Both jujube and wild jujube trees have many agronomic advantages, such as early fruit production, long flowering season and high tolerance to various biotic and abiotic stresses. And the bHLH gene family has a variety of functions such as flower and fruit development and is necessary for the normal growth and development in many plants [8, 16–22]. Compared with other TFs, bHLHs are involved in more reaction pathways and acted as some co-regulators on gene expression together with many other proteins.…”

Quantitative trait loci‐based genomics‐assisted prediction for the degree of apple fruit cover color

“…In QTL H11.1, the candidate gene MdCYP71D11 , which encodes a member of the cytochrome P450 mono‐oxygenase family, was predicted to be associated with DFC. In plants, CYP71D9 (F6H), CYP73A , CYP85E , CYP81 , and CYP93 were reported to participate in the flavonoid pathway (Tao et al., 2017; Tian, Zhang, Zhu, Xie, & Qin, 2018). However, the validation of these candidate genes and deciphering the genetic variation network controlling the DFC appeal extensive future dedications.…”

Genome-Wide Characterization and Analysis of the bHLH Transcription Factor Family in Suaeda aralocaspica, an Annual Halophyte With Single-Cell C4 Anatomy

“…With the completion of genome sequencing for multiple species, numerous plant bHLH proteins have been characterized, including 162 proteins in Arabidopsis ( Toledo-Ortiz et al, 2003 ), 167 in rice ( Li et al, 2006 ), 208 in maize ( Zhang et al, 2018 ), 437 in cotton ( Lu et al, 2018 ), 571 in wheat ( Wei and Chen, 2018 ), and 602 in Brassica napus ( Ke et al, 2020 ). The functions of many plant bHLH proteins have been described in detail, indicating their involvement in regulating diverse physiological and biochemical processes, such as light signal transmission ( Buti et al, 2020 ), plant hormone signaling ( Seo et al, 2011 ), iron uptake ( Ogo et al, 2007 ), anthocyanin and flavonoid biosynthesis ( Xu et al, 2017 ; Tian et al, 2018 ), and stomatal, root, and petal growth ( Ohashi-Ito and Bergmann, 2006 ; Szecsi et al, 2006 ; Kanaoka et al, 2008 ). For example, the Arabidopsis bHLH proteins PIF3 and PIF4 can directly interact with phytochrome in the signaling network of photoreceptors to control the expression of light-regulated genes ( Toledo-Ortiz et al, 2003 ).…”