In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing

Abstract

High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies.

The spatiotemporal profile of Dendrobium huoshanense and functional identification of bHLH genes under exogenous MeJA using comparative transcriptomics and genomics

“…The bHLH-MYC_N domain contains JID and TAD, which are responsible for the binding of JAZ to MYC2 and the transcriptional activation of MYC-targeted genes, respectively. DhMYC2 contains GDG motifs, suggesting their ability to bind JAZ proteins ( Song et al., 2022b ). The presence of RA[K/L]QAQ motifs in DhMYC2 suggests that it is a canonical MYC2 gene.…”

“…In normal growth conditions, JA is at a low level; when subjected to external stress, the JA content of the seedlings rapidly increased, which activates JA-responsive genes to increase resistance to environmental stimuli ( Zhu et al., 2017 ). JA also induced the expression of key enzymes in the terpenoid biosynthesis pathway and raised terpene alkaloid content in a short period of time ( Song et al., 2022b ). The bHLH genes have been widely investigated in both model plants and medicinal plants.…”

In-depth analysis of large-scale screening of WRKY members based on genome-wide identification

“…In this study, DoWRKY26 shared a high level of homology with AtWRKY18, 40, and 60; hence, it was suggested that WRKY26 might be involved in the transcriptional regulation of secondary metabolite biosynthetic genes (Figure 8). Gene duplications are critical to the rapid expansion of the genome and the evolution of gene families (Song et al, 2022c). Polyploidy drives species adaption, genetic diversity, and genome evolution.…”

“…Gene duplications are critical to the rapid expansion of the genome and the evolution of gene families ( Song et al, 2022c ). Polyploidy drives species adaption, genetic diversity, and genome evolution.…”

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

“…Thus, orchids cannot survive without mycorrhizal fungi (Rasmussen & Rasmussen, 2014). In recent years, there has been a growing interest in the genomics of orchids and ORM fungi to unravel the genetic mechanisms underlying orchid‐fungal interactions and the specificity of these symbiotic relationships (Chen et al ., 2022; Song et al ., 2022). The genomes of several orchid species (Cai et al ., 2015; Zhang et al ., 2016, 2017; Yang et al ., 2021; Jiang et al ., 2022; Li et al ., 2022) have been sequenced.…”