A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)

Abstract

Cymbidium goeringii, commonly known as the spring orchid, has long been favoured for horticultural purposes in Asian countries. It is a popular orchid with much demand for improvement and development for its valuable varieties. Until now, its reference genome has not been published despite its popularity and conservation efforts. Here, we report the de novo assembly of the C. goeringii genome, which is the largest among the orchids published to date, using a strategy that combines short‐ and long‐read sequencing and chromosome conformation capture (Hi‐C) information. The total length of all scaffolds is 3.99 Gb, with an N50 scaffold size of 178.2 Mb. A total of 29,556 protein‐coding genes were annotated and 3.55 Gb (88.87% of genome) repetitive sequences were identified. We constructed pseudomolecular chromosomes using Hi‐C, incorporating 89.4% of the scaffolds in 20 chromosomes. We identified 220 expanded and 106 contracted genes families in C. goeringii after divergence from its close relative. We also identified new gene families, resistance gene analogues and changes within the MADS‐box genes, which control a diverse set of developmental processes during orchid evolution. Our high quality chromosomal‐level assembly of C. goeringii can provide a platform for elucidating the genomic evolution of orchids, mining functional genes for agronomic traits and for developing molecular markers for accelerated breeding as well as accelerating conservation efforts.

Haplotype‐resolved genome assembly of Bletilla striata (Thunb.) Reichb.f. to elucidate medicinal value

“…The divergence time between the most closely related orchid plants B. striata and G. elata was estimated to be 55.1 Mya. Bletilla striata has experienced two WGD events, and the recent WGD was similar to that found in other orchid genomes (Ai et al., 2021; Chung et al., 2021; Niu et al., 2021; Yang, Gao, et al., 2021b; Zhang et al., 2017; Zhang et al., 2021), suggesting that this WGD was shared by all extant orchid genomes. There is sufficient evidence to confirm that WGD events have been frequent in the evolutionary history of flowering plant genomes, and they usually shape the evolutionary trajectory of genes and genomes, especially the genes related to plant‐specialized phenotypes and/or agronomic traits(Clark & Donoghue, 2017; Guo et al., 2013; Soltis & Soltis, 2016).…”

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

“…A chromosomalscale genome and chromosome linkage groups of P. aphrodite were first created, which contributed to the variation in labellum and pollinium morphology and structures (Chao et al, 2018). A chromosome-scale genome assembly of C. goeringii suggested several new gene families, resistance-related homologs and variations within the MADS-box genes may regulate a wide set of developmental processes during adaptive evolution (Chung et al, 2022). A haplotype-resolved genome of Bletilla striata reveals its evolutionary relationship with other orchids, which have experienced an ancient WGD event shared with monocots and a recent WGD event within all orchids.…”