Improved de novo Assembly of the Achlorophyllous Orchid Gastrodia elata.

Shanshan Chen,Wei Chen,Guanghui Zhang,Yang Dong,Wen Wang,Xiao Dong,Wanling Song,Yangzi Wang,Xiao Wang,Michael L Arnold,Jianhua Miao

doi:10.3389/fgene.2020.580568

Abstract

Achlorophyllous plants are full mycoheterotrophic plants with no chlorophyll and they obtain their nutrients from soil fungi. Gastrodia elata is a perennial, achlorophyllous orchid that displays distinctive evolutionary strategy of adaptation to the non-photosynthetic lifestyle. Here in this study, the genome of G. elata was assembled to 1.12 Gb with a contig N50 size of 110 kb and a scaffold N50 size of 1.64 Mb so that it helped unveil the genetic basics of those adaptive changes. Based on the genomic data, key genes related to photosynthesis, leaf development, and plastid division pathways were found to be lost or under relaxed selection during the course of evolution. Thus, the genome sequence of G. elata provides a good resource for future investigations of the evolution of orchids and other achlorophyllous plants.

Highlights

In the autotroph-dominant plant world, the symbiotic relationship between plants and fungi plays an indispensable role in the maintenance of ecosystem (Read, 1991)
We presented a high quality de novo assembly of the G. elata nuclear genome, which had a higher coverage, contig N50 size, and Benchmarking Universal Single-Copy Ortholog (BUSCO) completeness than that of a previous report (Yuan et al, 2018)
In the G. elata genome, we identified 20 Gastrodia antifungal protein (GAFP) genes, 10 GAFP genes in A. shenzhenica, and 0 in A. thaliana, which indicates that GAFP has expanded in G. elata (Supplementary Table 16)

Summary

INTRODUCTION

In the autotroph-dominant plant world, the symbiotic relationship between plants and fungi plays an indispensable role in the maintenance of ecosystem (Read, 1991). Compared with the genomes of photosynthetic orchid species, such as Phalaenopsis equestris (Cai et al, 2015), Apostasia Shenzhenica (Zhang et al, 2017), and Dendrobium officinale (Yan et al, 2015), the new G. elata nuclear genome and plastome assemblies showed key gene loss and relaxed selection related to its non-functional photosystem and retarded leaf development. These data demonstrated that the improved G. elata genome provides more insights into the genomic and evolutionary mechanisms underlying the morphological and physiological adaptations associated with a non-photosynthetic lifestyle

MATERIALS AND METHODS

RESULTS

CONCLUSION

DATA AVAILABILITY STATEMENT