Improved de novo Assembly of the Achlorophyllous Orchid Gastrodia elata

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

doi:10.3389/fgene.2020.580568

Improved de novo Assembly of the Achlorophyllous Orchid Gastrodia elata

Front Genet. 2020 Nov 19:11:580568. doi: 10.3389/fgene.2020.580568. eCollection 2020.

Authors

Shanshan Chen^{1

2}, Xiao Wang^{3

4}, Yangzi Wang⁵, Guanghui Zhang⁶, Wanling Song⁵, Xiao Dong⁵, Michael L Arnold⁷, Wen Wang^{3

8

9}, Jianhua Miao¹⁰, Wei Chen^{11

12

13}, Yang Dong^{5

10

11

13}

Affiliations

¹ School of Life Sciences, Zhengzhou University, Zhengzhou, China.
² BGI College, Zhengzhou University, Zhengzhou, China.
³ State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
⁴ Jiaxing Synbiolab Biotechnology Co., Ltd., Jiaxing, China.
⁵ College of Biological Big Data, Yunnan Agricultural University, Kunming, China.
⁶ The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China.
⁷ Department of Genetics, University of Georgia, Athens, GA, United States.
⁸ Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.
⁹ Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
¹⁰ Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
¹¹ State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.
¹² College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.
¹³ Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China.

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.

Keywords: Gastrodia elata; achlorophyllous; genome; non-photosynthetic; relaxed selection.