Improved de novo Assembly of the Achlorophyllous Orchid Gastrodia elata

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

doi:10.3389/fgene.2020.580568

Frontiers in Genetics (Nov 2020)

Improved de novo Assembly of the Achlorophyllous Orchid Gastrodia elata

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

Affiliations

Shanshan Chen: School of Life Sciences, Zhengzhou University, Zhengzhou, China
Shanshan Chen: BGI College, Zhengzhou University, Zhengzhou, China
Xiao Wang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
Xiao Wang: Jiaxing Synbiolab Biotechnology Co., Ltd., Jiaxing, China
Yangzi Wang: College of Biological Big Data, Yunnan Agricultural University, Kunming, China
Guanghui Zhang: 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
Wanling Song: College of Biological Big Data, Yunnan Agricultural University, Kunming, China
Xiao Dong: College of Biological Big Data, Yunnan Agricultural University, Kunming, China
Michael L. Arnold: Department of Genetics, University of Georgia, Athens, GA, United States
Wen Wang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
Wen Wang: Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
Wen Wang: 0Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
Jianhua Miao: 1Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
Wei Chen: 2State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
Wei Chen: 3College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
Wei Chen: 4Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China
Yang Dong: College of Biological Big Data, Yunnan Agricultural University, Kunming, China
Yang Dong: 1Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
Yang Dong: 2State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
Yang Dong: 4Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China

DOI: https://doi.org/10.3389/fgene.2020.580568
Journal volume & issue: Vol. 11

Abstract

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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.

Published in Frontiers in Genetics

ISSN: 1664-8021 (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Science: Biology (General): Genetics
Website: http://journal.frontiersin.org/journal/genetics

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