The Gastrodia Elata Genome Provides Insights into Plant Adaptation to Heterotrophy

Overview

Journal Nat Commun

Specialty Biology

Date 2018 Apr 26

PMID 29691383

Citations 116

Authors

Yuan Yuan

Xiaohua Jin

Juan Liu

Xing Zhao

Junhui Zhou

Xin Wang

Deyi Wang

Changjiangsheng Lai

Wei Xu

JingWen Huang

Liangping Zha

Dahui Liu

Xiao Ma

Li Wang

Menyan Zhou

Zhi Jiang

Hubiao Meng

Huasheng Peng

Yuting Liang

Ruiqiang Li

Chao Jiang

Yuyang Zhao

Tiegui Nan

Yan Jin

Zhilai Zhan

Jian Yang

Wenkai Jiang

Luqi Huang

Affiliations

Soon will be listed here.

Abstract

We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.

Citing Articles

The multi-chromosomal structure of mitogenomes provided new insights into the accurate authentication of medicinal Dendrobium species.

Wang M, Yang J, Hou Z, Li C, Niu Z, Zhang B BMC Plant Biol. 2025; 25(1):202.

PMID: 39955482 PMC: 11829489. DOI: 10.1186/s12870-025-06240-3.

Features and evolutionary adaptations of the mitochondrial genome of W. W. Sm.

Chen R, Rao R, Wang C, Zhu D, Yuan F, Yue L Front Plant Sci. 2025; 15:1509669.

PMID: 39902196 PMC: 11788303. DOI: 10.3389/fpls.2024.1509669.

Genome-wide identification of carboxyesterase family members reveals the function of GeCXE9 in the catabolism of parishin A in Gastrodia elata.

Yan Y, Jiang M, Wang X Plant Cell Rep. 2025; 44(2):45.

PMID: 39885015 DOI: 10.1007/s00299-025-03426-9.

Mitochondrial Genome Characteristics Reveal Evolution of and Phylogenetic Relationships.

Liu X, Luo H, Liu Z, Yang B Int J Mol Sci. 2025; 26(2).

PMID: 39859280 PMC: 11765986. DOI: 10.3390/ijms26020562.

Insights into the Genomic Background of Nine Common Chinese Medicinal Plants by Flow Cytometry and Genome Survey.

An C, Li D, Lu L, Liu C, Xu X, Xie S Plants (Basel). 2025; 13(24.

PMID: 39771235 PMC: 11679336. DOI: 10.3390/plants13243536.

References

Stamatakis A . RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006; 22(21):2688-90. DOI: 10.1093/bioinformatics/btl446. View

Tsai C, Wu K, Chiang T, Huang C, Chou C, Li S . Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes. BMC Genomics. 2016; 17:212. PMC: 4784368. DOI: 10.1186/s12864-016-2508-6. View

Leister D . Chloroplast research in the genomic age. Trends Genet. 2002; 19(1):47-56. DOI: 10.1016/s0168-9525(02)00003-3. View

Punta M, Coggill P, Eberhardt R, Mistry J, Tate J, Boursnell C . The Pfam protein families database. Nucleic Acids Res. 2011; 40(Database issue):D290-301. PMC: 3245129. DOI: 10.1093/nar/gkr1065. View

Kanehisa M, Goto S . KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999; 28(1):27-30. PMC: 102409. DOI: 10.1093/nar/28.1.27. View

Llorens C, Futami R, Covelli L, Dominguez-Escriba L, Viu J, Tamarit D . The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res. 2010; 39(Database issue):D70-4. PMC: 3013669. DOI: 10.1093/nar/gkq1061. View

Xu Z, Wang H . LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007; 35(Web Server issue):W265-8. PMC: 1933203. DOI: 10.1093/nar/gkm286. View

Heckman D, Geiser D, Eidell B, STAUFFER R, Kardos N, Hedges S . Molecular evidence for the early colonization of land by fungi and plants. Science. 2001; 293(5532):1129-33. DOI: 10.1126/science.1061457. View

Aggarwal G, Ramaswamy R . Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER. J Biosci. 2002; 27(1 Suppl 1):7-14. DOI: 10.1007/BF02703679. View

10.

Garcia K, Delaux P, Cope K, Ane J . Molecular signals required for the establishment and maintenance of ectomycorrhizal symbioses. New Phytol. 2015; 208(1):79-87. DOI: 10.1111/nph.13423. View

11.

Cox K, Layne D, Scorza R, Schnabel G . Gastrodia anti-fungal protein from the orchid Gastrodia elata confers disease resistance to root pathogens in transgenic tobacco. Planta. 2006; 224(6):1373-83. DOI: 10.1007/s00425-006-0322-0. View

12.

Simao F, Waterhouse R, Ioannidis P, Kriventseva E, Zdobnov E . BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210-2. DOI: 10.1093/bioinformatics/btv351. View

13.

Jurka J, Kapitonov V, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J . Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005; 110(1-4):462-7. DOI: 10.1159/000084979. View

14.

Li L, Stoeckert Jr C, Roos D . OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13(9):2178-89. PMC: 403725. DOI: 10.1101/gr.1224503. View

15.

Trapnell C, Pachter L, Salzberg S . TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009; 25(9):1105-11. PMC: 2672628. DOI: 10.1093/bioinformatics/btp120. View

16.

Kretzschmar T, Kohlen W, Sasse J, Borghi L, Schlegel M, Bachelier J . A petunia ABC protein controls strigolactone-dependent symbiotic signalling and branching. Nature. 2012; 483(7389):341-4. DOI: 10.1038/nature10873. View

17.

Steinbiss S, Willhoeft U, Gremme G, Kurtz S . Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Res. 2009; 37(21):7002-13. PMC: 2790888. DOI: 10.1093/nar/gkp759. View

18.

Zhang G, Xu Q, Bian C, Tsai W, Yeh C, Liu K . The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. Sci Rep. 2016; 6:19029. PMC: 4709516. DOI: 10.1038/srep19029. View

19.

Bai Y, Yin H, Bi H, Zhuang Y, Liu T, Ma Y . De novo biosynthesis of Gastrodin in Escherichia coli. Metab Eng. 2016; 35:138-147. DOI: 10.1016/j.ymben.2016.01.002. View

20.

Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View