Data supporting multiple independent losses of nitrogen-fixing root nodule symbiosis.

Dataset type: Genomic
Data released on April 16, 2018

The complex symbiosis of plants root nodules with nitrogen-fixing bacteria enables their survival on nitrogen-poor soils and has a major impact on global nitrogen cycles and food production. It is restricted to a small subset of plant species belonging to four closely related orders of flowering plants, the Fabales, Fagales, Cucurbitales and Rosales (FaFaCuRo) clade. Of the 30 families within this clade, only 10 contain nodulating species and these are phylogenetically scattered throughout the clade. The evolutionary and molecular basis for this scattered distribution has to date remained unclear.
To facilitate comparative phylogenetic analysis covering the FaFaCuRo clade, the genomes of eight nodulating and three closely related non-nodulating plant species have been sequenced and the data is presented here for download.
Whole genome sequencing for the ten newly sequenced genomes was performed using Illumina sequencing technology (HISEQ2000 and HISEQ4000 sequencing technology) at BGI-Shenzhen. Hierarchical library construction strategy was applied utilising multiple pair-end libraries with insert sizes of 170, 250, 350, 500, and 800bp and mate-pair libraries with insert sizes of 2, 5, 10, and 20kb. Most of the paired-end and mate-pair libraries were prepared from large genomic fragments, typically 20-40kb in size or even larger. For more detailed information on the assembly pipeline see the published paper.
Making up this dataset, the legume species selected for this purpose comprise of two non-nodulator species, Nissolia schottii and Cercis canadensis, and two nodulators, Chamaecrista fasciculata and the touch-sensitive Mimosa pudica. Six actinorhizal model species representing the Cucurbitales (Datisca glomerata), Fagales (Alnus glutinosa and Casuarina glauca) and Rosales (Discaria trinervis, Dryas drummondii and Purshia tridentata) were selected alongside one closely related non-nodulator (Begonia fuchsioides, Cucurbitales).
The 10 newly sequenced genomes was combined with 27 already sequenced angiosperm genomes and a phylogenetic analysis on 22 candidate genes was conducted. Here we provide not only the assembly and annotation files of the newly sequenced genomes but also the data files produced in our analysis of them. It is hoped these data will aid in the battle for global food security by elucidating the means to transfer the symbiotic capacity to major crop plants that are currently depending on the application of chemical nitrogen fertilizer.

Additional details

Read the peer-reviewed publication(s):

Griesmann, M., Chang, Y., Liu, X., Song, Y., Haberer, G., Crook, M. B., … Cheng, S. (2018). Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science, eaat1743. doi:10.1126/science.aat1743

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Accessions (data generated as part of this study):

BioProject: PRJNA374770

File NameSample IDData TypeFile FormatSizeRelease Date 
AlignmentsFASTA123.79 KB2018-11-03
Phylogenetic treeUNKNOWN4.21 KB2018-11-03
AlignmentsFASTA26.83 KB2018-11-03
AlignmentsFASTA18.45 KB2018-11-03
Phylogenetic treeUNKNOWN1.98 KB2018-11-03
AlignmentsFASTA16.36 KB2018-11-03
AlignmentsFASTA29.94 KB2018-11-03
Phylogenetic treeUNKNOWN2.09 KB2018-11-03
AlignmentsFASTA7.48 KB2018-11-03
AlignmentsFASTA24.21 KB2018-11-03
Displaying 1-10 of 66 File(s).
Date Action
May 30, 2018 Dataset publish
July 4, 2018 Manuscript Link added : 10.1126/science.aat1743