The Medicago truncatula DMI2, DMI3, IPD3, CASTER/POLLUX and VAPYRIN sequences were used as queries, as in a previous study39 (link), to search against the genomes and transcriptomes from species listed in Supplementary Table 11 using tBLASTn73 (link). For liverworts and ferns from the 1KP data set32 (link), non-annotated transcriptomes were used as targets, with the longest open reading frame of each contig extracted and translated. For A.filiculoides and S.cucullata, both the annotated gene models and the unannotated scaffolds were used. All hits that matched already annotated gene models were discarded prior to subsequent analyses. No homologues were identified in the two fern genomes for IPD3 and VAPYRIN. Protein sequences for DMI2/SYMRK, DMI3/CCaMK and CASTOR/POLLUX were aligned using MAFFT89 (link). The best substitution model for each alignment (JTT for all alignments) was determined using MEGA6 (ref.124 (link)). Phylogenetic trees were generated using RAxML100 (link) on the CIPRES platform125 , and node support was assessed with 100 rapid bootstrap pseudoreplicates.
Li F.W., Brouwer P., Carretero-Paulet L., Cheng S., de Vries J., Delaux P.M., Eily A., Koppers N., Kuo L.Y., Li Z., Simenc M., Small I., Wafula E., Angarita S., Barker M.S., Bräutigam A., dePamphilis C., Gould S., Hosmani P.S., Huang Y.M., Huettel B., Kato Y., Liu X., Maere S., McDowell R., Mueller L.A., Nierop K.G., Rensing S.A., Robison T., Rothfels C.J., Sigel E.M., Song Y., Timilsena P.R., Van de Peer Y., Wang H., Wilhelmsson P.K., Wolf P.G., Xu X., Der J.P., Schluepmann H., Wong G.K, & Pryer K.M. (2018). Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants, 4(7), 460-472.
Publication 2018
Castor Fern Genomes LiverwortsMedicago truncatula Protein sequences Transcriptomes
Corresponding Organization : Ithaca College
Other organizations :
Utrecht University, Ghent University, Dalhousie University, Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Université Toulouse III - Paul Sabatier, Centre National de la Recherche Scientifique, Duke University, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, University of Arizona, California State University, Fullerton, ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Pennsylvania State University, Bielefeld University, Taiwan Forestry Research Institute, Max Planck Institute for Plant Breeding Research, The University of Tokyo, VIB-UGent Center for Plant Systems Biology, Philipps University of Marburg, Utah State University, University of California, Berkeley, University of Louisiana at Lafayette, University of Pretoria, University of Alberta
The Medicago truncatula DMI2, DMI3, IPD3, CASTER/POLLUX and VAPYRIN sequences were used as queries
dependent variables
No homologues were identified in the two fern genomes for IPD3 and VAPYRIN
control variables
A previous study39 (link) was used as a reference point for the species and sequences examined
Annotations
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