Data access for the 1,000 Plants (1KP) project

Abstract

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.

Functional Characterization of UDP-apiose Synthases from Bryophytes and Green Algae Provides Insight into the Appearance of Apiose-containing Glycans during Plant Evolution

“…amino acid sequence identity to Arabidopsis AXS1/UAS1 were identified in monocots, mosses, liverworts, hornworts, and streptophyte green algae (Table 1) using publically available data from The 1,000 Plants (1KP) Project (22) and the Phytozome genomics portal. No UAS-like homologs were detected in the available transcriptomes of chlorophyte green algae.…”

“…The recent availability of the sequenced genome of the moss Physcomitrella patens (21) and publically available transcriptomic data for other avascular land plants and for green algae produced by the 1,000 Plants (1KP) Project (22) allowed us to re-examine this hypothesis.…”

Azolla, a little fern with massive green potential

“…Tma12 has a high similarity to chitinbinding proteins (Pfam PF03067), but its evolutionary origin is unknown. Here, we found a Tma12 homologue to be present in the Salvinia genome (henceforth ScTma12), as well as in a few 1,000 Plants (1KP) 32 fern transcriptomes, but not in Azolla or any other publicly available plant genomes. Phylogenetic analyses position the fern Tma12 sequences together with bacterial sequences, and are most closely related to the chitin-binding proteins from Chloroflexi (Fig.…”

“…This pathway is highly conserved in all land plants 39 , except for those that have lost the AM symbiosis 40,41 , such as A. thaliana and three aquatic angiosperms 40,41 . We investigated whether the CSP might have been co-opted during the evolution of the Azolla-Nostoc symbiosis by searching for six essential CSP genes in the Azolla and Salvinia genomes, as well as in transcriptomic data from other ferns in the 1KP data set 32 (Supplementary Table 11). Although DMI2 (also known as SYMRK), DMI3 (also known as CCaMK), IPD3 (also known as CYCLOPS) and VAPYRIN were found in other ferns, the Azolla and Salvinia genomes completely lacked orthologues (Fig.…”

“…We used BLASTp 73 to search for Tma12 (Genbank accession: JQ438776) homologues in Phytozome 95 , 1KP transcriptomes 32 and the NCBI Genbank non-redundant protein database. Although Tma12 homologues are present in fern transcriptomes and in the S. cucullata genome, no significant hit was found in any other plant genomes or transcriptomes.…”