Gossypium australe (G2) genome CRI assembly v1.1
About the assembly
The Gossypium australe PA1801(G2-lz) genome was sequenced and assembled with a combination of four technologies: Pacbio single-molecule real-time (SMRT) sequencing, paired-end sequencing, optical mapping (DLS) and Illumina short-read Hi-C. Assembly with these complementary data types proceeded in a stepwise fashion, producing progressively improved assemblies stored under
Cai, Y., Cai, X., Wang, Q., Wang, P., Zhang, Y., Cai, C., Xu, Y., Wang, K., Zhou, Z., Wang, C., Geng, S., Li, B., Dong, Q., Hou, Y., Wang, H., Ai, P., Liu, Z., Yi, F., Sun, M., An, G., Cheng, J., Zhang, Y., Shi, Q., Xie, Y., Shi, X., Chang, Y., Huang, F., Chen, Y., Hong, S., Mi, L., Sun, Q., Zhang, L., Zhou, B., Peng, R., Zhang, X. and Liu, F. (2019) Genome sequencing of the Australian wild diploid species Gossypium austral highlights disease resistance and delayed gland morphogenesis. Plant Biotechnol. J., https://doi.org/10.1111/pbi.13249
The chromosomes (pseudomolecules) and scaffolds for G. australe genome. These files belong to the CRI-G2 Assembly v1.1
The predicted gene model, their alignments and proteins for G. australe genome. These files belong to the CRI-G2 Assembly 1.1
All annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar. Each data type page will provide a description of the available files and links do download. Alternatively, you can use the FTP repository for bulk download.
Marker alignments were performed by the CottonGen Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map marker sequences from CottonGen to the Gossypium australe genome assembly. Markers required 90% identity over 97% of their length. For SSRs & RFLPs, gap size was restricted to 1000bp or less with less than 2 gaps. For dbSNPs and Indels gap size was restricted to 2bp with less than 2 gaps. The available files are in GFF3 format. Markers available in CottonGen are linked to JBrowse.
Transcript alignments were performed by the CottonGen Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the G. australe genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.
Homology of the Gossypium australe CRI Genome v1.1 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2018-05) and 1e-6 for the Arabidoposis proteins (TAIR10), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format.
Functional annotation files for the Gossypium australe CRI Genome v1.1 are available for download below. The Gossypium australe CRI Genome proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).