| Analysis Name | Eragrostis nindensis MSU_Enin_2.1 Assembly & Annotation |
| Sequencing technology | PacBio |
| Assembly method | CANU v. 1.8 |
| Release Date | 2020-04-17 |
Pardo J, Man Wai C, Chay H, Madden CF, Hilhorst HWM, Farrant JM, VanBuren R. Intertwined signatures of desiccation and drought tolerance in grasses. Proc Natl Acad Sci U S A. 2020 May 5;117(18):10079-10088. doi: 10.1073/pnas.2001928117.
AbstractDesiccation tolerance likely evolved independently several times in grasses, providing an ideal comparative system to identify genetic elements controlling this trait. Using comparative genomics, we identified genomic and expression changes distinguishing the desiccation-tolerant grass Eragrostis nindensis from its desiccation-sensitive crop relative Eragrostis tef. We expanded these analyses to include several cereals to identify broadly conserved and divergent patterns during water stress. We found that the distinction between drought and desiccation in grasses is subtle, where genes with essential roles in seed development are broadly expressed under water stress. Thus we propose that seeds and leaves share common sets of coregulated genes of likely ancient origin, with only a few genes uniquely expressed for desiccation tolerance.
Assembly statistics
| Genome size | 986.2 Mb |
| Total ungapped length | 986.2 Mb |
| Number of contigs | 4,366 |
| Contig N50 | 521 kb |
| Contig L50 | 423 |
| GC percent | 46 |
| Genome coverage | 63.0x |
| Assembly level | Contig |
The Eragrostis nindensis MSU_Enin_2.1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | Eragrostis_nindensis.faa.gz |
The Eragrostis nindensis MSU_Enin_2.1 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Eragrostis_nindensis.gff.gz |
| CDS sequences (FASTA file) | En_cds.fa.gz |
| Protein sequences (FASTA file) | En_pep.fa.gz |
Functional annotation for the Eragrostis nindensis MSU_Enin_2.1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Eragrostis_nindensis.Pfam.tsv.gz |
Summary
| Query | Contig | Size(bp) | Coordinates | tBLASTn Hit | tBLASTn %ID | Domain |
| DUF247I-S1 | Contig_28 | 2750635 | 1250331-1252016 | Cpurpureus | 69 | DUF247 |
| DUF247I-S2 | Contig_98 | 1356931 | 828766-830409 | Cpurpureus | 65 | DUF247 |
| DUF247I-S3 | Contig_688 | 366405 | 236179-237840 | Cpurpureus | 64 | DUF247 |
| DUF247I-S4Ψ | Contig_1600 | 148969 | 94729-95409 | Pvirgatum | 68 | DUF247 |
| DUF247II-S1 | Contig_28 | 2750635 | 1245974-1247605 | Pvirgatum | 61 | DUF247 |
| DUF247II-S2 | Contig_98 | 1356931 | 834907-836535 | Pvirgatum | 57 | DUF247 |
| DUF247II-S3Ψ | Contig_688 | 366405 | 242246-242827 | Pvirgatum | 68 | DUF247 |
| DUF247II-S4 | Contig_1600 | 148969 | 100700-102319 | Pvirgatum | 64 | DUF247 |
| HPS10-S1 | Contig_28 | 2750635 | 1553432-1553550,1553695-1553863 | Pvaginatum | 55 | - |
| HPS10-S2 | Contig_98 | 1356931 | 832801-832963,833050-833159 | Pvaginatum | 67 | - |
| HPS10-S3 | Contig_688 | 366405 | 239547-239709,239825-239931 | Pvaginatum | 61 | - |
| HPS10-S4 | Contig_1600 | 148969 | 98105-98267,98383-98489 | Pvaginatum | 61 | - |
| DUF247I-Z1 | Contig_116 | 1255800 | 638520-640085 | Pvaginatum | 61 | DUF247 |
| DUF247I-Z2 | Contig_418 | 527687 | 374324-375883 | Pvaginatum | 58 | DUF247 |
| DUF247I-Z3Ψ | Contig_499 | 472456 | 420558-421688 | Pvaginatum | 46 | DUF247 |
| DUF247I-Z4 | Contig_1512 | 162405 | 64047-65663 | Pvaginatum | 57 | DUF247 |
| DUF247II-Z1 | Contig_116 | 1255800 | 643122-644780 | Pvaginatum | 48 | DUF247 |
| DUF247II-Z2 | Contig_418 | 527687 | 377860-379527 | Pvaginatum | 47 | DUF247 |
| DUF247II-Z3Ψ | Contig_499 | 472456 | 424555-425979 | Pvaginatum | 65 | DUF247 |
| DUF247II-Z4 | Contig_1512 | 162405 | 60519-62189 | Pvaginatum | 48 | DUF247 |
| HPS10-Z1 | Contig_13 | 3680791 | 1226289-1226395,1226574-1226709 | Pvaginatum | 72 | - |
| HPS10-Z2 | Contig_116 | 1255800 | 636211-636346,636524-636627 | Pvaginatum | 38 | - |
| HPS10-Z3 | Contig_418 | 527687 | 372584-372719,373060-373166 | Pvaginatum | 36 | - |
| HPS10-Z4 | Contig_418 | 527687 | 376697-376847,376932-377041 | Pvaginatum | 51 | - |
| HPS10-Z5 | Contig_499 | 472456 | 418293-418428,418604-418713 | Pvaginatum | 72 | - |
| HPS10-Z6 | Contig_1512 | 162405 | 44826-45000,45058-45164 | Pvaginatum | 70 | - |
Nucleotide
Protein