| Analysis Name | Poa annua FRR_PoAnn_1.0 Assembly & Annotation |
| Sequencing technology | PacBio RSII |
| Assembly method | hifiasm v. 0.14-r312 |
| Release Date | 2022-12-16 |
Robbins MD, Bushman BS, Huff DR, Benson CW, Warnke SE, Maughan CA, Jellen EN, Johnson PG, Maughan PJ. Chromosome-Scale Genome Assembly and Annotation of Allotetraploid Annual Bluegrass (Poa annua L.). Genome Biol Evol. 2023 Jan 4;15(1):evac180. doi: 10.1093/gbe/evac180.
AbstractPoa annua L. is a globally distributed grass with economic and horticultural significance as a weed and as a turfgrass. This dual significance, and its phenotypic plasticity and ecological adaptation, have made P. annua an intriguing plant for genetic and evolutionary studies. Because of the lack of genomic resources and its allotetraploid (2n = 4x = 28) nature, a reference genome sequence would be a valuable asset to better understand the significance and polyploid origin of P. annua. Here we report a genome assembly with scaffolds representing the 14 haploid chromosomes that are 1.78 Gb in length with an N50 of 112 Mb and 96.7% of BUSCO orthologs. Seventy percent of the genome was identified as repetitive elements, 91.0% of which were Copia- or Gypsy-like long-terminal repeats. The genome was annotated with 76,420 genes spanning 13.3% of the 14 chromosomes. The two subgenomes originating from Poa infirma (Knuth) and Poa supina (Schrad) were sufficiently divergent to be distinguishable but syntenic in sequence and annotation with repetitive elements contributing to the expansion of the P. infirma subgenome.
Assembly statistics
| Genome size | 1.8 Gb |
| Total ungapped length | 1.8 Gb |
| Number of chromosomes | 14 |
| Number of scaffolds | 26 |
| Scaffold N50 | 112.3 Mb |
| Scaffold L50 | 5 |
| Number of contigs | 188 |
| Contig N50 | 65.4 Mb |
| Contig L50 | 8 |
| GC percent | 45.5 |
| Genome coverage | 49.0x |
| Assembly level | Chromosome |
The Poa annua FRR_PoAnn_1.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | Poa_annua.faa.gz |
The Poa annua FRR_PoAnn_1.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Poa_annua.gff.gz |
| CDS sequences (FASTA file) | Pa_cds.fa.gz |
| Protein sequences (FASTA file) | Pa_pep.fa.gz |
Functional annotation for the Poa annua FRR_PoAnn_1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Poa_annua.Pfam.tsv.gz |
Summary
| Query | Chromosome | Size(bp) | Coordinates | tBLASTn Hit | tBLASTn %ID | Domain |
| DUF247I-S | Pa6A | 102273047 | 9845836-9847431 | LpSDUF247-I_chromosome1 | 79 | DUF247 |
| DUF247I-S | Pa6B | 73030011 | 10540492-10542084 | LpSDUF247-I_chromosome1 | 90 | DUF247 |
| DUF247II-S | Pa6A | 102273047 | 9836419-9838074 | LpSDUF247-II_chromosome1 | 83 | DUF247 |
| DUF247II-S | Pa6B | 73030011 | 10417284-10418936 | LpSDUF247-II_chromosome1 | 90 | DUF247 |
| HPS10-S | Pa6A | 102273047 | 9843279-9843390,9843468-9843604 | LpsS_contig11029 | 63 | - |
| HPS10-S | Pa6B | 73030011 | 10538859-10538976,10539050-10539183 | LpsS_contig11029 | 57 | - |
| DUF247I-ZΨ | Pa1A | 320692588 | 313508507-313509592 | LrDUF247I-Z | 59 | DUF247 |
| DUF247I-Z | Pa1B | 98219837 | 91174745-91176355 | LpZDUF247-I_chromosome2 | 58 | DUF247 |
| DUF247I-Z | Pa1B | 98219837 | 91169584-91171194 | LpZDUF247-I_chromosome2 | 58 | DUF247 |
| DUF247I-Z | Pa1B | 98219837 | 91164422-91166032 | LpZDUF247-I_chromosome2 | 58 | DUF247 |
| DUF247II-ZΨ | Pa1A | 320692588 | 313526242-313526832 | LrDUF247II-Z | 72 | DUF247 |
| DUF247II-Z | Pa1B | 98219837 | 91184737-91186371 | Amyosuroides | 46 | DUF247 |
| HPS10-Z | Pa1A | 320692588 | 313510660-313510843,313510933-313511024 | LpsZ_contig55097 | 53 | - |
| HPS10-Z | Pa1B | 98219837 | 91184013-91184097,91184266-91184366 | LpsZ_contig4538 | 42 | - |
Nucleotide
Protein