Panicum hallii HAL2 Assembly and Gene Annotation

About Panicum hallii HAL2

Panicum hallii, commonly known as Hall's panicgrass (2n = 2x = 19), is a perennial grass in the Panicum genus which is native to the south/southwestern regions of the United States of America and into southern Mexico. It is a genetic model for C4 photosynthesis perennial grasses, which are drought-tolerant and yield high biomass. This genome corresponds to assembly PhalliiHAL_v2.1 of ecotype HAL2 of Panicum hallii var. Hallii.

Assembly

Two genotypes of Panicum hallii were sequenced using a whole genome shotgun strategy at the DOE Joint Genome Institute (USA) and the HudsonAlpha Institute for Biotechnology (USA). Sequencing effort for HAL2 included one Illumina 800 bp insert 2 × 250 fragment library (150 × ) and a total of 89.5x of PACBIO reads (average subread length 11.8 kb). FIL2 sequencing was similar, with one Illiumina 500 bp insert 2 × 150 fragment library (100 × ) and a total of 95.87x of PACBIO reads (average subread length 9.6 kb). Assembly was performed with MECAT and polished using QUIVER. A 325,613-marker genetic map from shallow resequencing of a RIL population was used to identify and correct mis-joins in the assemblies.

Annotation

PERTRAN and PASA were used to produce 92,211 (HAL2) and 111,325 (FIL2) transcript assemblies from ~1100 M (HAL2) and ~1200 M (FIL2) 2 × 150 paired-end Illumina RNA-seq reads. Loci were determined by transcript assembly alignments and/or EXONERATE alignments of proteins from Arabidopsis thaliana, soybean, Kitaake rice, sorghum, foxtail millet, Brachypodium distachyon, grape and Swiss-Prot proteomes. Gene models were predicted by a combination of methods. The best-scoring predictions for each locus were selected and penalized if overlapped with repeats. High-confidence transcripts were called. Gene models with >30% transposable element Pfam domains were culled, as well as gene models with a short single exon, without protein domains or with weak expression.

References

  1. The genomic landscape of molecular responses to natural drought stress in Panicum hallii.
    JT Lovell, J Jenkins, DB Lowry, S Mamidi, A Sreedasyam, X Weng, K Barry, J Bonnette, B Campitelli, C Daum et al. 2018. Nature Communications. 9, Article number: 5213

Picture credit: Copyright Bob Harms

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyPhalliiHAL_v2.1, INSDC Assembly GCA_003061485.1,
Database version98.1
Base Pairs486,463,734
Golden Path Length487,473,734
Genebuild by08
Genebuild methodGenerated from ENA annotation
Data sourceEuropean Nucleotide Archive

Gene counts

Coding genes33,263
Gene transcripts42,523

About this species