Panicum hallii HAL2 Assembly and Gene Annotation

About Panicum hallii

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 2x250 fragment library (150x) 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 2x150 fragment library (100x) 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) 2x150 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.