Monthly Archives: October 2015

Genome sequencing of 9 species from the genus, Hymenoscyphus.

The Contributors

Christine Sambles, Karen Moore, Exeter Sequencing Service, Mick Kershaw, Chris Thornton, Murray Grant and David Studholme.
University of Exeter, Devon.

Summary

Genome sequencing and assembly of 9 different species from the Hymenoscyphus genus.

Table 1: The 9 sequenced species with NCBI GenBank and Short Read Archive (SRA) accession numbers:

Species Strain GenBank accession SRA accession
Hymenoscyphus fructigenus CBS 650.92 LKUV00000000 SRX1322313
Hymenoscyphus scutula CBS 480.97 LKTO00000000 SRX1322311
Hymenoscyphus varicosporoides CBS 651.66 LLCF00000000 SRX1322314
Hymenoscyphus repandus CBS 341.76 LLCE00000000 SRX1322310
Hymenoscyphus salicellus CBS 111550 LLCD00000000 SRX1322295
Hymenoscyphus fraxineus CBS 133217 LLCC00000000 SRX1322294
Hymenoscyphus infarciens CBS 122016 LLCB00000000 SRX1322117
Hymenoscyphus herbarum (Calycina herbarum) CBS 466.73 LLEY00000000 SRX1325539
Hymenoscyphus laetus* CBS 340.76 LLCA00000000 SRX1322158

*ITS phylogenetic analysis suggests this is not a Hymenoscyphus spp. but is more likely to be a species from the Phaeosphaeria genus.

Table 2: Assembly statistics of the 9 sequenced Hymenoscyphus spp. genomes:

Species Strain Genome size (bp) # contigs N50 % GC
Hymenoscyphus fructigenus CBS 650.92 61,124,938 504 373,842 43.09
Hymenoscyphus scutula CBS 480.97 63,226,382 2,591 72,955 41.07
Hymenoscyphus varicosporoides CBS 651.66 31,978,795 206 585,492 46.36
Hymenoscyphus repandus CBS 341.76 42,813,648 925 226,427 45.61
Hymenoscyphus salicellus CBS 111550 57,952,665 9,749 9,574 44.34
Hymenoscyphus fraxineus CBS 133217 51,524,987 4,749 24,374 43.65
Hymenoscyphus infarciens CBS 122016 68,152,485 1,714 156,341 37.56
Hymenoscyphus herbarum CBS 466.73 69,308,136 529 325,154 41.67
Hymenoscyphus laetus* CBS 340.76 36,473,783 471 257,815 51.89

Fig 1: ITS phylogenetic tree of 8 sequenced genomes and other member of the Helotiales order, not including H. laetus (putatively a Phaeosphaeria spp.)

hym_9species