The genome of the crustacean Parhyale hawaiensis: a model for animal development, regeneration, immunity and lignocellulose digestion

Damian Kao; Alvina G. Lai; Evangelia Stamataki; Silvana Rosic; Nikolaos Konstantinides; Erin Jarvis; Alessia Di Donfrancesco; Natalia Pouchkina-Stantcheva; Marie Sémon; Marco Grillo; Heather Bruce; Suyash Kumar; Igor Siwanowicz; Andy Le; Andrew Lemire; Michael B. Eisen; Cassandra Extavour; William E. Browne; Carsten Wolff; Michalis Averof; Nipam H. Patel; Peter Sarkies; Anastasios Pavlopoulos; A. Aziz Aboobaker

High levels of heterozygosity and polymorphism in the Parhyale genome 224 To estimate the level of heterozygosity in genes we first identified transcribed regions of the genome by 225 mapping back transcripts to the assembly. Where these regions appeared in a single contig in the 226 assembly, heterozygosity was calculated using information from mapped reads. Where these regions 227 appeared in more than one contig, because haplotypes had assembled independently, heterozygosity was 228 calculated using an alignment of the genomic sequences corresponding to mapped transcripts and 229 information from mapped reads. This allowed us to calculate heterozygosity for each gene within the 230 sequenced individual (Supplemental Data 9). We then calculated the genomic coverage of all transcribed 231 regions in the genome and found, as expected, they fell broadly into two categories with higher and lower 232 read coverage ( Figure 6A ; Supplemental Data 9). Genes that fell within the higher read coverage group 233 had a lower mean heterozygosity (1.09% of bases displaying polymorphism), which is expected as more 234 reads were successfully mapped. Genes that fell within the lower read coverage group had a higher is not substantially different between genes from the higher (0.88%) versus lower coverage group genes 244 (0.73%; Figure 6C ). This analysis suggests that within captive laboratory populations of Parhyale there is 245 considerable additional polymorphism distributed across genes, irrespective of whether or not they have 246 relatively low or high heterozygosity in the individual male we sequenced. In addition the single male we 247 have sequenced provides an accurate reflection of polymorphism of the wider laboratory population and 248 the established Chicago-F strain does not by chance contain unusually divergent haplotypes. We also 249 performed an assessment of polymorphism on previously cloned Parhyale developmental genes, and To further evaluate the extent of polymorphism across the genome, we mapped the genomic reads to a set 256 of previously Sanger-sequenced BAC clones of the Parhyale Hox cluster from the same Chicago-F line 257 from which we sequenced the genome of an adult male. [18] . We detected SNPs at a rate of 1.3 to 2.5% 258 among the BACs (Table 3) and also additional sequence differences between the BACs and genomic 259 reads, confirming that additional polymorhism exists in the Chicago-F line beyond that detected between 260 in the haplotypes of the individual male we sequenced. 261 Overlapping regions of the contiguous BACs gave us the opportunity to directly compare Chicago-F 262 haplotypes and accurately observe polynucleotide polymorphisms, that are difficult to detect with short 263 reads that do not map when polymorphisms are large, but are resolved by longer Sanger reads. (Figure 264 7A). Since the BAC clones were generated from a pool of Chicago-F animals, we expected each 265 sequenced BAC to be representative of one haplotype. Overlapping regions between BAC clones could 266 potentially represent one or two haplotypes. We found that the genomic reads supported the SNPs 267 observed between the overlapping BAC regions. We found relatively few base positions with evidence 268 supporting the existence of a third allele. This analysis revealed many insertion/deletion (indels) with 269 some cases of indels larger than 100 base pairs ( Figure 7B ). The finding that polynucleotide with Scr in the first maxillary se