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

major small RNA pathways, including 4 argonaute family members, 2 PIWI family members, and 499 orthologs of D. melanogaster Dicer-1 and Dicer-2, drosha and loquacious, (Figure 14 , Supplemental 500 Figure 1 ). Among Argonaute genes, Parhyale has 1 AGO-1 ortholog and 3 AGO-2 orthologs, which is 501 presumably a malacostraca-specific expansion. While Parhyale only has 2 PIWI family members, other 502 crustacean lineages have clearly undergone independent expansions of this protein family. Unlike in C. 503 elegans, many mammals, fish and insects (but not D. melanogaster), we did not find any evidence in the 504 Parhyale genome for the SID-1 (systemic RNA interference defective) transmembrane protein that is 505 essential for systemic RNAi [125] [126] [127] . Species without a SID-1 ortholog can silence genes only in a 506 cell-autonomous manner [128] . This feature has important implications for future design of RNAi 507 experiments in Parhyale. 508 We also assessed the miRNA and putative long non-coding RNAs (lncRNA) content of Parhyale using The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/065789 doi: bioRxiv preprint Conserved linkages have also been observed between miRNAs and Hox genes in Bilateria [137] [138] [139] [140] [141] .