RT Journal Article SR Electronic T1 Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria JF bioRxiv FD Cold Spring Harbor Laboratory SP 045708 DO 10.1101/045708 A1 David A. Baltrus A1 Kevin Dougherty A1 Kayla R. Arendt A1 Marcel Huntemann A1 Alicia Clum A1 Manoj Pillay A1 Krishnaveni Palaniappan A1 Neha Varghese A1 Natalia Mikhailova A1 Dimitrios Stamatis A1 T. B. K. Reddy A1 Chew Yee Ngan A1 Chris Daum A1 Nicole Shapiro A1 Victor Markowitz A1 Natalia Ivanova A1 Nikos Kyrpides A1 Tanja Woyke A1 A. Elizabeth Arnold YR 2016 UL http://biorxiv.org/content/early/2016/03/25/045708.abstract AB Fungi interact closely with bacteria both on the surfaces of hyphae, and within their living tissues (i.e., endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts, and can mediate a diverse phenotypic traits in their hosts. Although EHB have been observed in many major lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features found across all EHB strains. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, genomes of these facultative EHB resemble those of closely related strains isolated from environmental sources. Although all analyzed genomes encode structures that can be used to interact with eukaryotic hosts, we find no known pathways that facilitate intimate EHB-fungal interactions in all strains. We isolated two strains with nearly identical genomes from different classes of fungi, consistent with previous suggestions of horizontal transfer of EHB across endophytic hosts. Because bacteria are differentially present during the fungal life cycle, these genomes could shed light on the mechanisms of plant growth promotion by fungal endophytes during the symbiotic phase as well as degradation of plant material during saprotrophic and reproductive phases. Given the capacity of EHB to influence fungal phenotypes, these findings illuminate a new dimension of fungal biodiversity.