De novo transcriptome assembly of the hydrocoral Millepora alcicornis (branching fire coral) from the Caribbean Ingrid C. Ortiz-González, Ramón E. Rivera-Vicéns, Nikolaos V. Schizas ⁎ University of Puerto Rico at Mayagüez, Department of Marine Sciences, P.O. Box 9000, Mayagüez, 00681, PR, USA abstract article info Article history: Received 20 October 2016 Received in revised form 28 November 2016 Accepted 29 November 2016 Available online xxxx The hydrocoral Millepora is found in shallow tropical/subtropical regions around the globe and is considered an important reef-building organism. Millepora alcicornis is the most common species in the Atlantic Ocean, and can be found from 0.5 to 50 m deep. It is distributed from the tropical/subtropical eastern western Atlantic Ocean, in- cluding Bermuda, Brazil, and on the east in Tenerife of the Canary Islands, the Cape Verde Archipelago and Ascen- sion Island. No genomic information is available for this ecologically important group. Here, we report de novo transcriptome assembly of M. alcicornis sampled from Puerto Rico, Caribbean. We used paired-end sequencing (Illumina HiSeq4000, 2 × 150 bp) and obtained 76,518,693 reads. Transcriptome assembly was performed using Trinity, producing a total of 479,982 transcripts with an average size of 553 bp and a N50 of 749. Data was normalized using RSEM and filtered by a TPM of 3. Open reading frames (ORFs) from the filtered transcripts were obtained by TransDecoder using the hydrozoan Hydra vulgaris protein sequences as reference, generating 16,024 putative ORFs. Blast searches showed that 25.8% (4137) of the ORFs matched H. vulgaris and 24.6% matched other anthozoan cnidarians (i.e. Nematostella vectensis = 1621, Exaiptasia pallida = 1280, Acropora digitifera = 1050). Gene ontology generated by Blast2GO resulted in a total of 7220 ORFs associated with molec- ular function, 4917 with biological processes, and 2989 with cellular components. A general overview will be pre- sented of the first assembled M. alcicornis transcriptome with emphasis on shared genes among Hydrozoans and Scyphozoans. © 2016 Elsevier B.V. All rights reserved. Keywords: Transcriptome De novo assembly Puerto Rico Coral Hydrozoan Hydrocoral 1. Introduction Hydrocorals of the genus Millepora are a relatively rich-species genus with 18 species distributed around the globe. They inhabit reefs at depths between 0.5 m down to 50 m (Lewis, 2006) and usually grow upright in finger-like branches, leaf-like, or blade-like patterns. Millepora spp. grows also over other substrata such as rocks, piers, man- grove roots, living corals, gorgonians and sponges (Banaszak et al., 2003; Lewis, 2006; Wahle, 1980). Milleporids provide habitat for many species such as small fish, ophiuroids, barnacles, micro-crusta- ceans among others. In the Caribbean, milleporids are important reef builders and are commonly found in shallow and turbulent waters forming dense reef rims contributing to the stabilization and complexity of the carbonate structure (Edmunds, 1999; Lewis, 2006). Millepora alcicornis (Linneaus 1758) is the most widely dispersed fire coral in the Atlantic in comparison with the other seven species in the same ocean. It has an extensive distribution from the tropical/sub- tropical western Atlantic Ocean, including Brazil, to the west coast of Af- rica in Cape Verde Archipelago, and Ascension Island (Amaral et al., 2008; Clemente et al., 2011; de Weerdt and Glynn, 1991; Hoeksema et al., 2014; Morri et al., 2000). More recently, M. alcicornis was reported from the southeastern coast of Tenerife but this record has been deemed as a recent invasion to the Canary Islands (Clemente et al., 2011; López et al., 2015). Dispersion during the medusoid stage may not be as effec- tive due to the short pre-competency period time of the hydromedusae in the water column (Edmunds, 1999; Lewis, 2006). However, asexual reproduction through fragmentation of this branching hydrocoral is substantial during disturbances (Edmunds, 1999; Lewis, 2006) and may contribute more to the dispersal. In addition, the success of M. alcicornis to settle to distant locations can be attributed to transporta- tion through ballast waters of large vessels and fouling of hulls (Clemente et al., 2011; López et al., 2015). Despite the prevalence of Millepora in shallow water reefs, there is uncertainty on the number of true species in the genus. All the previous studies aiming to identify Millepora species are mainly based on mor- phological characters such as number, diameter and distance of gastropores and dactylopores, the presence or absence of the ampullae, and the shape, texture and character of the corallum (Boshma, 1948; de Weerdt and Glynn, 1991). This method has not produced consensus re- sults to distinguish species because of the great morphological variabil- ity within and between species (Amaral et al., 2002; Lewis, 2006). In fact, the most recently described species from Brazil, M. laboreli (Amaral et al., 2008), was based exclusively on morphological Marine Genomics xxx (2016) xxx–xxx ⁎ Corresponding author. E-mail address: nschizas@gmail.com (N.V. Schizas). MARGEN-00494; No of Pages 4 http://dx.doi.org/10.1016/j.margen.2016.11.005 1874-7787/© 2016 Elsevier B.V. All rights reserved. Contents lists available at ScienceDirect Marine Genomics journal homepage: www.elsevier.com/locate/margen Please cite this article as: Ortiz-González, I.C., et al., De novo transcriptome assembly of the hydrocoral Millepora alcicornis (branching fire coral) from the Caribbean, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2016.11.005