Shaadi Mehr; Aida Verdes; Rob DeSalle; John Sparks; Vincent Pieribone; David F Gruber

“ The sex pheromone attractin has been suggested by previous authors as a potential phylogenetic marker [58] . As part of our annotation pipeline, we have identified seven sequences homologous to attractin in the transcriptome of Hermodice carunculata. A phylogenetic analysis was performed to evaluate the potential of the H. carunculata attractin protein as a reliable phylogenetic marker for polychaete systematics and evolutionary studies. ”

“ Housekeeping genes are required for the maintenance of essential basal cellular functions and consequently, under normal conditions, they are expressed in all cells regardless of tissue type or developmental stage [54] . They are especially interesting because they represent the minimal set of genes required to sustain life and they can be used as comparative controls for experimental and computational studies [54] , for example, to assess the suitability of transcriptome datasets for gene discovery [50] . ”

“ Hermodice carunculata is also a winter reservoir and spring-summer vector for the coral-bleaching pathogen Vibrio shiloi [9] and plays a complex and potentially ecologically important role in coral reef ecosystem health.
Amphinomidae is a well-delineated clade within aciculate polychaetes and it comprises approximately 200 described species from 25 genera [10] - [11] . Amphinomids are distributed worldwide and are known to inhabit intertidal, continental shelf and shallow reef communities, with a few species also recorded from the deep-sea [11] . ”

“ This analysis showed that genetic divergence is low among samples across the Atlantic Ocean, and these particular three genes do not reflect any genetic basis for the observed morphological differences (e.g., variable filament abundance) among populations. Therefore, identification of informative loci for phylogeographic application is necessary. However, a different study using COI sequences has found that Eurythoe complanata represents a complex of three genetically distinct and morphologically indistinguishable lineages inhabiting the Atlantic and Pacific Oceans. ”

“ This is expected, as C. teleta and H. carunculata are both polychaete annelids, as opposed to H. robusta, a leech (Clitellata) . In total, 15,841 transcripts had a significant hit (70% length homology) in both datasets. Furthermore, 29,819 of these ORFs showed homology to P. jeffreysi and 36,033 to E. complanata. Of these ORFs, 23,441 were homologous to both Paramphinome jeffreysi and Eurythoe complanata. These shared sequences can be used for future genome annotation of both annelids and amphinomids, respectively (data available upon request) . ”

“ One of the important aspects of mining the transcriptomic data is assigning function to individual transcripts. Functional annotation is an effective way to categorize genes into physiological classes to assist in understanding the large quantity of transcripts and for evaluating functional differences between subgroups of sequences. ”

“ Results and discussion Sequencing andde novoassembly
Total RNA was extracted from the body-segment H. carunculata. The (A) + RNA was isolated, sheered to smaller fragments, and reverse transcribed to make cDNA for sequencing with Hi-Seq Illumina 1000. Four hundred million paired-end strand-unspecific reads were obtained from one lane of one plate, generating 32.4 gigabase pairs (Gbp) of raw data that were uploaded to NCBI. Reads were checked for Phred-like quality scores above the Q30 level with FastQC [31] . ”

“ The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32 (Database issue) :D258–61.14681407↑ Zdobnov EM, Apweiler R. InterProScan–an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001;17:847–8.10.1093/bioinformatics/17.9.84711590104↑ Mulder NJ, Apweiler R: The InterPro database and tools for protein domain analysis. Curr Protoc Bioinforma 2008, Chapter 2:Unit 2 7.↑ Hofmann K, Bucher P, Falquet L, Bairoch A. The PROSITE database, its status in 1999. ”

“ Nature. 2011;471:95–U113.10.1038/nature09864213688311 2 Colgan DJ, Hutchings PA, Beacham E. Multi-gene analyses of the phylogenetic relationships among the Mollusca, Annelida, and Arthropoda. Zool Sci. 2008;47:338–51.↑ Giribet G. Assembling the lophotrochozoan (=spiralian) tree of life. Philos Trans R Soc L B Biol Sci. 2008;363:1513–22.10.1098/rstb.2007.22411 2 Salzet M, Tasiemski A, Cooper E. Innate immunity in lophotrochozoans: the annelids. ”