Interspecific Differential Expression Analysis of RNA-Seq Data Yields Insight into Life Cycle Variation in Hydractiniid Hydrozoans

Abstract

Hydrozoans are known for their complex life cycles, which can alternate between an asexually reproducing polyp stage and a sexually reproducing medusa stage. Most hydrozoan species, however, lack a free-living medusa stage and instead display a developmentally truncated form, called a medusoid or sporosac, which generally remains attached to the polyp. Although evolutionary transitions in medusa truncation and loss have been investigated phylogenetically, little is known about the genes involved in the development and loss of this life cycle stage. Here, we present a new workflow for evaluating differential expression (DE) between two species using short read Illumina RNA-seq data. Through interspecific DE analyses between two hydractiniid hydrozoans, Hydractinia symbiolongicarpus and Podocoryna carnea, we identified genes potentially involved in the developmental, functional, and morphological differences between the fully developed medusa of P. carnea and reduced sporosac of H. symbiolongicarpus. A total of 10,909 putative orthologs of H. symbiolongicarpus and P. carnea were identified from de novo assemblies of short read Illumina data. DE analysis revealed 938 of these are differentially expressed between P. carnea developing and adult medusa, when compared with H. symbiolongicarpus sporosacs, the majority of which have not been previously characterized in cnidarians. In addition, several genes with no corresponding ortholog in H. symbiolongicarpus were expressed in developing medusa of P. carnea. Results presented here show interspecific DE analyses of RNA-seq data to be a sensitive and reliable method for identifying genes and gene pathways potentially involved in morphological and life cycle differences between species.

The genome of the jellyfish Aurelia and the evolution of animal complexity

“…As important as gene co-option appears in Aurelia's evolution, we did discover multiple gene family expansions that could be candidate drivers of medusa development, as well as many taxonomically restricted genes that are upregulated in the polypto-medusa transition. This finding is consistent with previous studies that have leveraged high-throughput sequencing to holistically examine medusa development, and broadly support the hypothesis that this life stage is generated from a combination of modified gene regulation as well as gene gain and loss 23,[51][52][53] . However, our analyses allow us to further hypothesize that taxonomically restricted genes are not overrepresented in the polyp-to-medusa transition, and that changes in gene content appear just as common in the anthozoans as they are in Aurelia.…”

Differential Gene Expression Between Polymorphic Zooids of the Marine BryozoanBugulina stolonifera

“…These results are difficult to compare with other studies on polymorphic colonies, as few have addressed differential gene expression across polymorphs. From a methodological context, siphonophores have been used as a model to compare assembly techniques ( Siebert et al 2011 ), and other studies have focused on examining different life stages in the biphasic life cycle of a hydrozoan ( Sanders and Cartwright 2015 ). Even with bryozoans, levels of expression have been studied to select candidate developmental genes for body patterning (especially the lophophore and digestive tract) ( Wong et al 2014 ), but this study compared larval and whole-colony data, without discerning among polymorphic zooids, as done here.…”

Frizzled3 expression and colony development in hydractiniid hydrozoans

“…Animal Care. Animal care was performed as in Sanders and Cartwright (2015b). For in situ hybridizations young colonies were reared and fixed for downstream analysis.…”