Comprehensive Metatranscriptome Analysis of the Reef-Building Holobiont Millepora complanata

Abstract

Hydrocorals from the genus Millepora (Phylum Cnidaria, Class Hydrozoa) are conspicuous organisms commonly found in shallow waters of tropical regions. These cnidarians, which are considered the second reef builders in the world (Rojas-Molina et al., 2012), are vital components of marine ecosystems and provide habitat for many coral reef-dependent communities (Lewis, 2006). The genus Millepora includes calcareous hydroids that are not classified in the group of true stony corals (Radwan and Aboul-Dahab, 2004). Milleporids are commonly known as “fire corals” due to their ability to inflict painful wounds in human epithelial tissues through the secretion of toxins (Radwan, 2002), which are stored in the nematocysts (Shiomi et al., 1989; David et al., 2008). Millepora complanata is a common resident of the Mesoamerican Reef System in the Mexican Caribbean (Ibarra-Alvarado et al., 2007). This organism inhabits shallow water and the reef crest (Stromgren, 1976) where it forms plate-like colonies composed of multiple clones (Lewis, 1991). Like many scleractinian corals and other cnidarians, M. complanata lives in mutualistic symbiosis with dinoflagellate algae of the family Symbiodiniaceae (commonly known as zooxanthellae) (Davy et al., 2012). Dinoflagellates reside in the symbiosomes, which are phagosome-derived vacuoles within cnidarian gastrodermal cells (Lehnert et al., 2014). Symbiodiniaceae algae provide photosynthetic fixed carbon to their host, in exchange, cnidarians supply their symbionts with nitrogenous compounds (Sproles et al., 2018). Within host tissues, coral-associated symbionts may reach population densities of several millions per square centimeter and the holobiont may contain more than one Symbiodiniaceae genus (LaJeunesse, 2002). Diverse studies have analyzed the symbiotic relationship between stony corals (class Anthozoa) and their symbionts (Furla et al., 2005; Davy et al., 2012; Gusmão et al., 2020; Tivey et al., 2020; Xiang et al., 2020). However, hydrocoral-Symbiodiniaceae symbiosis is poorly understood. Investigations on the mutualistic relationship between reef-building cnidarians and Symbiodiniaceae algae have increased in the “omics age” (Meyer and Weis, 2012; Bi et al., 2019; Simona, 2019) and the sea anemone Exaiptasia diaphana, formerly known as Aiptasia pallida, has been widely employed as a model to study cnidarian endosymbiosis (Lehnert et al., 2012; Tortorelli et al., 2020). A gene expression analysis of cnidarian-algae association in Anthopleura elegantissima evidenced a complex modulation of host gene expression related to oxidative stress, apoptosis, cell proliferation, cell adhesion, and lipid metabolism (Rodriguez-Lanetty et al., 2006). It has been demonstrated that reef-building cnidarians are also associated with a diverse community of bacteria and other microorganisms (Tandon et al., 2020). These microorganisms are key components of the coral holobiont and play a major role in nutrient cycling, which is fundamental for reef development (Rajasabapathy et al., 2020). Environmental stressors, such as UV radiation and high temperature can lead to “bleaching,” the disruption of the symbiosis between cnidarians and Symbiodiniaceae (Hughes et al., 2017). Unfortunately, the frequency and seriousness with which bleaching occurs have increased in recent years, seriously compromising coral populations around the world (Sully et al., 2019). Considering that perturbations induced by climate change have threatened the integrity and resilience of marine ecosystems, several investigations have analyzed the bleaching phenomenon, using transcriptomic approaches to understand the molecular mechanisms underlying the responses of cnidarians and symbionts to heat stress (Mayfield et al., 2011, 2014; Pinzón et al., 2015). Investigations aimed at characterizing the transcriptomes of reef-building cnidarians have focused on species of the class Anthozoa (Kitchen et al., 2015; Kenkel and Bay, 2017; Pootakham et al., 2018; Veglia et al., 2018; Rivera-García et al., 2019; Ryu et al., 2019; Chiu et al., 2020). Regarding organisms of the class Hydrozoa, analysis of the transcriptomes from Hydractinia echinata and Hydra vulgaris showed the presence of evolutionary-conserved proteins and hitherto undescribed sequences in metazoans (Soza-Ried et al., 2010; Wenger and Galliot, 2013). However, with respect to de novo transcriptome assemblies of cnidarians of the genus Millepora, only one study has been reported on the branching hydrocoral M. alcicornis from the Caribbean (Ortiz-González et al., 2017). RNA-seq-based transcriptomic approaches have become powerful tools directed toward recognizing all the expressed genes codified by a genome under certain conditions. Additionally, generation of new gene catalogs enables identification of ortholog sequences across related taxa. In this study, we used a metatranscriptomic sequencing approach to describe, for first time, the metatranscriptome of M. complanata and its associate symbionts in order to generate a new reference metatranscriptome of reef-building cnidarians of the class Hydrozoa. Fragments of M. complanata colonies (~10 cm) were collected by SCUBA (Self-Contained Underwater Breathing Apparatus) diving at the Parque Nacional Arrecife located in Puerto Morelos, Quintana Roo, México (21°00′00′′ and 20°48′33′′ North latitude and 86°53′14.40′′ and 86°46′38.94′′ West longitude), during November 2016 (Permit No PFP/DGOPA-139/15). Samples were immediately frozen in liquid nitrogen and transported to the “Laboratorio de Investigación Química y Farmacológica de Productos Naturales in the Universidad Autónoma de Querétaro,” Queretaro,...