Maternal effects in coral fitness are reflected in gene expression patterns
Maternal effects in recruit survival and size previously reported forA. loripes x A. tenuis hybrid corals (Table 1) were consistent with their gene expression patterns. At the time when the corals were sampled for gene expression analyses, the hybrid LT and its maternal purebred LL had higher survival compared to the hybrid TL and its maternal purebred TT under both ambient and elevated conditions. Although the corals did not differ in size at seven months of age, maternal effects in size were evident by one year of age (Table 1). Maternal effects have previously been reported for other Indo-PacificAcropora hybrid corals obtained via laboratory crossing. These include effects in: 1) morphology of interspecific hybrids from anA. pulchra x A. millepora cross (Willis et al., 2006), 2) survival of interspecific hybrid larvae from an A. florida xA. intermedia cross (Isomura et al., 2013), and 3) thermal tolerance of intraspecific A. millepora hybrid larvae from a higher and lower latitude population. In contrast, paternal effects were found in morphology of natural interspecific hybrids of A. palmata and A. cervicornis from the Caribbean (Vollmer & Palumbi, 2002), and additive effects in survival (i.e., hybrid survival was intermediate between the parental offspring) were observed in experimentally produced intraspecific hybrids of A. milleporafrom a higher and lower latitude cross (van Oppen et al., 2014).
While a few studies have reported maternal effects in coral fitness and morphology, little is known about maternal effects in gene expression. In addition to the coral host, the host-associated microbiome can also have an impact on host gene expression (Barfield et al., 2018; Buerger et al., 2020; Helmkampf et al., 2019). In our study, however, the bacterial and microalgal endosymbiont communities of the corals were similar at the time of sampling (Table 1). The consistency between host gene expression and phenotypic results thus suggests that maternal host-related factors were likely the drivers behind the observed fitness differences. A large number of differentially expressed genes (~2000 DEGs) were found when comparing offspring groups that had different maternal parent species (i.e., between the hybrid TL and its paternal purebred LL, and between the reciprocal hybrids), but not when the groups shared the same maternal parent species (i.e., only 40 DEGs between the hybrid LT and its maternal purebred LL). Maternal effects were evident in these corals based on PCA, heatmap and volcano plots. While a statistical comparison cannot be made back to the parental purebred TT due to small sample size, gene expression of hybrid TL was similar to the only TT sample tested based on PCA and the heatmap was indicative of maternal effects. The four samples omitted from the main analyses because of their small library sizes also supported the presence of maternal effects, although inferences drawn from these samples should be taken with caution.
In our study, however, no mitochondrial genes were differentially expressed and PCA and heatmap of mitochondrial genes did not show maternal patterns. In other words, evidence of maternal gene expression patterns was only found in the nuclear genes, but not in the mitochondrial genes or via mito-nuclear crosstalk in this study (although note that only seven mitochondrial genes were available for comparison post-filtering).
Several studies have reported maternal effects in gene expression including in a perennial herb (Videvall et al., 2016), coral (Dixon et al., 2015), pipefish (Beemelmanns & Roth, 2016) and stickleback (Metzger & Schulte, 2016; Mommer & Bell, 2014; Shama et al., 2016), and maternal environments have also been demonstrated to affect DNA methylation of sea urchin (Strader et al., 2020). Videvall et al. (2016) showed that gene expression patterns were distinct between parental populations of 12-week-old seedling of the perennial herbArabidopsis lyrata , and expression in intraspecific hybrids was frequently more similar to that of the maternal than paternal population. Only 15 DEGs were found between the hybrid produced in one direction and its maternal population, yet > 8800 DEGs were found when compared to its paternal population (Videvall et al., 2016). Interestingly, maternal effects were weaker in the hybrid cross of the other direction, with 334 and 661 DEGs observed when compared to its maternal and paternal population respectively (Videvall et al., 2016). Only one previous study has examined maternal effects in coral hybrid gene expression and only coral larvae were studied. Consistent with our findings, Dixon et al. (2015) showed that gene expression of intraspecific A. millepora hybrid larvae was similar to that of their maternal population (i.e., up to 2,000 genes in hybrids followed the expression patterns of the maternal population). In these studies (Dixon et al., 2015 and Videvall et al., 2016) however, maternal effects were examined in early life stages only (i.e., 12-week-old seedling and 6-day-old larvae). Our results show that maternal effects can continue to influence gene expression of hybrid corals up to the age of at least seven months, indicating the potential long-term nature of maternal effects.
While differences in gene expression patterns were obvious between reciprocal hybrids as well as between the hybrid TL and its paternal purebred, it was unclear what pathways and mechanisms were linked to these differences and underpinned observed phenotypic differences (Chan et al., 2018). Gene ontology (GO) analyses revealed underrepresentation of a very broad GO category, “cytosol”, in both pairs of comparison. It is also possible that maternal provisioning had long-lasting effects in offspring (that were seven months old) and was responsible for the phenotypic and gene expression differences (i.e., poorly provisioned offspring may exhibit pervasive differences in transcription). Future studies on maternal effects in corals will benefit from quantifying differences in maternal provisioning between the parental species, such as lipid/protein content of eggs and early larvae.
In contrast, clear pathways involved in maternal effects were observed in the intraspecific A. millepora hybrid larvae (Dixon et al., 2015). Analyses of cellular component categories of tolerance-associated genes (i.e., genes for which expression levels prior to stress predicted the probability of larval survival under stress) showed enrichment of nuclear-encoded mitochondrial membrane components in hybrid coral larvae whose parents come from a warmer latitude (Dixon et al., 2015). The most upregulated GO categories were energy production and conversion, and encompassed mitochondrial proteins, suggesting mitochondrial protein variation in larvae may have contributed to maternal effects in thermal tolerance (Dixon et al., 2015).
The difference in GO associated patterns between these two studies may be due to 1) the parental populations chosen for hybridization, 2) the symbiotic/aposymbiotic nature of the corals and 3) the life stage of the corals. Parental populations of the same species from different latitudes were selected in Dixon et al. (2015), whereas parental populations of two different species from the same reef were chosen for this study. The differences in parental thermal regimes in Dixon et al. (2015) may lead to clearer maternal effects in thermal stress-related GO categories. Moreover, gene expression responses of aposymbiotic larvae in Dixon et al. ( 2015) were likely different from coral recruits (in this study) that were associated with a high density of microalgal endosymbionts. The effects of maternal provisioning on gene expression is also likely to be stronger in early larvae than in seven-month-old recruits. Hence, the contrasting results of the two studies are unsurprising. Further, mitochondrial genes may not show maternal patterns if maternal provisioning was responsible for the phenotypic maternal patterns observed in these corals.