Two divergent haplogroups of a sacsin-like gene in Acropora corals.

Reef-building corals are declining due to environmental changes. Sacsin is a member of the heat shock proteins and has been reported as a candidate protein associated with the stress response in Acropora corals. Recently, high nucleotide diversity and the persistence of two divergent haplogroups of sacsin-like genes in Acropora millepora have been reported. While it was not clear when the two haplogroups have split and whether the haplogroups have persisted in only A. millepora or the other lineages in the genus Acropora. In this study, we analyzed a genomic region containing a sacsin-like gene from Acropora and Montipora species. Higher nucleotide diversity in the sacsin-like gene compared with that of surrounding regions was also observed in A. digitifera. This nucleotide diversity is derived from two divergent haplogroups of a sacsin-like gene, which are present in at least three Acropora species. The origin of these two haplogroups can be traced back before the divergence of Acropora and Montipora (119 Ma). Although the link between exceptionally high genetic variation in sacsin-like genes and functional differences in sacsin-like proteins is not clear, the divergent haplogroups may respond differently to envionmental stressors and serve in the adaptive phsiological ecology of these keystone species.

Presence-absence polymorphisms of single-copy genes in the stony coral Acropora digitifera.

BACKGROUND: Despite the importance of characterizing genetic variation among coral individuals for understanding phenotypic variation, the correlation between coral genomic diversity and phenotypic expression is still poorly understood. RESULTS: In this study, we detected a high frequency of genes showing presence-absence polymorphisms (PAPs) for single-copy genes in Acropora digitifera. Among 10,455 single-copy genes, 516 (5%) exhibited PAPs, including 32 transposable element (TE)-related genes. Five hundred sixteen genes exhibited a homozygous absence in one (102) or more than one (414) individuals (n = 33), indicating that most of the absent alleles were not rare variants. Among genes showing PAPs (PAP genes), roughly half were expressed in adults and/or larvae, and the PAP status was associated with differential expression among individuals. Although 85% of PAP genes were uncharacterized or had ambiguous annotations, 70% of these genes were specifically distributed in cnidarian lineages in eumetazoa, suggesting that these genes have functional roles related to traits related to cnidarians or the family Acroporidae or the genus Acropora. Indeed, four of these genes encoded toxins that are usually components of venom in cnidarian-specific cnidocytes. At least 17% of A. digitifera PAP genes were also PAPs in A. tenuis, the basal lineage in the genus Acropora, indicating that PAPs were shared among species in Acropora. CONCLUSIONS: Expression differences caused by a high frequency of PAP genes may be a novel genomic feature in the genus Acropora; these findings will contribute to improve our understanding of correlation between genetic and phenotypic variation in corals.

Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. 'macula'.

BACKGROUND: The molecular basis of the incipient stage of speciation is still poorly understood. Cichlid fish species in Lake Victoria are a prime example of recent speciation events and a suitable system to study the adaptation and reproductive isolation of species. RESULTS: Here, we report the pattern of genomic differentiation between two Lake Victoria cichlid species collected in sympatry, Haplochromis pyrrhocephalus and H. sp. 'macula,' based on the pooled genome sequences of 20 individuals of each species. Despite their ecological differences, population genomics analyses demonstrate that the two species are very close to a single panmictic population due to extensive gene flow. However, we identified 21 highly differentiated short genomic regions with fixed nucleotide differences. At least 15 of these regions contained genes with predicted roles in adaptation and reproductive isolation, such as visual adaptation, circadian clock, developmental processes, adaptation to hypoxia, and sexual selection. The nonsynonymous fixed differences in one of these genes, LWS, were reported as substitutions causing shift in absorption spectra of LWS pigments. Fixed differences were found in the promoter regions of four other differentially expressed genes, indicating that these substitutions may alter gene expression levels. CONCLUSIONS: These diverged short genomic regions may have contributed to the differentiation of two ecologically different species. Moreover, the origins of adaptive variants within the differentiated regions predate the geological formation of Lake Victoria; thus Lake Victoria cichlid species diversified via selection on standing genetic variation.

Presence-Absence Polymorphisms of Highly Expressed FP Sequences Contribute to Fluorescent Polymorphisms in Acropora digitifera.

Despite many hypotheses regarding the roles of fluorescent proteins (FPs), their biological roles and the genetic basis of FP-mediated color polymorphisms in Acropora remain unclear. In this study, we determined the genetic mechanism underlying fluorescent polymorphisms in A. digitifera. Using a high-throughput sequencing approach, we found that FP gene sequences in FP multigene family exhibit presence-absence polymorphism among individuals. A few particular sequences in short-to-middle wavelength emission and middle-to-long wavelength emission clades were highly expressed in adults, and different sequences were highly expressed in larvae. These highly expressed sequences were absent in the genomes of individuals with low total FP gene expression. In adults, presence-absence differences of the highly expressed FP sequences were consistent with measurements of emission spectra of corals, suggesting that presence-absence polymorphisms of these FP sequences contributed to the fluorescent polymorphisms. The functions of recombinant FPs encoded by highly expressed sequences in adult and larval stages were different, suggesting that expression of FP sequences with different functions may depend on the life-stage of A. digitifera. Highly expressed FP sequences exhibited presence-absence polymorphisms in subpopulations of A. digitifera, suggesting that presence-absence status is maintained during the evolution of A. digitifera subpopulations. The difference in FPs between adults and larvae and the polymorphisms of highly expressed FP genes may provide key insight into the biological roles of FPs in corals.

Visual adaptation in Lake Victoria cichlid fishes: depth-related variation of color and scotopic opsins in species from sand/mud bottoms.

BACKGROUND: For Lake Victoria cichlid species inhabiting rocky substrates with differing light regimes, it has been proposed that adaptation of the long-wavelength-sensitive (LWS) opsin gene triggered speciation by sensory drive through color signal divergence. The extensive and continuous sand/mud substrates are also species-rich, and a correlation between male nuptial coloration and the absorption of LWS pigments has been reported. However, the factors driving genetic and functional diversity of LWS pigments in sand/mud habitats are still unresolved. RESULTS: To address this issue, nucleotide sequences of eight opsin genes were compared in ten Lake Victoria cichlid species collected from sand/mud bottoms. Among eight opsins, the LWS and rod-opsin (RH1) alleles were diversified and one particular allele was dominant or fixed in each species. Natural selection has acted on and fixed LWS alleles in each species. The functions of LWS and RH1 alleles were measured by absorption of reconstituted A1- and A2-derived visual pigments. The absorption of pigments from RH1 alleles most common in deep water were largely shifted toward red, whereas those of LWS alleles were largely shifted toward blue in both A1 and A2 pigments. In both RH1 and LWS pigments, A2-derived pigments were closer to the dominant light in deep water, suggesting the possibility of the adaptation of A2-derived pigments to depth-dependent light regimes. CONCLUSIONS: The RH1 and LWS sequences may be diversified for adaptation of A2-derived pigments to different light environments in sand/mud substrates. Diversification of the LWS alleles may have originally taken place in riverine environments, with a new mutation occurring subsequently in Lake Victoria.

Acropora digitifera Encodes the Largest Known Family of Fluorescent Proteins that Has Persisted during the Evolution of Acropora Species.

Fluorescent proteins (FPs) are well known and broadly used as bio-imaging markers in molecular biology research. Many FP genes were cloned from anthozoan species and it was suggested that multi-copies of these genes are present in their genomes. However, the full complement of FP genes in any single coral species remained unidentified. In this study, we analyzed the FP genes in two stony coral species. FP cDNA sequences from Acropora digitifera and Acropora tenuis revealed the presence of a multi-gene family with an unexpectedly large number of genes, separated into short-/middle-wavelength emission (S/MWE), middle-/long-wavelength emission (M/LWE), and chromoprotein (CP) clades. FP gene copy numbers in the genomes of four A. digitifera colonies were estimated as 16-22 in the S/MWE, 3-6 in the M/LWE, and 8-12 in the CP clades, and, in total, 35, 31, 33, and 33 FP gene copies per individual shown by quantitative PCR. To the best of our knowledge, these are the largest sets of FP genes per genome. The fluorescent light produced by recombinant protein products encoded by the newly isolated genes explained the fluorescent range of live A. digitifera, suggesting that the high copy multi-FP gene family generates coral fluorescence. The functionally diverse multi-FP gene family must have existed in the ancestor of Acropora species, as suggested by molecular phylogenetic and evolutionary analyses. The persistence of a diverse function and high copy number multi-FP gene family may indicate the biological importance of diverse fluorescence emission and light absorption in Acropora species.

Genetic diversity of fluorescent protein genes generated by gene duplication and alternative splicing in reef-building corals.

INTRODUCTION: Reef-building corals (Scleractinia) exhibit various colors, of which fluorescent proteins (FPs) are a major determinant. Gene duplication is considered a major mechanism in the generation of the FP gene family and color diversity. Examining gene duplication events and subsequent evolution may improve our understanding of FP gene family diversity. RESULTS: We isolated a novel FP gene family from one individual of Montipora sp., which we named monGFP (GFP gene from Montipora sp.). This gene family consists of at least four genes that produce at least six different cDNA sequences. The sequences were categorized into two types based on the length of cDNA; this difference is attributed to alternative splicing. Although the amino acid sequences were different, the emission spectra of the monGFP variants were nearly identical (518-521 nm). In addition to this gene family, we isolated ten paralogous AdiFP10 (Adi-Fluorescent protein-10 gene from Acropora digitifera) sequences from cDNA of two Acropora species, A. digitifera and A. tenuis. Based on our phylogenetic analysis, five sequences from A. digitifera and four sequences from A. tenuis appeared to be in a different cluster from AdiFP10, suggesting a new FP gene cluster. The FP sequences were likely to have been generated independently in each species or generated by gene duplications in the ancestral lineage of Acropora, followed by extensive gene conversion within each species. CONCLUSION: Our results clarify a part of the diversification process of FP genes during the evolutionary history of Montipora and Acropora species. Our analyses of monGFP indicate that FPs translated from different splicing variants and gene copies have evolved without changes in the function of fluorescence, and gene copies have been evolved under purifying selection. On the other hand, AdiFP10 paralogs and other RFP genes in Acropora species may have diversified their functions. Identification of conserved and divergent modes of evolution after the duplication of FP genes may reflect variation in the biological roles of different FPs.