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

Abstract

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.

Keywords: Expression difference; Genome diversity; Structural variation.

Fig. 1

PAP in the Acropora digitifera genome. (a) An example of a PAP region lacking coverage. The genomic location of a CDS (LOC107329567) is shown with a gray arrow on the scaffold (NW_015442398.1). The read coverage (0 to 50) across the scaffold is shown in gray for a control and three samples. Dotted lines indicate the approximate start and end positions of the area with no read coverage. (b) Boundaries of absent alleles in A. digitifera and A. tenuis. The sequence from the scaffold (NW_015442476.1) was used as an A. digitifera present allele. The genomic locations of two genes are shown with light gray arrows on the line representing the scaffold sequence. Existing genomic regions are shown in dark gray in both present and absent alleles of A. digitifera and A. tenuis. The A. digitifera specific deletion is indicated by dashed lines. The sequence predicted from the length of a PCR product for the A. tenuis present allele is surrounded by a dashed line, insertions specific to absent alleles are shown by light gray boxes. The locations of the 5′ junction and 3′ junction are indicated by black arrows

Fig. 2

Characterization of PAPs in 33 A. digitifera and six A. tenuis individuals. (a) The frequencies of single-copy genes under functional constraint (47%: 10,455) and multiple-copy genes or single-copy genes without functional constraint (53%: 11,917) for all CDSs (22,372). (b) The frequencies of PAPs (5%: 516) and non-PAPs (95%: 9939) for single-copy genes under functional constraint. (c) The frequencies of PAPs on single scaffolds. (d) The frequencies of each presence–absence status for 516 genes (PAPs in A. digitifera) in A. tenuis

Fig. 3

Expressions of genes showing PAPs. (a) The frequencies of expression (49%) and no expression (51%) for all PAP genes. (b) PAP genes were classified into five categories based on RPKM values: RPKM = 0, 1 ≤ RPKM < 5, 5 ≤ RPKM < 10, 10 ≤ RPKM< 50, 50 ≤ RPKM. The y-axis indicates the number of genes in each category. (c) Differences in gene expressions among individuals of A. digitifera. Rows are the 51 PAPs with complete matches between presence–absence patterns and expression patterns. Columns indicate the expression levels (RPKM) of three samples

Fig. 4

Characteristics of PAPs and non-PAPs. The frequencies of PAPs that were uncharacterized (55%), characterized with the suffix “-like or prefix “probable-” (30%), and annotated (15%) (a) and non-PAP genes (b). Distribution of the homologous genes for PAPs (c) and non-PAP genes (d)