Cross-Species Comparison

Headline statistics across Acropora pulchra, Porites evermanni, and Pocillopora tuahiniensis. Species are distinguished by colour and abbreviation labels throughout.

Interpret cross-species differences cautiously. Genome assembly quality varies substantially among the three taxa (see the reference genome quality table below and Methods), which affects transcript and interaction counts. Sequence conservation does not imply conserved regulatory function.

Reference genome quality

The three species were mapped to genome assemblies of differing contiguity and completeness. Assembly fragmentation (low N50) can fragment gene models and 3′/5′UTR annotation, which in turn affects miRNA-binding prediction and transcript/interaction counts. Treat cross-species differences in the tables below with this in mind. P. tuahiniensis reads were mapped to a congeneric P. meandrina assembly.

Species	Reference genome assembly	Genome size	Contig/scaffold N50	Protein-coding genes
A. pulchra	Acropora pulchra (Conn et al., 2025; GCA_044231415.1)	518 Mbp	17.8 Mbp	40,518
P. evermanni	Porites evermanni (Noel et al., 2023; GCA_942486025.1) · browser	497 Mbp	0.17 Mbp	40,389
P. tuahiniensis	Pocillopora meandrina (Stephens et al., 2022)	377 Mbp	10 Mbp	31,840

N50 is a contiguity metric: a higher value means the assembly is built from longer contiguous pieces. Values here span two orders of magnitude (P. evermanni ≈ 0.17 Mbp vs. A. pulchra ≈ 17.8 Mbp), so the P. evermanni assembly is substantially more fragmented. BUSCO completeness and assembly level are reported in each source publication (see Methods & Caveats).

Acropora pulchra

Apul · 40,518 protein-coding genes

miRNAs: 39
lncRNAs: 31,491
Global CpG methylation: 9.92%
Predicted miRNA–mRNA interactions: 49,220
Sig. coexpressed miRNA–mRNA (p<0.05): 2,222
Predicted miRNA–lncRNA interactions: 564
Putative ceRNA lncRNAs: 117
Epi-miRNA target pairs: 35
Mean prop. positive targets: 0.68

Porites evermanni

Peve · 40,389 protein-coding genes

miRNAs: 45
lncRNAs: 10,090
Global CpG methylation: 7.24%
Predicted miRNA–mRNA interactions: 24,055
Sig. coexpressed miRNA–mRNA (p<0.05): 1,267
Predicted miRNA–lncRNA interactions: 175
Putative ceRNA lncRNAs: 41
Epi-miRNA target pairs: 15
Mean prop. positive targets: 0.49

Pocillopora tuahiniensis

Ptuh · 31,840 protein-coding genes

miRNAs: 37
lncRNAs: 16,153
Global CpG methylation: 4.04%
Predicted miRNA–mRNA interactions: 17,523
Sig. coexpressed miRNA–mRNA (p<0.05): 902
Predicted miRNA–lncRNA interactions: 564
Putative ceRNA lncRNAs: 161
Epi-miRNA target pairs: 16
Mean prop. positive targets: 0.53

Comparative charts

miRNA count

miRNA count
Series	Value
A. pulchra	39
P. evermanni	45
P. tuahiniensis	37

lncRNA count

lncRNA count
Series	Value
A. pulchra	31,491
P. evermanni	10,090
P. tuahiniensis	16,153

Global CpG methylation

Aggregated across all samples (WGBS).

Global CpG methylation
Series	Value (%)
A. pulchra	9.92
P. evermanni	7.24
P. tuahiniensis	4.04

Putative ceRNA lncRNAs

A small fraction of the total lncRNAs (see lncRNA count); most lncRNAs were not predicted to act as ceRNAs.

Putative ceRNA lncRNAs
Series	Value
A. pulchra	117
P. evermanni	41
P. tuahiniensis	161

Epi-miRNA target pairs

Epi-miRNA target pairs
Series	Value
A. pulchra	35
P. evermanni	15
P. tuahiniensis	16

Mean per-miRNA proportion of positively coexpressed targets

A. pulchra miRNAs trend toward more positive target coexpression.

Mean per-miRNA proportion of positively coexpressed targets
Series	Value
A. pulchra	0.68
P. evermanni	0.49
P. tuahiniensis	0.53

Predicted binding region distribution

Counts of predicted miRNA-binding edges by region in the significantly coexpressed (p<0.05) network. A. pulchra miRNAs are more CDS-biased.

Species	CDS	5′UTR	3′UTR	lncRNA
A. pulchra	1,739	217	266	564
P. evermanni	835	224	208	175
P. tuahiniensis	499	200	203	564

Epi-miRNA target categories

Category	A. pulchra	P. evermanni	P. tuahiniensis
DNA methylation & reading	2	1	0
Histone modification & variants	5	2	5
Chromatin signaling	4	1	0
Ubiquitin signaling	8	6	3
RNA modification	6	0	1
ncRNA biogenesis & silencing	6	5	7
ADP-ribosylation	4	0	0

miR-100 comparison

miR-100 is one of four miRNAs conserved across all three species. Its target coexpression is starkly species-divergent: almost exclusively negative in A. pulchra and P. tuahiniensis, but almost entirely positive in P. evermanni. Sequence conservation does not imply conserved regulatory function.

A. pulchra · miR-100

negative

Interactions (p<0.05): 215
Positive / negative: 8 / 207
mRNA / lncRNA targets: 176 / 39
CDS / UTR binding: 148 / 28

Epi-machinery targets:

USP31 (Ubiquitin signaling, negative)
TRMT1 (RNA modification, negative)

Enriched functions: metabolic & transport processes; lipid and amino acid handling; expression regulation.

P. evermanni · miR-100

positive

Interactions (p<0.05): 325
Positive / negative: 320 / 5
mRNA / lncRNA targets: 269 / 56
CDS / UTR binding: 210 / 59

Epi-machinery targets:

UBE3A (Ubiquitin signaling, positive)

Enriched functions: immune & signaling pathways; toll-like receptor signaling; calcium ion binding.

P. tuahiniensis · miR-100

negative

Interactions (p<0.05): 96
Positive / negative: 11 / 85
mRNA / lncRNA targets: 65 / 31
CDS / UTR binding: 51 / 14

Epi-machinery targets: none recovered

Enriched functions: calcium ion binding.

Interaction, direction, and binding counts are computed from the loaded p<0.05 network; epi-machinery targets and enriched functions are from the manuscript (Results, Table 2). Emphasis: conserved sequence ≠ conserved regulatory function.

Methylation & conserved orthogroups

109orthogroups methylated in all three

1,507A. pulchra uniquely methylated orthogroups

1,518P. evermanni uniquely methylated orthogroups

226P. tuahiniensis uniquely methylated orthogroups