Michael Sweet

Global syntheses of 16S rRNA metabarcoding data rely on combining datasets, yet amplicon sequence variants generated with different primer pairs can rarely be compared directly. Existing approaches correct batch effects statistically or aggregate taxonomically; none first establishes whether the sequences are positionally comparable. We present SeCAT (Sequence Consensus Amplicon Trimming), a Nextflow pipeline that maps every study’s variants onto a 16S rRNA full-length reference alignment, determines the largest window shared across studies, and tests by simulation whether trimming to that window degrades community structure before any data are merged. Applied to thirteen marine studies sequenced with three primer sets, twelve converged on a consensus window with a median trimmed read length of 249 bp (9,582 alignment columns). Degradation tests across twelve studies and six taxonomic ranks (72 study-rank combinations) returned 31 passes, 38 cautions and three confirmed failures. Eleven studies (682 samples after filtering) were harmonised (trimmed to the window and merged), collapsing 20,891 primer-specific variants into 12,667 MetaASVs, trimmed sequences deduplicated across studies. Harmonisation preserved community structure at family level (Mantel r = 1.00; Procrustes mZ < 0.001) without adding between-study variance (|ΔRZ| < 0.001). Alpha diversity, including observed richness, was recovered across all levels (intraclass correlations 0.93–1.00), whereas sequence-level congruence was moderate (Procrustes mZ = 0.52), as expected where between-study similarity at sequence level exists only after harmonisation. The harmonised output supports synthesis from aggregated ranks down to exact sequences. By establishing positional comparability before merging, SeCAT opens the archive of primer-fragmented 16S rRNA surveys to sequence-level synthesis.

Coral reefs are diverse marine ecosystems that provide ecological functions and economic and social benefits across over 100 tropical countries. Warming driven by climate change is a primary threat to coral reefs and is increasing the frequency of global coral bleaching events. Here we reassessed the IUCN Red List status of 892 reef-building coral species, first assessed in 2008 ¹. Because species-level population trends are unavailable for most reef-building corals, population reductions were inferred using proxies based on global coral cover trends and projected annual severe bleaching under SSP2-4.5, both over three decades, adjusted using trait-based estimates of species vulnerability. Of the 774 species with sufficient data to be assessed, 340 (44%) were classified as threatened under IUCN Red List criteria. Thirty-three species were assessed as Critically Endangered, 251 as Endangered, and 56 as Vulnerable, most due to risk of population reduction associated with projected thermal stress. These findings predate the three hottest years on record and the fourth global coral bleaching event (2023-2025), and the first exceedance for an annual mean of the 1.5^oC global warming threshold. The findings reinforce the importance of limiting further warming to maintain coral biodiversity and reef ecosystem function. The Red List assesses the relative extinction risk of species, whereby species are placed in categories of increasing risk by comparing their population size, decline and geographic range against standardised thresholds. The Red List does not predict whether or when a species may go extinct. As the ranges of coral species remain under-surveyed, future assessments would be strengthened by species-level population data and thermal-stress and recovery metrics that better capture range-representative dynamics.

We present a genome assembly from a specimen of Siderastrea siderea (massive starlet coral; Cnidaria; Anthozoa; Scleractinia; Rhizangiidae). The genome sequence has a total length of 831.10 megabases. Most of the assembly (97.77%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.39 kilobases. Gene annotation of this assembly by Ensembl identified 36,569 protein-coding genes.

We present a genome assembly from a specimen of Montipora capitata (rice coral; Cnidaria; Anthozoa; Scleractinia; Acroporidae). The genome sequence has a total length of 689.31 megabases. Most of the assembly (99.26%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.87 kilobases. Gene annotation of this assembly by Ensembl identified 44 675 protein-coding genes.

We present a genome assembly from a specimen of Orbicella franksi (boulder star coral; Cnidaria; Anthozoa; Scleractinia; Merulinidae). The genome sequence has a total length of 496.97 megabases. Most of the assembly (95.24%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.08 kilobases. Gene annotation of this assembly by Ensembl identified 28 996 protein-coding genes.

We present a genome assembly from a specimen of Acropora cervicornis (staghorn coral; Cnidaria; Anthozoa; Scleractinia; Acroporidae). The genome sequence has a total length of 328.68 megabases. Most of the assembly (99.07%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.26 kilobases. Gene annotation of this assembly by Ensembl identified 24,579 protein-coding genes. From the metagenome data, we recovered two bins, of which one was a high-quality MAG.

We present a genome assembly from a colony sample of Acropora cf. manni (staghorn coral; Cnidaria; Anthozoa; Scleractinia; Acroporidae). The assembly contains two haplotypes with total lengths of 459.26 megabases and 489.30 megabases. Most of haplotype 1 (94.39%) is scaffolded into 14 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 18.48 kilobases. Metagenome binning recovered one bacterial bin from the phylum Chlamydiota.

We present a genome assembly from a specimen of Siderastrea radians (lesser starlet coral; Cnidaria; Anthozoa; Scleractinia; Rhizangiidae). The genome sequence has a total length of 807.19 megabases. Most of the assembly (94.17%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.38 kilobases. Gene annotation of this assembly by Ensembl identified 47 051 protein-coding genes. From the metagenome data, we recovered two binned metagenomes assigned to the bacterial phylum Bacteroidota and class Bacteroidia.

We present a genome assembly from a specimen of Meandrina meandrites (maze coral; Cnidaria; Anthozoa; Scleractinia; Meandrinidae). The genome sequence has a total length of 551.16 megabases. Most of the assembly (99.25%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.2 kilobases. Gene annotation of this assembly by Ensembl identified 30 464 protein-coding genes. We recovered two bins from the metagenome data.