Seq’ and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs

Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems

Seq’ and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs

Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems

DESIGNING PHYLOGENOMIC TOOLS TO DISENTANGLE THE EVOLUTION OF STONY CORALS

Ph.DDOCTOR OF PHILOSOPHY (FOS

Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia)

10.1016/j.ympev.2019.01.012Molecular Phylogenetics and Evolution13412-2

Complete mitochondrial genome of the sea star Archaster typicus (Asteroidea: Archasteridae)

10.1080/23802359.2019.1666676Mitochondrial DNA Part B423130-313

Complete mitochondrial genome of the sea star Archaster typicus (Asteroidea: Archasteridae)

The complete mitochondrial genome of the widespread and common Indo-Pacific sea star Archaster typicus has been sequenced in this study. The mitogenome is 16,230 base pairs (bp) in length, with 13 protein coding genes (PCGs), 22 tRNAs and 2 rRNAs. Gene order of its PCGs and rRNAs matches those of nine other asteroid taxa included for comparison in this study, and it has a similar nucleotide composition of 33.08% A, 26.38% T, 25.53% C and 15.01% G nucleotides. Phylogenetic analyses place A. typicus as the sister group to Acanthaster spp., consistent with previous inferences

Autecology of the common fishtail palm, Caryota mitis (Arecaceae), in Singapore

10.1080/23818107.2020.1717612Botany Letters16702265-27

Phylogeny and morphology of Himerometroidea (Echinodermata: Crinoidea) feather stars in Singapore

Evaluating the diversity of crinoids (Echinodermata: Crinoidea) in Singapore accurately has been challenging due in part to inadequacies in crinoid taxonomy. Most species descriptions have neither incorporated morphological variation of juveniles into diagnostic characters nor analysed species’ molecular phylogenetic affinities. In this study, we performed detailed morphological examination and phylogenetic analyses of the mitochondrial cytochrome c oxidase subunit I marker on Himerometroidea crinoids collected from the Singapore Strait, and showed that specimens could not be reliably identified to species based on existing taxonomic descriptions. Specifically, juveniles identified as Heterometra spp. and Zygometra sp., and adults as H. cf. producta, solely based on morphological features were revealed to comprise three distinct species: Zygometra cf. comata, Heterometra schlegelii, and Dichrometra sp. The juveniles were found to have sizes smaller than the ranges given in existing descriptions, with considerable variabilities in traits that limited the utility of morphology for species taxonomy. Features contributing to misidentification of specimens and their application in past species diagnoses are discussed. Revised descriptions of these species, as well as the recently revised Homalometra crenulata, are also presented. More broadly, this study emphasises the need to revisit diagnoses of crinoid species according to various ontogenetic stages and to uncover more congruent morphological characters based on a robust molecular phylogeny

Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms

10.1093/molbev/msaa262Molecular Biology and Evolution383981-98

Spirobranchus bakau sp. nov. from Singapore: yet another species of S. kraussii-complex (Polychaeta: Serpulidae)

10.11646/zootaxa.5040.1.2ZOOTAXA5040133-6