Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan.

Background: This paper describes two datasets: species occurrences, which were determined by environmental DNA (eDNA) metabarcoding and their associated DNA sequences, originating from a research project which was carried out along the Houdong River (), Jiaoxi Township, Yilan, Taiwan. The Houdong River begins at an elevation of 860 m and flows for approximately 9 km before it empties into the Pacific Ocean. Meandering through mountains, hills, plains and alluvial valleys, this short river system is representative of the fluvial systems in Taiwan. The primary objective of this study was to determine eukaryotic species occurrences in the riverine ecosystem through the use of the eDNA analysis. The second goal was, based on the current dataset, to establish a metabarcoding eDNA data template that will be useful and replicable for all users, particularly the Taiwan community. The species occurrence data are accessible at the Global Biodiversity Information Facility (GBIF) portal and its associated DNA sequences have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI, respectively. A total of 12 water samples from the study yielded an average of 1.5 million reads. The subsequent species identification from the collected samples resulted in the classification of 432 Operational Taxonomic Units (OTUs) out of a total of 2,734. Furthermore, a total of 1,356 occurrences with taxon matches in GBIF were documented (excluding 4,941 incertae sedis, accessed 05-12-2023). These data will be of substantial importance for future species and habitat monitoring within the short river, such as assessment of biodiversity patterns across different elevations, zonations and time periods and its correlation to water quality, land uses and anthropogenic activities. Further, these datasets will be of importance for regional ecological studies, in particular the freshwater ecosystem and its status in the current global change scenarios. New information: The datasets are the first species diversity description of the Houdong River system using either eDNA or traditional monitoring processes.

The observation records from whale and dolphin watching inshore of Hualien, eastern Taiwan.

Background: The eastern waters of Taiwan have been lacking baseline and research data for several years. This study was initiated by Kuroshio Ocean Education Foundation (KOEF) in collaboration with the Turumoan whale-watching company since 1998, collecting long-term ecological data for cetaceans in the inshore of Hualien, eastern Taiwan. This dataset includes 10,675 records of cetacean sightings from June 1998 to December 2021. Collection of cetacean sighting records was paused for one year in 2001 due to budgetary reasons. All of the sighting records were collected by whale-watching boat guides that were trained by KOEF. Following a standardised protocol, guides used a handheld GPS device and cetacean sighting record sheets to document information about the cetacean species identification, location, time, number of individuals, the presence of mother-calf pairs and mixed-species groups and other states of each sighting during a whale-watching tour. The collection of citizen-science data during this period has significantly advanced Taiwan's cetacean baseline data in the study area. Additionally, we make data available to the public in the form of citizen-science, making a substantial contribution to the advancement of ocean scientific research. We have published the dataset on Global Biodiversity Information Facility, allowing users around the world to download the dataset. New information: This is currently the largest dataset of cetacean sighting records in Taiwan (last updated on 2023-09-05). We have also recorded several species on the International Union for Conservation of Nature (IUCN) Red List categorised as "Data Deficient" during our survey inshore of Hualien, eastern Taiwan, including Ginkgo-toothed beaked whales (Mesoplodonginkgodens Nishiwaki & Kamiya, 1958), Omura's whales (Balaenopteraomurai Wada, Oishi & Yamada, 2003) and killer whales (Orcinusorca (Linnaeus, 1758)). There are also sperm whales (Physetermacrocephalus Linnaeus, 1758), categorised as "Vulnerable" in the IUCN Red List and false killer whales (Pseudorcacrassidens (Owen, 1846)), categorised as "Near Threatened". This study is also the first and only long-term study that has documented cetaceans in the study area.

Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization.

BACKGROUND: The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host. RESULTS: Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. CONCLUSIONS: The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts.

Prevalence, complete genome, and metabolic potentials of a phylogenetically novel cyanobacterial symbiont in the coral-killing sponge, Terpios hoshinota.

Terpios hoshinota is an aggressive, space-competing sponge that kills various stony corals. Outbreaks of this species have led to intense damage to coral reefs in many locations. Here, the first large-scale 16S rRNA gene survey across three oceans revealed that bacteria related to the taxa Prochloron, Endozoicomonas, SAR116, Ruegeria, and unclassified Proteobacteria were prevalent in T. hoshinota. A Prochloron-related bacterium was the most dominant and prevalent cyanobacterium in T. hoshinota. The complete genome of this uncultivated cyanobacterium and pigment analysis demonstrated that it has phycobiliproteins and lacks chlorophyll b, which is inconsistent with the definition of Prochloron. Furthermore, the cyanobacterium was phylogenetically distinct from Prochloron, strongly suggesting that it should be a sister taxon to Prochloron. Therefore, we proposed this symbiotic cyanobacterium as a novel species under the new genus Candidatus Paraprochloron terpiosi. Comparative genomic analyses revealed that 'Paraprochloron' and Prochloron exhibit distinct genomic features and DNA replication machinery. We also characterized the metabolic potentials of 'Paraprochloron terpiosi' in carbon and nitrogen cycling and propose a model for interactions between it and T. hoshinota. This study builds a foundation for the study of the T. hoshinota microbiome and paves the way for better understanding of ecosystems involving this coral-killing sponge.

A dataset of sea turtle occurrences around the Taiwan coast.

Background: We describe a dataset of sea turtle sightings around the coast of Taiwan and its islands (Hoh and Fong 2022). This data collection was initiated by TurtleSpot Taiwan, a citizen-science project that collects sea turtle sighting data. This dataset includes 3,515 sighting data dated from March 2010, except most of the data (n = 3,128; 89%) were collected between June 2017 to December 2021. Sightings were reported by citizen scientists to the Facebook Group of TurtleSpot Taiwan by providing occurrence information. We also requested photos and videos for species identification and to record any physical abnormality of the turtle, if observable. In addition to recording data often associated with an occurrence, TurtleSpot aims to identify each sea turtle up to the individual level using the Photo Identification (Photo ID) method. Hence, if photos of left facial scutes were available, the sighted individual can be identified and given a unique turtle ID. In total, 762 individuals were assigned a turtle ID, comprising 723 Greens (Cheloniamydas), 38 Hawksbills (Eretmochelysimbricata) and one Olive Ridley (Lepidochelysolivacea) turtle. This dataset is now publicly opened in Global Biodiversity Information Facility (GBIF) and available for download. It is hoped that the data may assist in future ecological studies and the development of conservation measures. New information: This dataset contains 3,515 occurrence records of sea turtles (Cheloniidae) and is currently the largest public dataset of sea turtle sighting records in Taiwan. Post-publication of this dataset to the GBIF platform demonstrated that the number of Green sea turtle Cheloniamydas records in Taiwan is one of the largest in the world (last accessed date: 15-10-2022). The data served as the foundation for understanding biogeography and sea turtle ecology in Taiwan's coastal waters.