Long-read sequencing and genome assembly of natural history collection samples and challenging specimens.

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assembled the 3.

Improved species assignments across the entire genus using targeted sequencing.

Accurate species identification of the mosquitoes in the genus is of crucial importance to implement malaria control measures and monitor their effectiveness. We use a previously developed amplicon panel (ANOSPP) that retrieves sequence data from multiple short nuclear loci for any species in the genus. Species assignment is based on comparison of samples to a reference index using -mer distance.

Single candidate gene for salt tolerance of (Ohwi) Ohwi & Ohashi identified by QTL mapping, whole genome sequencing and triplicated RNA-seq analyses.

Salt tolerance has been an important issue as a solution for soil salinization and groundwater depletion. To challenge this issue, genetic diversity of wild plants must be harnessed. Here we report a discovery of a candidate gene for salt tolerance in , one of the coastal species in the genus .

Cost-efficient PCR based DNA barcoding of marine invertebrate specimens with NovaSeq amplicon sequencing.

Background: The marine environment harbors high biodiversity; however, it is poorly understood. Nucleotide sequence data of all marine organisms should be accumulated before natural and/or anthropogenic environmental changes jeopardize the marine environment. In this study, we report a cost-effective and easy DNA barcoding method.

Mitochondrial metagenomics reveal the independent colonization of the world's coasts by intertidal oribatid mites (Acari, Oribatida, Ameronothroidea).

Oribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.

Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species (Thelypteridacea, Polypodiales).

Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern--and its diploid parental species, () and ().

Complete Genome Sequence of , filamentous colony-making Chroococcales with the analysis of FraC gene influencing filament integrity.

The complete genome of was sequenced. The genome size is 4.02 Mbp, including 3886286 bp circular chromosome and four circular plasmids (31516, 42453, 38085 and 24903 bp).

DNA metabarcoding focusing on the plankton community: an effective approach to reconstruct the paleo-environment.

DNA metabarcoding (DNA-MB) targeting the whole plankton community is a promising approach in studies of sediment samples from water bodies, but its effectiveness in ancient material is not well demonstrated. We applied DNA-MB of plankton in a sediment core to reconstruct the paleo-environment of Lake Shinji, Japan, through a marine lagoon/freshwater lake transition during the past 2300 years. We interpreted core-sample plankton taxonomy and habitat by reference to the modern plankton community in water samples.

DNA metabarcoding focused on difficult-to-culture protists: An effective approach to clarify biological interactions.

DNA metabarcoding on a single organism is a promising approach to clarify the biological interactions (e.g., predator-prey relationships and symbiosis, including parasitism) of difficult-to-culture protists.

Development of a High-Quality/Yield Long-Read Sequencing-Adaptable DNA Extraction Method for Crop Seeds.

Genome sequencing is important for discovering critical genes in crops and improving crop breeding efficiency. Generally, fresh, young leaves are used for DNA extraction from plants. However, seeds, the storage form, are more efficient because they do not require cultivation and can be ground at room temperature.

Phosphate starvation response precedes abscisic acid response under progressive mild drought in plants.

Drought severely damages crop production, even under conditions so mild that the leaves show no signs of wilting. However, it is unclear how field-grown plants respond to mild drought. Here, we show through six years of field trials that ridges are a useful experimental tool to mimic mild drought stress in the field.

Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat.

Common buckwheat, Fagopyrum esculentum, is an orphan crop domesticated in southwest China that exhibits heterostylous self-incompatibility. Here we present chromosome-scale assemblies of a self-compatible F. esculentum accession and a self-compatible wild relative, Fagopyrum homotropicum, together with the resequencing of 104 wild and cultivated F.

Two new species of the bathyal holothurian genus Pannychia (Elasipodida, Laetmogonidae) from Japanese waters.

Sea cucumbers are one of the most common large animals in the deep-sea benthic communities, and those of the genus Pannychia are particularly abundant in the bathyal North Pacific Ocean. In Japanese waters, three species of Pannychia have been reported, mainly from the northern and eastern parts of the country. Here, we describe two new species from the western part of Japan.

Complete chloroplast and mitochondrial genomes of Kindb. (Ditrichaceae, Bryophyta).

The moss family Pottiaceae is one of the most diverse lineages of the subclass Dicranidae (haplolepideous mosses). Nevertheless, the phylogenetic relationships of Pottiaceae with other Dicranidae families remain unclear. To better understand the ancestral genomic structure and evolution of the Pottiaceae, herein, we present the chloroplast and mitochondrial genomes of (Ditrichaceae, Bryophyta).

Systematic position of the genus Metacanthocephalus Yamaguti, 1959 (Palaeacanthocephala: Echinorhynchida) inferred from molecular evidence, with a redescription of Metacanthocephalus ovicephalus (Zhukov, 1960).

The familial affiliation of the echinorhynchid palaeacanthocephalan genus Metacanthocephalus has been uncertain, with the three families Echinorhynchidae, Leptorhynchoididae, and Rhadinorhynchidae having been suggested as its parent taxon. In this study, adult individuals of Metacanthocephalus ovicephalus from the intestine of the cresthead flounder Pseudopleuronectes schrenki (new host) and the dark flounder Pseudopleuronectes obscurus in Hokkaido, Japan, were examined. Using three gene markers (mitochondrial cytochrome c oxidase subunit I; nuclear 18S and 28S rRNA genes) determined from two specimens of M.

Mite secretions from three traditional mite-ripened cheese types: are ripened French cheeses flavored by the mites (Acari: Astigmata)?

The opisthonotal glands of Astigmata contain monoterpenes, aromatics, aliphatics, and other volatile compounds; some of these compounds act as pheromones and have antifungal effects. This study analyzed volatile compounds secreted by mites on three traditional mite-ripened cheeses from producers (Milbenkäse from Germany, Mimolette and Artisou from France). The mites obtained from various traditional ripened French cheeses (Mimolette, Laguiole, Salers, and Cantal vieux) from stores were also investigated.

Complete mitochondrial genome of a sea cucumber, (Echinodermata, Holothuroidea, Apodida, Synaptidae).

We determined the complete mitochondrial genome sequence of a holothurian belonging to the order Apodida. The complete mitogenome of was 16,410 bp in length and consisted of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The orders of PCGs and rRNAs did not match those of any recorded holothurian mitogenomes.

Do 'cheese factory-specific' mites (Acari: Astigmata) exist in the cheese-ripening cabinet?

To determine whether the mites used in the ripening process of traditional cheeses are genetically unique to cheese factories, we investigated mites from three types of traditional cheeses, that use mites in the ripening process: 'Würchwitzer Milbenkäse' from Germany and 'Mimolette' and 'Artisou' from France. In addition, traditional ripened cheeses were purchased from cheese specialty stores in France (Mimolette) and Japan ('Laguiole' from France) as well as stores in temporary markets in France ('Salers' and 'Cantal vieux') and the mites obtained from those cheeses were analyzed in this study. Partial sequences of the 28S rRNA gene (28S) were determined and used to reconstruct a phylogenetic tree.

A New Species of the Anchovy Genus Lacepède 1803 from North Sumatra, Indonesia, and Redescriptions of Baldwin 1984 and Kimura, Hori and Shibukawa 2009 (Teleostei: Clupeiformes: Engraulidae).

sp. nov. is described here, and and are redescribed.

Complete mitochondrial genomes of two snail mite: and (Acariformes, Prostigmata, Ereynetidae).

We determined the mitochondrial genome sequences of two snail mites, and . The length of the entire mitogenome of these two species is 15,078 bp and 15,148 bp long, respectively. Both of them contain 13 proteins, two rRNAs, and 22 tRNAs for a total of 37 gene products.

Genome Assembly of Stinkhorn Mushroom (Basidiomycota, Fungi) Using Illumina and Nanopore Sequencing Data.

We report the reference genome of isolate MO-923, which was isolated from Chichijima Island, the Ogasawara (Bonin) Islands, Japan. Oxford Nanopore Technologies MinION and Illumina sequence reads were assembled using NECAT and polished using Pilon to yield a 36.51-Mb genome with 10,625 predicted protein-coding genes.

Patterns of diversification of the operculate land snail genus Cyclophorus (Caenogastropoda: Cyclophoridae) on the Ryukyu Islands, Japan.

The Ryukyu Islands, an island chain in southwestern Japan, originated from land masses that separated from the Eurasian continent due to the formation of sea barriers about 1.55 million years ago. In this study, we investigated the phylogenetic relationships of the operculate land snail genus Cyclophorus (Caenogastropoda: Cyclophoridae) in the Ryukyu Archipelago and surrounding regions based on DNA sequence data.