Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology.

Pacific saury (Cololabis saira) is a commercially important small pelagic fish species in Asia. In this study, we conducted the first-ever whole genome sequencing of this species, with single molecule, real-time (SMRT) sequencing technology. The obtained high-fidelity (HiFi) long-read sequence data, which amount to ~30-folds of its haploid genome size that was measured with quantitative PCR (1.17 Gb), were assembled into contigs. Scaffolding with Hi-C reads yielded a whole genome assembly containing 24 chromosome-scale sequences, with a scaffold N50 length of 47.7 Mb. Screening of repetitive elements including telomeric repeats was performed to characterize possible factors that need to be resolved towards 'telomere-to-telomere' sequencing. The larger genome size than in medaka, a close relative in Beloniformes, is at least partly explained by larger repetitive element quantity, which is reflected in more abundant tRNAs, in the Pacific saury genome. Protein-coding regions were predicted using transcriptome data, which resulted in 22,274 components. Retrieval of Pacific saury homologs of aquaporin (AQP) genes known from other teleost fishes validated high completeness and continuity of the genome assembly. These resources are available at https://treethinkers.nig.ac.jp/saira/ and will assist various molecular-level studies in fishery science and comparative biology.

Development of the caudal-fin skeleton reveals multiple convergent fusions within Atherinomorpha.

BACKGROUND: The caudal fin of teleosts is a highly diverse morphological structure and a valuable source of information for comparative analyses. Within the Atherinomorpha a high variation of conditions of the caudal-fin skeleton can be found. These range from complex but basal configurations to simple yet derived configurations. When comparing atherinomorph taxa, it is often difficult to decide on the homology of skeletal elements if only considering adult specimens. However, observing the development of caudal-fin skeletons allows one to evaluate complex structures, reveal homologies and developmental patterns, and even reconstruct the grundplan of the examined taxa. RESULTS: We studied the development of the caudal-fin skeleton in different atheriniform, beloniform and cyprinodontiform species using cleared and stained specimens. Subsequently we compared the development to find similarities and differences in terms of 1) which structures are formed and 2) which structures fuse during ontogeny. For many structures, i.e., the parhypural, the epural(s), the haemal and neural spines of the preural centra and the uroneural, there were either no or only minor differences visible between the three taxa. However, the development of the hypurals revealed a high variation of fusions within different taxa that partly occurred independently in atheriniforms, beloniforms and cyprinodontiforms. Moreover, comparing the development of the ural centra exposed two ways of formation of the compound centrum: 1) in atheriniforms and the beloniforms Oryzias and Hyporhamphus limbatus two ural centra develop and fuse during ontogeny while 2) in cyprinodontiforms and Exocoetidae (Beloniformes) only a single ural centrum is formed during ontogeny. CONCLUSIONS: We were able to reconstruct the grundplan of the developmental pattern of the caudal-fin skeleton of the Atheriniformes, Beloniformes and Cyprinodontiformes as well as their last common ancestors. We found two developmental modes of the compound centrum within the Atherinomorpha, i.e., the fusion of two developing ural centra in atheriniforms and beloniforms and the development of only one ural centrum in cyprinodontiforms. Further differences and similarities for the examined taxa are discussed, resulting in the hypothesis that the caudal-fin development of a last common ancestor to all atherinomorphs is very much similar to that of extant atheriniforms.

Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae).

Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study, we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using micro-computed tomographic (µCT) scanning and geometric morphometrics, we quantified body shape, size, and vertebral counts of 31 belonid species. We then examined the pattern and tempo of body shape and size evolution using phylogenetic comparative methods. Our results show that transitions from marine to freshwater habitats have altered the adaptive landscape for needlefishes and expanded morphospace relative to marine taxa. We provide further evidence that freshwater taxa attain reduced sizes either through dwarfism (as inferred from axial skeletal reduction) or through developmental truncation (as inferred from axial skeletal loss). We propose that transitions to freshwater habitats produce morphological novelty in response to novel prey resources and changes in locomotor demands. We find that repeated invasions of different habitats have prompted predictable changes in morphology.

The complete mitochondrial genome of the Pacific needlefish Strongylura anastomella (Belonidae, Beloniformes) from Korea.

Belonidae is a good model for investigating speciation and biogeography. To obtain basic information on the phylogeny of Belonidae, we determined the complete mitogenome of Strongylura anastomella using next-generation sequencing. The complete mitogenome is 16,534 bp in length and consists of 2 rRNAs, 22 tRNAs, 13 protein-coding genes and a control region. The nucleotide composition is 31.1% A, 29.8% T, 14.5% G and 24.6% C, with an AT bias (60.9%). The gene direction and position were similar to those of other Beloniformes. Belonidae and Scomberesocidae were separated in the phylogenetic tree based on complete mitogenomes. Further study is required to clarify the phylogenetic relationships among Belonidae and families within Beloniformes.

Complete mitochondrial genome of the Korean flying fish Cheilopogon doederleinii (Beloniformes, Exocoetidae): mitogenome characterization and phylogenetic analysis.

The Korean flying fish, Cheilopogon doederleinii, is a marine fish species belonging to the family Exocoetidae. In this study, I report for the first time the sequencing and assembly of the complete mitochondrial genome of C. doederleinii. The complete mitochondrial genome is 16,525 bp long and includes 13 protein-coding, 22 tRNA, and 2 rRNA genes. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 10 species showed that C. doederleinii is clustered with C. arcticeps and grouped with the other Exocoetidae species. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution.