Recombinant Mitochondrial Genomes Reveal Recent Interspecific Hybridization between Invasive Salangid Fishes.

The interspecific recombination of the mitochondrial (mt) genome, if not an experimental artifact, may result from interbreeding of species with broken reproductive barriers, which, in turn, is a frequent consequence of human activities including species translocations, habitat modifications, and climate change. This issue, however, has not been addressed for Protosalanx chinensis and other commercially important and, simultaneously, invasive salangid fishes that were the product of successful aquaculture in China. To assess the probability of interspecific hybridization, we analyzed the patterns of diversity and recombination in the complete mitochondrial (mt) genomes of these fishes using the GenBank resources.

Multiple bacterial partners in symbiosis with the nudibranch mollusk Rostanga alisae.

The discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host's ecology. Of particular interest are nudibranchs that unprotected by a shell and feed mainly on sponges. The symbiotic association of the nudibranch Rostanga alisae with bacteria was supported by ample evidence, including an analysis of cloned bacterial 16S rRNA genes and a fluorescent in situ hybridization analysis, and microscopic observations.

Genetic Evidence for a Mixed Composition of the Genus (Cottoidei: Cottidae) Necessitates Generic Realignment.

Sculpin fishes belonging to the family Cottidae represent a large and complex group, inhabiting a wide range of freshwater, brackish-water, and marine environments. Numerous studies based on analysis of their morphology and genetic makeup frequently provided controversial results. In the present work, we sequenced complete mitochondrial (mt) genomes and fragments of nuclear ribosomal DNA (rDNA) of the fourhorn sculpin and some related cottids to increase the power of phylogenetic and taxonomic analyses of this complex fish group.

Complete mitochondrial genome of the Belligerent sculpin Megalocottus platycephalus (Cottoidei: Cottidae).

The complete mitochondrial (mt) genome was sequenced in two specimens of the Belligerent sculpin by high-throughput sequencing technology (Ion S5 platform). The sequences are 16,673 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mt genomes published previously. Comparison of the two mt genomes now obtained with other complete mt genomes available in GenBank reveals an affinity to the sculpin fishes from the genus .

Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins.

Mitochondrial (mt) genomes of the sea urchins and demonstrate the identical patterns of intraspecific length variability of the gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only.

Complete mitochondrial genome of the great sculpin (Cottoidei: Cottidae).

The complete mitochondrial genome was sequenced in two specimens of the great sculpin by high-throughput sequencing technology (Ion S5 platform). The genome sequences are 16,651 and 16,652 bp in size, and the gene arrangement, composition, and size are similar to the other sculpin mitochondrial genomes published previously. Overall base composition of the complete mitochondrial DNA is A (26.

Complete mitochondrial genome of the surf smelt (Osmeriformes, Osmeridae).

The complete mitochondrial genome was sequenced in two individuals of the surf smelt . The genome sequences are 16,762 and 16,771 bp in size, and the gene arrangement, composition, and size are very similar to the other smelt mitochondrial genomes published previously. The difference between two genomes studied is 0.

Complete mitochondrial genome of the Arctic rainbow smelt (Osmeriformes, Osmeridae).

The complete mitochondrial genome was sequenced in two individuals of the Arctic rainbow smelt . The genome sequences are 16,615 and 16,616 bp in size, and the gene arrangement, composition, and size are very similar to the other smelt mitochondrial genomes published previously. The difference between the two genomes studied is 0.

Complete mitochondrial genome of the European smelt (Osmeriformes, Osmeridae).

The complete mitochondrial (mt) genome was sequenced in two individuals of the European smelt . The genome sequences are 16,608 and 16,609 bp in size, and the gene arrangement, composition, and size are very similar to the other smelt mt genomes previously published. The difference between the two genomes studied is low, 0.

Complete Mitochondrial Genomes of the Cherskii's Sculpin and Siberian Taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome.

The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii's sculpin . A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of studied here and the GenBank mt genome of (KJ956027).

Complete mitochondrial genome of the phenotypically-diverse sea urchin (Strongylocentrotidae, Echinoidea).

The complete mitochondrial genomes are sequenced in two individuals representing two morphological forms, 'usual' (U) and 'gray' (G), of the short-spined sea urchin . The genome sequences are 15,705 bp in size, and the gene arrangement, composition, and size are very similar to the other sea urchin mitochondrial genomes published previously. A low level of sequence divergence (  = 0.

Complete mitochondrial genome of the Sakhalin sculpin (Cottoidei: Cottidae).

The complete mitochondrial genome was sequenced in two individuals of the Sakhalin sculpin . The genome sequences are 16,526 and 16,527 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mitochondrial genomes published previously. The difference between the two genomes studied is low, 0.

Complete mitochondrial genome of the Volk's sculpin (Cottoidei: Cottidae).

The complete mitochondrial genome was sequenced in two individuals of the Volk's sculpin . The genome sequences are 16,519 and 16,536 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mitochondrial genomes published previously. The difference between the two genomes studied is relatively high, 3.

Complete mitochondrial genome of the Amur sculpin (Cottoidei: Cottidae).

The complete mitochondrial genome was sequenced in two individuals of the Amur sculpin . The genome sequences are 16,518 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin genomes published previously. The low level of sequence divergence detected between the genome of and the GenBank complete mitochondrial genome of the Cherskii's sculpin (KJ956027) may likely be due to recent divergence, historical hybridization, or presence of a new unrecognized taxonomic unit close to but erroneously identified as .

DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea).

Background: The sperm gene bindin encodes a gamete recognition protein, which plays an important role in conspecific fertilization and reproductive isolation of sea urchins. Molecular evolution of the gene has been extensively investigated with the attention focused on the protein coding regions. Intron evolution has been investigated to a much lesser extent.

Complete mitochondrial genome of the yellow-spotted grayling (Salmoniformes, Salmonidae).

The complete mitochondrial genome was sequenced in two individuals of yellow-spotted grayling . The genome sequences are 16,659 bp in size, and the gene arrangement, composition and size are very similar to the salmonid fish genomes published previously. The low level of sequence divergence detected between the genome of and the GenBank complete mitochondrial genomes of the (KJ866484) and (KF649073) may likely be due to recent divergence of the species and/or historical hybridization and interspecific replacement of mtDNA.

Complete mitochondrial genome of the stone char (Salmoniformes, Salmonidae).

The complete mitochondrial genome was sequenced in two individuals of stone char . The genome sequences are 16,654 bp in size, and the gene arrangement, composition and size are very similar to the salmonid fish genomes published previously. The low level of sequence divergence detected between the genome of and the GenBank complete mitochondrial genomes of the white char (KT266870 and KT266871), the Northern Dolly Varden char (KJ746618) and the Arctic char (AF154851) may likely be due to recent divergence and/or historical hybridization and interspecific replacement of mtDNA.

Complete mitochondrial genome of the Kamchatka grayling Thymallus mertensii (Salmoniformes, Salmonidae).

The complete mitochondrial genome was sequenced in two individuals of the Kamchatka grayling Thymallus mertensii. The genome sequences are 16 662 bp in size, and the gene arrangement, composition, and size are very similar to the salmonid fish genomes published previously. The low level of sequence divergence (0.

Complete mitochondrial genome of the white char Salvelinus albus (Salmoniformes, Salmonidae).

The complete mitochondrial genome was sequenced in two individuals of white char Salvelinus albus. The genome sequences are 16 653 bp in size, and the gene arrangement, composition, and size are very similar to the salmonid fish genomes published previously. The low level of sequence divergence detected between the genome of S.

Complete mitochondrial genomes of the anadromous and resident forms of the lamprey Lethenteron camtschaticum.

The complete mitochondrial genomes were sequenced in anadromous and resident forms of the lamprey Lethenteron camtschaticum. The sizes of the genomes in the two isolates are 16,245 and 16,295 bp. The gene arrangement, base composition, and size of the two sequenced genomes are similar to the lamprey genomes previously published.

Complete mitochondrial genome of Sakhalin taimen Parahucho perryi (Salmoniformes, Salmonidae) without two frame-disrupting indels in the ND4 gene.

The complete mitochondrial genome was sequenced in two individuals of Sakhalin taimen Parahucho perryi. The genome sizes were 16,652 bp and 16,653 bp in the two isolates. Gene arrangement, base composition, and size of the two sequenced haplotypes are very similar to the P.

Complete mitochondrial genomes of the Northern (Salvelinus malma) and Southern (Salvelinus curilus) Dolly Varden chars (Salmoniformes, Salmonidae).

The complete mitochondrial genomes were sequenced from the Northern and Southern Dolly Varden chars, Salvelinus malma and S. curilus. The genome sequences are 16,654 bp in size in both species, and the gene arrangement, composition, and size are very similar to the salmonid fish genomes published previously.

Complete mitochondrial genome of blunt-snouted lenok Brachymystax tumensis (Salmoniformes, Salmonidae).

The complete mitochondrial genomes were sequenced in two individuals of blunt-snouted lenok Brachymystax tumensis. The sizes of the genomes in the two isolates were 16,754 and 16,836; the difference was due to variable number of repeat sequences within the control region. The gene arrangement, base composition, and size of the two sequenced genomes are very similar to the B.

Complete mitochondrial genome of Siberian taimen, Hucho taimen not introgressed by the lenok subspecies, Brachymystax lenok and B. lenok tsinlingensis.

The complete mitochondrial genomes were sequenced in two individuals of Siberian taimen Hucho taimen. The sizes of the genomes were 16,833 and 16,914 in the two isolates, representing two haplotype groups previously detected. The gene arrangement, base composition, and size of the two sequenced genomes are very similar to the H.

Computational methods of identification of pseudogenes based on functionality: entropy and GC content.

Spectral entropy and GC content analyses reveal comprehensive structural features of DNA sequences. To illustrate the significance of these features, we analyze the β-esterase gene cluster, including the Est-6 gene and the ψEst-6 putative pseudogene, in seven species of the Drosophila melanogaster subgroup. The spectral entropies show distinctly lower structural ordering for ψEst-6 than for Est-6 in all species studied.