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Simple Summary: The present study aimed to characterize the complete mitochondrial genome of Streptopelia decaocto (Frivaldszky, 1838) and investigated the evolutionary relationships among species within the Columbidae family. The mtDNA full sequence length of S. decaocto was 17,160 bp. The mitogenome of S. decaocto comprised 13 PCGs, 22 tRNA genes, 2 rRNA genes, non-coding regions, and a control region. Analysis of the entire mtDNA of S. decaocto revealed consistently positive AT-skew values, except for nad3, nad6, and the D-loop. Conversely the GC-skew values were consistently negative, except for nad6. These findings suggest that S. decaocto belongs to the Columbinae subfamily. In this research, the mitochondrial genome of the Streptopelia decaocto was sequenced and examined for the first time to enhance the comprehension of the phylogenetic relationships within the Columbidae. The complete mitochondrial genome of Streptopelia decaocto (17,160 bp) was structurally similar to the recognized members of the Columbidae family, but with minor differences in gene size and arrangement. The structural AT content was 54.12%. Additionally, 150 mitochondrial datasets, representing valid species, were amassed in this investigation. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees and evolutionary time relationships of species were reconstructed based on cytb gene sequences. The findings from the phylogenetic evaluations suggest that the S. decaocto was classified under the Columbinae subfamily, diverging from the Miocene approximately 8.1 million years ago, indicating intricate evolutionary connections with its close relatives, implying a history of species divergence and geographic isolation. The diversification of the Columbidae commenced during the Late Oligocene and extended into the Miocene. This exploration offers crucial molecular data for the S. decaocto, facilitating the systematic taxonomic examination of the Columbidae and Columbiformes, and establishing a scientific foundation for species preservation and genetic resource management. [ABSTRACT FROM AUTHOR]

Simple Summary: The water environment in Laizhou Bay has experienced mild eutrophication in recent years, impacting the interactions between environmental factors, microorganisms, and aquatic species. The metagenomic analysis of 142 samples from various water layers revealed that Oplegnathus punctatus mariculture significantly increases microbial abundance and complexity in the culture area. These alterations were more noticeable in sediments compared to seawater. Cyanobacteria and Candidatus Micrarchaeota in seawater, and Actinobacteria and Thaumarchaeota in sediments show notably higher abundances in the mariculture area, indicating shifts in microbial community structure due to aquaculture practices. Antibiotic resistance genes (ARGs) in sediments are highly sensitive to environmental variables, particularly oxygen solubility and salinity. This indicates that Oplegnathus punctatus mariculture can impact the occurrence and spread of antibiotic resistance in marine ecosystems. The study underscores the intricate and dynamic relationships between microorganisms, environmental conditions, and ARGs, highlighting the need for region-specific strategies in managing marine resources sustainably. (1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism–environment–ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources. [ABSTRACT FROM AUTHOR]

In the present study, the complete mitochondrial genome of Lepidozona coreanica was sequenced and described. The complete mitogenome sequence of L. coreanica is 16,572 bp long and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The base composition was AT biased (70.1%). The 13 PCGs of L. coreanica and the other 15 species of Polyplacophora were used for phylogenetic analysis using maximum-likelihood methods. The results showed that L. coreanica, Ischnochiton hakodadensis, and Chaetopleura apiculata are sister groups of the three lineages. [ABSTRACT FROM AUTHOR]

Acanthochitona rubrolineatus (Lischke, 1873) (Polyplacophora, Neoloricata, Cryptoplacidae) is an important species widely distributed in the middle and low tide zone of coastal intertidal zone along the China Sea coast. In recent years, the serious pollution of seawater has caused a sharp decline in the number of wild populations of A. rubrolineatus. Lacking of effective molecular markers limits the effective protection and management of this species. Studies for the isolation and characterization of 135 A. rubrolineatus SNP markers were carried out. The frequency of minor allele ranges from 0.0125 to 0.5000. The observed heterozygosity and expected heterozygosity are 0.0000-0.9750, 0.0731–0.6696, respectively. The inbreeding value varies from − 0.2902 to 0.9966. Among them, there are 27 sites markablely differently from Hardy-Weinberg equilibrium (P < 0.05). The study of the polymorphic SNPs will provide a therotical basis for further analysis of population genetic analysis on A. rubrolineatus. [ABSTRACT FROM AUTHOR]

In this study, the complete mitogenome of Grapsus albolineatus (Lamarck, 1818) (Crustacea: Grapsoidea) was sequenced. The mitogenome of G. albolineatus was a circular molecule with 15,578 bp length. Its nucleotide composition was 26.81% A, 16.37% G, 34.51% T, and 22.31% C. It comprised 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA). All PCGs were initiated by ATN codons, except for the atp8 and nad1 genes. Ten PCGs used a common stop codon of TAA or TAG, and the other three ended with a truncated stop codon (a single stop nucleotide T). Phylogenetic analysis revealed that G. albolineatus was closely related to species from the genera Pachygrapsus and Metopograpsus. [ABSTRACT FROM AUTHOR]

Sargassum is one of the most important genera of the family Sargassaceae in brown algae and is used to produce carrageenan, mannitol, iodine, and other economic substances. Here, seven complete plastid genomes of Sargassum ilicifolium var. conduplicatum, S. graminifolium, S. phyllocystum, S. muticum, S. feldmannii, S. mcclurei , and S. henslowianum were assembled using next-generation sequencing. The sizes of the seven circular genomes ranged from 124,258 to 124,563 bp, with two inverted regions and the same set of plastid genes, including 139 protein-coding genes (PCGs), 28 transfer (t)RNAs, and 6 ribosomal (r)RNAs. Compared with the other five available plastid genomes of Fucales, 136 PCGs were conserved, with two common ones shared with Coccophora langsdorfii , and one with S. fusiforme and S. horneri. The co-linear analysis identified two inversions of trnC(gca) and trnN(gtt) in ten Sargassum species, against S. horneri and C. langsdorfii. The phylogenetic analysis based on the plastid genomes of 55 brown algae (Phaeophyceae) showed four clades, whose ancient ancestor lived around 201.42 million years ago (Mya), and the internal evolutionary branches in Fucales started to be formed 92.52 Mya, while Sargassum species were divided into two subclades 14.33 Mya. Our novel plastid genomes provided evidence for the speciation of brown algae and plastid genomic evolution events. [ABSTRACT FROM AUTHOR]

Mollusca is the largest marine phylum, comprising about 23% of all named marine organisms, Mollusca systematics are still in flux, and an increase in human activities has affected Molluscan reproduction and development, strongly impacting diversity and classification. Therefore, it is necessary to explore the mitochondrial genome of Mollusca. The Mollusca mitochondrial database (MODB) was established for the Life and Health Big Data Center of Yantai University. This database is dedicated to collecting, sorting and sharing basic information regarding mollusks, especially their mitochondrial genome information. We also integrated a series of analysis and visualization tools, such as BLAST, MUSCLE, GENEWISE and LASTZ. In particular, a phylogenetic tree was implemented in this database to visualize the evolutionary relationships between species. The original version contains 616 species whose mitochondrial genomes have been sequenced. The database provides comprehensive information and analysis platform for researchers interested in understanding the biological characteristics of mollusks. Database URL : http://modb.ytu.edu.cn/ [ABSTRACT FROM AUTHOR]

In this study, 38 single nucleotide polymorphism (SNP) markers were developed and characterized in Patelloida pygmaea. The minor allele frequency raged from 0.0833 to 0.5000. The observed heterozygosity varied from 0.0000 to 1.000, and the expected heterozygosity varied from 0.1197 to 0.5496. Polymorphic information content ranged from 0.1103 to 0.4316. The inbreeding coefficient values varied from − 0.3330 to 0.8686. Eleven loci showed significant deviations from the Hardy–Weinberg equilibrium (P < 0.05). The polymorphic SNPs will be useful for the further studies of population genetics and natural resource conservation of P. pygmaea. [ABSTRACT FROM AUTHOR]

The transition of terrestrial snakes to marine life ∼10 Ma is ideal for exploring adaptive evolution. Sea snakes possess phenotype specializations including laterally compressed bodies, paddle-shaped tails, valvular nostrils, cutaneous respiration, elongated lungs, and salt glands, yet, knowledge on the genetic underpinnings of the transition remains limited. Herein, we report the first genome of Shaw's sea snake (Hydrophis curtus) and use it to investigate sea snake secondary marine adaptation. A hybrid assembly strategy obtains a high-quality genome. Gene family analyses date a pulsed coding-gene expansion to ∼20 Ma, and these genes associate strongly with adaptations to marine environments. Analyses of selection pressure and convergent evolution discover the rapid evolution of protein-coding genes, and some convergent features. Additionally, 108 conserved noncoding elements appear to have evolved quickly, and these may underpin the phenotypic changes. Transposon elements may contribute to adaptive specializations by inserting into genomic regions around functionally related coding genes. The integration of genomic and transcriptomic analyses indicates independent origins and different components in sea snake and terrestrial snake venom; the venom gland of the sea snake harbors the highest PLA2 (17.23%) expression in selected elapids and these genes may organize tandemly in the genome. These analyses provide insights into the genetic mechanisms that underlay the secondary adaptation to marine and venom production of this sea snake. [ABSTRACT FROM AUTHOR]

Streptopelia orientalis is an important commercial species, and natural populations have declined dramatically in recent years because of the application of traditional Chinese medicine. The effective conservation and management of S. orientalis have been limited without sufficient molecular markers. In this study, we reported the isolation and characterization of 89 SNP markers in S. orientalis. The minor allele frequency raged from 0.0417 to 0.4792. The observed heterozygosity and expected heterozygosity ranged from 0.0000 to 0.9583 and from 0.0816 to 0.5098, respectively. Polymorphic information content ranged from 0.0767 to 0.3746. The inbreeding coefficient values varied from − 0.3149 to 0.8686. Only four loci showed significant deviations from the Hardy–Weinberg equilibrium (P < 0.05). The polymorphic SNPs will be helpful for the further population genetic analysis and natural resource conservation of S. orientalis. [ABSTRACT FROM AUTHOR]

In this study, 26 single nucleotide polymorphism (SNP) markers were developed and characterized in Nipponacmea schrenckii. The minor allele frequency raged from 0.0238 to 0.3571. The observed heterozygosity and expected heterozygosity ranged from 0.0000 to 0.2381 and from 0.0929 to 0.4866, respectively. Polymorphic information content ranged from 0.0866 to 0.3538. The inbreeding coefficient values varied from − 0.0582 to 0.9985. Four loci showed significant deviations from the Hardy–Weinberg equilibrium (P < 0.01). The polymorphic SNPs will be helpful for the further population genetic analysis and natural resource conservation of N. schrenckii. [ABSTRACT FROM AUTHOR]

Algae are the oldest taxa on Earth, with an evolutionary relationship that spans prokaryotes (Cyanobacteria) and eukaryotes. A long evolutionary history has led to high algal diversity. Their organelle DNAs are characterized by uniparental inheritance and a compact genome structure compared with nuclear genomes; thus, they are efficient molecular tools for the analysis of gene structure, genome structure, organelle function and evolution. However, an integrated organelle genome database for algae, which could enable users to both examine and use relevant data, has not previously been developed. Therefore, to provide an organelle genome platform for algae, we have developed a user-friendly database named Organelle Genome Database for Algae (OGDA, http://ogda.ytu.edu.cn/). OGDA contains organelle genome data either retrieved from several public databases or sequenced in our laboratory (Laboratory of Genetics and Breeding of Marine Organism [MOGBL]), which are continuously updated. The first release of OGDA contains 1055 plastid genomes and 755 mitochondrial genomes. Additionally, a variety of applications have been integrated into this platform to analyze the structural characteristics, collinearity and phylogeny of organellar genomes for algae. This database represents a useful tool for users, enabling the rapid retrieval and analysis of information related to organellar genomes for biological discovery. [ABSTRACT FROM AUTHOR]

Ischnochiton hakodaensis is one of Polyplacophora species, which plays an important role in the intertidal and subtidal ecosystems. In this study, the complete mitochondrial genome of I. hakodaensis was obtained with 15,139 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes. The overall base composition of the genome is 35.93% A, 13.51% G, 37.19% T, 13.38% C. The phylogenetic tree show that I. hakodaensis, Acanthopleura brevispinosa, Acanthopleura granulate, and Liolophura japonica constituted a sister clade along with Tonicia forbesii and Tonicia lamellose. [ABSTRACT FROM AUTHOR]

We describe the complete mitochondrial genome of the important Polyplacophora species, Acanthochitona rubrolineatus. The mitogenome sequence of A. rubrolineatus is 14,988 bp, and all genes show the typical gene arrangement conforming to the Mollusca consensus. The overall base composition of the genome is T 39.0%, C 12.4%, A 31.2% and G 17.4%. The cytochrome c oxidase subunit I (COI) sequence of A. rubrolineatus and other 111 species from Chitonida were used for phylogenetic analysis by Bayesian inference and maximum-likelihood methods. The results show that A. rubrolineatus, Acanthochitona achates, and Acanthochitona defilippi is sister group to three lineages, and both together as the sister group of A. rubrolineata. [ABSTRACT FROM AUTHOR]

Neorhodomela munita (Perestenko) Masuda 1982 is distributed in the coastal areas of Shandong and Liaoning in China, and also in Japan. In this study, the complete nucleotide sequence of the circular mitochondrial DNA of the red alga Neorhodomela munita has been determined. The complete mitochondrial DNA sequence of Neorhodomela munita was 25,318 bp in length with an overall GC content of 25.1% and encoded 23 protein-coding genes, two ribosomal RNAs and 24 transfer RNAs. Phylogenetic tree showed that Neorhodomela munita clustered together with Choreocolax polysiphoniae. The phylogenetic analysis may provide a better understanding of the evolution of the Rhodophyta species. [ABSTRACT FROM AUTHOR]

The polymerase chain reaction combined with direct sequencing was employed to deduce the variety of the grey-rumped pheasant populations in China. Totally 1079 basepair sequences of mitochondrial DNA (mtDNA) control-region gene were analyzed from 121 grey-rumped pheasants obtained from 13 Chinese localities, 76 variable sites resulted in 91 haplotypes. These populations possessed a high level of genetic diversity, indicating that during their evolution effective population size and polymorphism were not reduced by climatic fluctuations in the Pleistocene ice ages. Phylogenetic analysis indicates that all populations were clustered into two groups, western and eastern. The degree of population differentiation presumably results from a low gene flow (Nm - 0.33, Fst - 0.60, P < 0.001) between the two groups, and the divergence occurred in the years (2.1 × 105 - 2.2 × 105). The genetic structure of grey-rumped pheasants in China appears to be the result of the uplift of Qinghai-Tibet Plateau, the existence of Qinling Mountains and Liupan Mountains and cyclical climatic oscillations during the late Pleistocene. [ABSTRACT FROM AUTHOR]

Abstract: The ring-necked pheasants (Phasianus colchicus) are widely distributed in China. We used mitochondrial DNA control-region data to investigate the origin and past demographic changes in 139 ring-necked pheasants (P. colchicus) sampled from the species’ distribution range. A total of 1078 nucleotides from the control region of mitochondrial DNA were sequenced, and 88 polymorphic positions defined 102 haplotypes. High level of genetic diversity was detected in all populations studied which could be associated with the wide ecological distributions and niche variation. Phylogenetic analyses of all haplotypes identified five major clades. The haplotypes of Gray-rumped Pheasants existed in the three clades: A (western clade), B (eastern clade) and C (Sichuan Basin clade). Two haplotypes of Kirghiz Pheasants were in the clade B, and the rest haplotype of Kirghiz Pheasants formed the clade D. Only one haplotype from White-winged Pheasants made up clade E. The results of AMOVA showed a low gene flow (Nm=0.44) and significant genetic differentiation (Fst=0.31, P <0.001) among all populations. Based on the divergence time, we speculate that the divergence of the ring-necked pheasant occurring in the late Pleistocene may have resulted from three events: (1) the uplift of Qinghai-Tibet Plateau, (2) the existence of Qinling Mountains and Liupan Mountains, (3) the isolation of Sichuan Basin. Demographic population expansion was strongly confirmed by the non-significant mismatch distribution analysis. The described subspecies of the ring-necked pheasant could not be supported by the phylogeographical structuring. [Copyright &y& Elsevier]

Complete chloroplast genome of Sargassum horneri was obtained in this work. Circular mapping revealed that the complete chloroplast DNA sequences of S. horneri was 124,075 bp in length and had an overall AT content of 69.41%, including 139 protein-coding genes, 28 transfer RNA genes, and 6 ribosomal RNA genes. The phylogenetic tree shows that S. horneri and Sargassum confusum constituted a sister clade along with Fucus vesiculosus. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome ofCentropus sinensisis determined in this study. The circle genome with the 17 159 bp total length contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. Phylogenetic tree shows thatC. sinensiswas sister toC. unirufus. The mitogenome ofC. sinensiswill contribute to researches of mitogenomic evolution, phylogenetic relationship, and conservation genetics. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome ofHalcyon smyrnensiswas determined in this study. The mitogenomic length ofHalcyon smyrnensiswas 17 318 bp, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region. Phylogenetic analyses show thatH. leucocephala,H. pileataandH. smyrnensiscongregated together, and our sample was sister toH. pileata. [ABSTRACT FROM PUBLISHER]