Mitochondrial Genomes of Streptopelia decaocto: Insights into Columbidae Phylogeny.

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.

Macrogenomics Reveals Effects on Marine Microbial Communities during Oplegnathus punctatus Enclosure Farming.

(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.

Complete mitochondrial genome and phylogenetic analysis of Mancinella alouina.

BACKGROUND: The Muricidae family in the Class Gastropoda comprises numerous species with a vast range of morphological features and a worldwide presence. The phylogeny of the Muricidae has been analyzed in previous studies; however, the evolutionary relationships among the main branches of the Muricidae remain unknown. METHODS AND RESULTS: In the present study, the mitochondrial genome of Mancinella alouina was sequenced. The mitochondrial genome was found to be 16,671 bp in length and made up of 37 genes (13 protein-coding genes, 22 transfer RNA and 2 ribosomal RNA genes). The genome has an A-T-rich region (66.5% A + T content) and all of the PCGs use the ATN start codon and the TAG or TAA stop codons. The mitochondrial gene arrangement of Mancinella alouina is similar to that of other Muricidae, except for Ocinebrellus inornatus and Ceratostoma burnetti. On the basis of a flexible molecular clock model, time-calibrated phylogenetic results indicate that the genus Mancinella diverged roughly 18.09 Mya, and that the family Muricidae emerged in the Late Cretaceous. CONCLUSIONS: This study reveals the structural and sequence information features of the mitochondrial genome of Mancinella alouina. This study provides evidence for the relationships within the family Muricidae at the molecular level, and infer the divergence time. The results of phylogenetic analyses strongly support the current classification.

Deep machine learning identified fish flesh using multispectral imaging.

Food fraud is widespread in the aquatic food market, hence fast and non-destructive methods of identification of fish flesh are needed. In this study, multispectral imaging (MSI) was used to screen flesh slices from 20 edible fish species commonly found in the sea around Yantai, China, by combining identification based on the mitochondrial COI gene. We found that nCDA images transformed from MSI data showed significant differences in flesh splices of the 20 fish species. We then employed eight models to compare their prediction performances based on the hold-out method with 70% training and 30% test sets. Convolutional neural network (CNN), quadratic discriminant analysis (QDA), support vector machine (SVM), and linear discriminant analysis (LDA) models perform well on cross-validation and test data. CNN and QDA achieved more than 99% accuracy on the test set. By extracting the CNN features for optimization, a very high degree of separation was obtained for all species. Furthermore, based on the Gini index in RF, 11 bands were selected as key classification features for CNN, and an accuracy of 98% was achieved. Our study developed a successful pipeline for employing machine learning models (especially CNN) on MSI identification of fish flesh, and provided a convenient and non-destructive method to determine the marketing of fish flesh in the future.

Chromosome-level genome assembly of Przevalski's partridge (Alectoris magna).

Przevalski's partridge (Alectoris magna) is one of the birds in the genus Alectoris endemic to China. The distribution of A. magna was narrow, and it was only found in parts of the Qinghai, Gansu, and Ningxia provinces. A. magna was considered a monotypic species until it was distinguished into two subspecies. However, external morphological characteristics, rather than genetic differences or evolutionary relationships, are now commonly used as evidence of subspecies differentiation. In this study, a chromosome-level reference genome of A. magna has been constructed by combining Illumina, PacBio and Hi-C sequencing data. The 1135.01 Mb A. magna genome was ultimately assembled. The genome showed 96.9% completeness (BUSCO), with a contig N50 length of 23.34 Mb. The contigs were clustered and oriented on 20 chromosomes, covering approximately 99.96% of the genome assembly. Additionally, altogether 19,103 protein-coding genes were predicted, of which 95.10% were functionally annotated. This high-quality genome assembly could serve as a valuable genomic resource for future research on the functional genomics, genetic protection, and interspecific hybridization of A. magna.

The complete mitochondrial genome and phylogenetic analysis of Lepidozona coreanica (Reeve, 1847).

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.

Histopathological and transcriptomic analyses reveal the reproductive endocrine-disrupting effects of decabromodiphenyl ethane (DBDPE) in mussel Mytilus galloprovincialis.

The novel brominated flame retardant DBDPE has become a widespread environmental contaminant and could affect reproductive endocrine system in vertebrates. However, information about reproductive endocrine-disrupting effects of DBDPE on invertebrates is totally unknown. In this study, mussels Mytilus galloprovincialis were exposed to 1, 10, 50, 200 and 500 µg/L DBDPE for 30 days. Histopathological and transcriptomic analyses were performed to assess the reproductive endocrine-disrupting effects of DBDPE in mussels and the potential mechanisms. DBDPE promoted the gametogenesis in mussels of both sexes according to histological observation, gender-specific gene expression (VERL and VCL) and histological morphometric parameter analysis. Transcriptomic analysis demonstrated that DBDPE suppressed the genes related to cholesterol homeostasis and transport in both sexes via different LRPs- and ABCs-mediated pathways. DBDPE also disturbed nongenomic signaling pathway including signaling cascades (GPR157-IP3-Ca2+) in males and secondary messengers (cGMP) in females, and subsequently altered the expression levels of reproductive genes (VMO1, ZAN, Banf1 and Hook1). Additionally, dysregulation of energy metabolism in male mussels induced by DBDPE might interfere with the reproductive endocrine system. Overall, this is the first report that DBDPE evoked reproductive endocrine-disruptions in marine mussels. These findings will provide important references for ecological risk assessment of DBDPE pollution in marine environment.

Complete mitogenome and phylogenetic analysis of the tropical rocky shore crab Grapsus albolineatus (Lamarck, 1818) (Crustacea: Grapsoidea).

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.

The Complete Plastid Genomes of Seven Sargassaceae Species and Their Phylogenetic Analysis.

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.

The complete mitochondrial genome and phylogenetic analysis of Neorhodomela munita.

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.

MODB: a comprehensive mitochondrial genome database for Mollusca.

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/.

OGDA: a comprehensive organelle genome database for algae.

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.

The Genome of Shaw's Sea Snake (Hydrophis curtus) Reveals Secondary Adaptation to Its Marine Environment.

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.

The complete mitochondrial genome and phylogenetic analysis of Ischnochiton hakodaensis (Carpenter, 1893).

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.

The complete mitochondrial genome and phylogenetic analysis of Acanthochitona rubrolineatus (Lischke, 1873).

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.

The complete chloroplast genome of Sargassum horneri and its phylogenetic analysis.

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.

Complete mitochondrial genome of the greater Coucal, Centropus sinensis (Aves: Cuculiformes).

The complete mitochondrial genome of Centropus sinensis is 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 that C. sinensis was sister to C. unirufus. The mitogenome of C. sinensis will contribute to researches of mitogenomic evolution, phylogenetic relationship, and conservation genetics.

Complete mitochondrial genome and the phylogenetic position of Halcyon smyrnensis (Aves: Coraciiformes).

The complete mitochondrial genome of Halcyon smyrnensis was determined in this study. The mitogenomic length of Halcyon smyrnensis was 17 318 bp, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region. Phylogenetic analyses show that H. leucocephala, H. pileata and H. smyrnensis congregated together, and our sample was sister to H. pileata.

The phylogenetic position and speciation dynamics of the genus Perdix (Phasianidae, Galliformes).

The nuclear gene (c-mos) and mitochondrial genes (CYT B and ND2) sequences, representing 44 phasianid species and 26 genera (mainly distributed in China), were used to study the phylogeny of the genus Perdix, which comprises three partridge species. Maximum parsimony and Bayesian methods were employed, and the analysis of mitochondrial sequence data and the combined dataset showed that Perdix is specifically related either to typical pheasants or to Ithaginis. Phylogenetic trees also indicated that: (1) Perdix is monophyletic; (2) the Tibetan partridge (Perdix hodgsoniae) has been consistently placed as basal to all other Perdix, and the Daurian partridge (Perdix dauuricae) is placed sister to gray partridge (Perdix perdix); (3) the Daurian partridge subspecies przewalskii and Tibetan partridge subspecies hodgsoniae are basal to other subspecies in their species clade, respectively. Speciation in Perdix was likely promoted by the late Pliocene/early Pleistocene intensive uplift of the Tibetan Plateau and by Pleistocene glaciations.

Phylogeography of the ring-necked pheasant (Phasianus colchicus) in China.

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.