MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years

DNA metabarcoding analysis revealed a silent prevalence of environmental pathogenic Leptospira in urban area of Okinawa Island, Japan

Objective

Human activities, such as agriculture, environmental manipulation, and city development, have impacted the distribution of flora, fauna, and microbes (including potential human pathogens) at the global level. This study focused on the bacterial genus Leptospira, an organism causing leptospirosis that is prevalent in tropical and subtropical regions. We hypothesized that although only a few cases of leptospirosis have been reported in the urban region of main island of Okinawa Prefecture (Okinawa Island, OKI), Japan, Leptospira is present in these regions.

Methods

Thirty-four samples were collected from rivers in urban OKI and rural Ishigaki Island (ISG) and analyzed to determine the distribution of Leptospira and mammals using environmental DNA (eDNA) metabarcoding. High-throughput sequencing analysis was performed to sequence the polymerase chain reaction products of partial leptospiral 16S rRNA and vertebrate mitochondrial 12S rRNA genes from 16 and 18 river samples of OKI and ISG, respectively, including the waters collected from Leptospira-endemic areas in ISG.

Results

Leptospira noguchii and L. interrogans-related, two Leptospira species of the P1+ clade that are pathogenic to humans and mammals, were repeatedly detected in OKI and ISG, supporting our hypothesis. The sequence numbers of the five Leptospira species of P1- and P2 clades showed significant correlations with those of cattle (Bos taurus) in OKI; however, the potential host animals for P1+ species remain unclear. The total number of leptospiral sequences obtained from the ISG samples was correlated with the distance from the mountainous woodlands.

Conclusion

The pathogenic P1+ Leptospira was distributed in urban OKI, in addition to rural ISG. The factors correlated with leptospiral detection, that is, cattle eDNAs and the distance from mountainous forests in OKI and ISG, respectively, suggest the silent prevalence of Leptospira in urban and developing regions related to human activities. The findings of the present study provide insights into public health in cities with respect to climate change and possible flood damage.

Underwater drone-based eDNA metabarcoding reveals regional differences in fish communities and early detection of alien species around the Korean Peninsula

Coastal ecosystems surrounding the Korean Peninsula are undergoing rapid environmental changes driven by global climate warming, highlighting the need for efficient methods to monitor marine biodiversity. This study aimed to analyze fish communities across four coastal regions: the East Sea, South Sea, West Sea, and Jeju using environmental DNA (eDNA) metabarcoding. Underwater drones were employed to collect water samples. A total of 63 sampling sites were surveyed, detecting 167 fish species from 72 families, encompassing tropical, subtropical, temperate, boreal, polar, and deep-water taxa. The East Sea hosted a mix of cold- and warm-water species, while Jeju exhibited a relatively high proportion of tropical and subtropical fish. Additionally, 13 alien species were identified, underscoring the utility of eDNA for the early detection of non-native taxa expanding their ranges in response to ongoing warming trends. This study further validated that eDNA sampling using underwater drones offers a rapid, non-invasive approach to biodiversity assessments, effectively addressing many of the limitations associated with traditional survey techniques. Collectively, these findings highlight the potential of eDNA to generate critical and timely data on fish assemblages the emergence of alien species, providing valuable insights to inform proactive resource management, and climate change research in marine ecosystems.

Comparative Mitogenomics of Wonder Geckos (Sphaerodactylidae: Teratoscincus Strauch, 1863): Uncovering Evolutionary Insights into Protein-Coding Genes

Background: Comparative studies of selection pressures on mitochondrial genomes and protein-coding genes (PCGs) are scarce in the genus Teratoscincus (Strauch, 1863), particularly within Sphaerodactylidae. Given their close evolutionary relationship, Teratoscincus przewalskii (Strauch, 1887) and Teratoscincus roborowskii (Bedriaga, 1906) serve as ideal models for the characterization of mitochondrial genome sand analysis of selective pressure in this genus. Methods: In this study, we employed Sanger sequencing to sequence the mitochondrial genome of T. roborowskii (Bedriaga, 1906), and utilized sliding window analysis, selection pressure analysis etc. to compared it with that of its close relative, T. przewalskii (Strauch, 1887). Results: The results contain the genome composition, Ka/Ks values, AT/GC-skew, etc. Selection pressure analysis of PCGs across Teratoscincus (Strauch, 1863) species (including those in GenBank) revealed that most genes evolve slowly, with the exception of ATP8 and ND6, which exhibited faster evolutionary rates. Notably, the ND6 of T. roborowskii (Bedriaga, 1906) demonstrated rapid non-synonymous substitution rates which may contribute to the survival and reproductive success of the species by favoring advantageous mutations. Phylogenetic analysis for the mitochondrial genomes of Sphaerodactylidae, Phyllodactylidae, and Gekkonidae confirmed the distinctiveness of Sphaerodactylidae and the two Teratoscincus (Strauch, 1863) species. Conclusions: This study has advanced the understanding of adaptive evolution in Teratoscincus (Strauch, 1863) mitochondrial genomes, expanded the mitochondrial database of Sphaerodactylidae, and provided insights into the phylogenetic relationships of the genus.

The complete mitochondrial genome of Halichoeres margaritaceus (Actinopterygii, Labridae)

Halichoeres margaritaceus Valenciennes 1839 is a polygynous species of coral fish. We sequenced the complete mitochondrial genome of H. margaritaceus, and conducted a comprehensive analysis to reveal its characteristics. Results showed that the mitochondrial genome is a closed circular molecule comprising 16,710 bp. Phylogenetic analysis based on mitochondrial whole genome sequences revealed H. margaritaceus as a sister group of H. ornatissimus, H. tenuispinis, etc., with maximal support. This study presents, for the first time, the complete mitochondrial genome of H. margaritaceus, offering valuable insights that can aid in future research on the biodiversity and conservation management of this species.

Comparative mitogenomic analysis of Chinese cavefish Triplophysa (Cypriniformes: Nemacheilidae): novel gene tandem duplication and evolutionary implications

BACKGROUND

Cavefish exhibit significant morphological changes that result in trade-offs in metabolic requirements and energy utilization in perpetual darkness. As cellular "powerhouses", mitochondria play crucial roles in energy metabolism, suggesting that mitochondrial genes have likely experienced selective pressures during cavefish evolution.

RESULTS

This study presents the first assembly of the complete mitogenome of Triplophysa yangi, a typical cavefish species in China. The mitogenome is 17,068 bp long, marking the longest recorded for the genus Triplophysa, and includes 13 protein-coding genes (PCGs), 2 rRNAs, 25 tRNAs, and a noncoding control region. An ~ 500 bp insertion between ND2 and WANCY regions was observed, comprising a large intact tandem repeat unit (A'-N'-OL'-C') flanked by two unannotated sequences (U1/U2). The evolutionary origin of this repeat unit may involve either in situ duplication events with subsequent functional divergence-where neofunctionalization, subfunctionalization, or pseudogenization drove differential mutation rates between paralogs-or alternatively, horizontal acquisition from exogenous genetic material that became functionally integrated into the ancestral T. yangi mitogenome through co-option mechanisms. Phylogenetic analyses revealed two major clades within Triplophysa-epigean and hypogean lineages-consistent with previous classifications, while cave-restricted species exhibited signs of parallel evolution within the hypogean lineage. Selective pressure analysis indicated that the hypogean lineage (cave-dwelling groups, II & III) have a significantly increased ratio of nonsynonymous to synonymous substitution rates (ω) compared to the epigean lineage (surface-dwelling group, I), suggesting a combination of adaptive selection and relaxed functional constraints in cave-dwelling species.

CONCLUSIONS

The duplication of tRNAs in T. yangi and the potential positive selection sites identified in Triplophysa cavefish further indicated adaptive evolution in mitochondrial PCGs in response to extreme subterranean conditions.

Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Crucian carp (Carassius carassius), a member of the carp family (Cyprinidae), is known for its remarkable anoxia tolerance. The physiological responses and adaptations to anoxia are well documented, but there is a need for better understanding of the molecular regulation and evolutionary mechanisms behind these adaptations. Here we present a high-quality, functionally annotated, chromosome-level genome assembly that can facilitate such further studies. Genomic DNA was obtained from a wild-caught crucian carp specimen and used for PacBio long-read, Illumina short-read and Hi-C sequencing. Short-read mRNA data were used for structural annotation using the BRAKER3 pipeline, while PacBio long-read RNA sequencing data were used for annotation of untranslated regions and refinement of gene-isoform relationships, using the PASA pipeline. The full assembly had a contig-level N50 of 15Mbp in 290 scaffolds and 98.6% of the total length (1.65Gbp) placed in 50 chromosomes. Structural annotation resulted in 82,557 protein-coding transcripts (in 45,667 genes), with a BUSCO completeness of 99.6% and of which 77,370 matched a protein in the UniProtKB/Swiss-Prot database.

Environmental DNA metabarcoding: Current applications and future prospects for freshwater fish monitoring

Fish, as the top predators in freshwater, greatly contribute to maintain ecosystem stability. There has been a sharp decline in freshwater fish stocks due to multiple factors, both natural and anthropogenic. Effective and accurate monitoring of freshwater fish is necessary to inform on ecosystem health and guide environmental management practices. Traditional survey methods are gradually unable to meet the growing monitoring needs. Environmental DNA (eDNA) metabarcoding provides a high sensitivity, fast and affordable approach for surveying and monitoring of aquatic biology. However, due to the limitations of incomplete databases and non-standardized procedures, the use of eDNA techniques for monitoring freshwater fish remains less mature compared to traditional fish monitoring methods. To systematically review the current applications and future prospects of the eDNA metabarcoding for freshwater fish monitoring, this article: (i) summarizes relevant researches on freshwater fish monitoring using eDNA technology (e.g., methodologies, resource surveys, habitat assessments, etc.) over the past decade. (ii) outlines the methodology of eDNA metabarcoding in freshwater fish monitoring, proposes a standardized process for eDNA methods, and suggests ways to eliminate detection errors. (iii) analyzes the current challenges of the eDNA metabarcoding application in resource surveys and ecological quality assessments of freshwater fish. The eDNA technology can be used as a better alternative or supplement to traditional survey methods for monitoring the diversity, biomass, population distribution, and spawning behaviors of freshwater fish, in particular, it has a prominent advantage in monitoring endangered and rare fish species. (iv) investigates the application of eDNA technology in investigating the impact of human activities and invasive species on freshwater fish, and emphasizes the eDNA's potential in assessing the impacts of water projects (e.g., dam construction or removal, water diversion project) on fish habitats, and the effectiveness of fish passage and invasive fish control efforts. (v) discusses the future prospects of eDNA-based freshwater fish monitoring, both in terms of technology and application. This review provides a guidance for the future development and application of eDNA technology in freshwater fish monitoring and ecological quality assessments.

Exploring technical improvements for environmental nucleic acids-based biodiversity assessment and management in coastal ecosystems

Assessing and conserving marine biodiversity remain critical global challenges, particularly in highly disturbed coastal regions. The use of environmental DNA (eDNA)-metabarcoding has revolutionized biodiversity assessment and management; however, the prevalence of both false positives and negatives continues to be a significant concern. To address these technical errors, we tested two potential methodological improvements in the highly disturbed Guangdong-Hong Kong-Macao Greater Bay Area: (1) the use of random whole-genome amplification (WGA) to reduce false negatives derived from low eDNA concentration, and (2) the application of environmental RNA (eRNA)-metabarcoding to mitigate false positives arising from eDNA contamination by human activities. Using fish communities as our target, we found that WGA enhanced downstream PCR amplification for metabarcoding but significantly reduced the detection of rare taxa, altered community structure, and increased false negatives (p < 0.001 for all tests). Interestingly, WGA led to higher levels of false negatives in more biodiverse communities. eDNA-metabarcoding revealed that 20.9%-23.6% of detected taxa were pure freshwater species (false positives) incapable of surviving in estuarine and coastal regions, highlighting the often-overlooked eDNA contamination in disturbed coastal ecosystems. In contrast, eRNA-metabarcoding significantly reduced false positives (p < 0.001), with error taxa accounting for only 2.5%-6.3% of all detections. Comparisons between eDNA and eRNA metabarcoding further revealed differences in their rare taxa recovery capacity. The findings provide critical insights into method selection for biodiversity assessment and management in highly disturbed coastal regions and highlight the need for further technical improvement of eDNA and eRNA-based biodiversity monitoring and conservation in aquatic ecosystems.

Selecting Competent Reverse Transcription Strategies to Maximise Biodiversity Recovery With eRNA Metabarcoding

Both environmental DNA (eDNA) and environmental RNA (eRNA) have been widely adopted for biodiversity assessment. While eDNA often persists longer in environments, eRNA offers a more current view of biological activities. In eRNA metabarcoding, extracted eRNA is reverse transcribed into complementary DNA (cDNA) for metabarcoding. However, the efficacy of various reverse transcription strategies has not been evaluated. Here we compared the biodiversity recovery efficiency of three strategies: random priming with hexamers, oligo(dT) priming and taxa-specific priming using Mifish-U for fish in both high- and low-biodiversity regions. Our results demonstrate that reverse transcription strategies significantly impact biodiversity recovery. Random priming consistently detected the highest number of taxa in both low- and high-biodiversity regions. In low-biodiversity areas, oligo(dT) performed comparably to random hexamers; however, in high-biodiversity regions, random hexamers outperformed oligo(dT), particularly in recovering rare taxa. While taxa-specific priming was comparable to the other strategies for high-abundance taxa, it was less effective for rare taxa, thus limiting its utility for comprehensive biodiversity assessment. These differences are largely due to the multiple binding sites for random hexamers compared to the fewer or absent sites with oligo(dT) and taxa-specific primers under high eRNA degradation. Combining random hexamers and oligo(dT) significantly improved taxa recovery, especially for low-abundance species, supporting its best practice in eukaryotes. For prokaryotes or genes lacking polyadenylation, random priming is favoured over taxa- or gene-specific priming. Collectively, these findings underscore the critical importance of selecting appropriate reverse transcription strategies in eRNA metabarcoding, with significant implications for effective biodiversity monitoring and conservation efforts.

The complete mitochondrial genome of the common dace Leuciscus leuciscus (Teleostei: Leuciscidae)

This study presents, for the first time, the complete mitochondrial genome of the Common Dace (Leuciscus leuciscus (Linnaeus 1758)), in association with a voucher specimen from the Swedish Natural History Museum. The complete mitogenome length is 16,603 bp and comprises 13 protein-coding-genes (PCGs), 22 tRNAs, 2 rRNAs, and one non-coding control region. A maximum likelihood phylogenetic reconstruction based on 13 PCGs of Leuciscids species confirm the monophyly of the Leuciscus genus. Furthermore, this reconstruction has corroborated the placement of other Leuciscus species in this genus as L. leuciscus is the type species of this genus.

Environmental DNA/RNA metabarcoding for noninvasive and comprehensive monitoring and assessment of marine fishes

Marine fisheries resources are under increasing threat, necessitating the development of new effective monitoring and management strategies. Environmental DNA (eDNA) and RNA (eRNA) metabarcoding has emerged as a non-invasive and sensitive alternative method for monitoring fish biodiversity and fisheries resources and assessing the fisheries impact of anthropogenic activities. Here, we summarize crucial technical details about eDNA metabarcoding for marine fish monitoring and provide meta-analytical trends in primer selection and sample size, assessment standards, fish and fisheries databases, reference fish genomic databases, and other relevant metrics. The pressing need for better reference databases and standardization methods is discussed. We further highlight the potency of emerging eDNA metabarcoding studies for monitoring global fish diversity and revealed regional study hotspots in South China, Atlantic and Mediterranean Seas. The innovative advances in using eDNA/eRNA metabarcoding for fish diversity monitoring and assessment from the detection of rare or invasive species to branching applications in biomass estimation, population genetics, food web analysis, fish migration and feeding studies were reviewed. We also explore the potential of eRNA metabarcoding as an upcoming extension of eDNA metabarcoding in marine fish monitoring and assessment with improved functional relevance. We envision the integration of eDNA/eRNA metabarcoding-based fish monitoring methods with traditional monitoring approaches to significantly improve marine fish surveillance, ecological research, and conservation efforts.

Use of 3D chaos game representation to quantify DNA sequence similarity with applications for hierarchical clustering

A 3D chaos game is shown to be a useful way for encoding DNA sequences. Since matching subsequences in DNA converge in space in 3D chaos game encoding, a DNA sequence's 3D chaos game representation can be used to compare DNA sequences without prior alignment and without truncating or padding any of the sequences. Two proposed methods inspired by shape-similarity comparison techniques show that this form of encoding can perform as well as alignment-based techniques for building phylogenetic trees. The first method uses the volume overlap of intersecting spheres and the second uses shape signatures by summarizing the coordinates, oriented angles, and oriented distances of the 3D chaos game trajectory. The methods are tested using: (1) the first exon of the beta-globin gene for 11 species, (2) mitochondrial DNA from four groups of primates, and (3) a set of synthetic DNA sequences. Simulations show that the proposed methods produce distances that reflect the number of mutation events; additionally, on average, distances resulting from deletion mutations are comparable to those produced by substitution mutations.

An optimized eDNA protocol for fish tracking in estuarine environments

Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It is increasingly used for detecting rare and invasive species, assessing biodiversity loss and monitoring fish communities, as it is considered a cost-effective and noninvasive approach. Some environments, however, can be challenging for eDNA analyses. Estuarine systems are highly productive, complex environments, but samples collected from these settings may exhibit PCR inhibition and a low fish read recovery. Here we present an approach for detecting fish in turbid, highly productive estuarine systems. The workflow includes bead-based extraction, inhibition removal, high fidelity and specificity DNA polymerase (Platinum SuperFi II) and multiplexing the universal MiFish primers. By applying this hybrid method to a variety of complex estuarine samples with known inhibition, we have more than doubled the number of recovered fish species while removing most of the off-target amplification.

Complete Mitochondrial Genome of Niphon spinosus (Perciformes: Niphonidae): Genome Characterization and Phylogenetic Analysis

The species Niphon spinosus (Cuvier, 1829) is the only representative of the family Niphonidae and the genus Niphon, and its taxonomic history is complicated; it is still unclear in a phylogenetic sense. In this study, we report the complete mitochondrial genome of N. spinosus (OP391482), which was determined to be 16,503 bp long with biased A + T contents (53.8%) using next-generation technology. The typical set of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and one control region (D-loop) are included in the mitochondrial genome. The H-strand encoded 28 genes (14 tRNA, 2 rRNA, and 12 PCGs), and D-loop, whereas the L-strand encoded the remaining 9 genes (8 tRNA and ND6). Its nucleotide composition, gene arrangement, codon usage patterns, and tRNA secondary structures are identical with other members of the Percoidei suborder. Furthermore, we reconstructed phylogenetic trees based on the 13 PCGs. The resulting phylogenetic trees showed N. spinosus placing as a separate lineage within the family Niphonidae, its close relationship to Trachinus draco (Trachinidae), and the clustering of major subfamilies like Luciopercinae and Percinae of the Percoidei suborder. These findings will contribute to future studies on the evolutionary history, population genetics, molecular taxonomy, and phylogeny of N. spinosus and related species.

Assembly of Mitochondrial Genomes Using Nanopore Long-Read Technology in Three Sea Chubs (Teleostei: Kyphosidae)

Complete mitochondrial genomes have become markers of choice to explore phylogenetic relationships at multiple taxonomic levels and they are often assembled using whole genome short-read sequencing. Herein, using three species of sea chubs as an example, we explored the accuracy of mitochondrial chromosomes assembled using Oxford Nanopore Technology (ONT) Kit 14 R10.4.1 long reads at different sequencing depths (high, low and very low or genome skimming) by comparing them to 'gold' standard reference mitochondrial genomes assembled using Illumina NovaSeq short reads. In two species of sea chubs, Girella nigricans and Kyphosus azureus, ONT long-read assembled mitochondrial genomes at high sequencing depths (> 25× whole [nuclear] genome) were identical to their respective short-read assembled mitochondrial genomes. Not a single 'homopolymer insertion', 'homopolymer deletion', 'simple substitution', 'single insertion', 'short insertion', 'single deletion' or 'short deletion' were detected in the long-read assembled mitochondrial genomes after aligning each one of them to their short-read counterparts. In turn, in a third species, Medialuna californiensis, a 25× sequencing depth long-read assembled mitochondrial genome was 14 nucleotides longer than its short-read counterpart. The difference in total length between the latter two assemblies was due to the presence of a short motif 14 bp long that was repeated (twice) in the long read but not in the short-read assembly. Read subsampling at a sequencing depth of 1× resulted in the assembly of partial or complete mitochondrial genomes with numerous errors, including, among others, simple indels, and indels at homopolymer regions. At 3× and 5× subsampling, genomes were identical (perfect) or almost identical (quasiperfect, 99.5% over 16,500 bp) to their respective Illumina assemblies. The newly assembled mitochondrial genomes exhibit identical gene composition and organisation compared with cofamilial species and a phylomitogenomic analysis based on translated protein-coding genes suggested that the family Kyphosidae is not monophyletic. The same analysis detected possible cases of misidentification of mitochondrial genomes deposited in GenBank. This study demonstrates that perfect (complete and fully accurate) or quasiperfect (complete but with a single or a very few errors) mitochondrial genomes can be assembled at high (> 25×) and low (3-5×) but not very low (1×, genome skimming) sequencing depths using ONT long reads and the latest ONT chemistries (Kit 14 and R10.4.1 flowcells with SUP basecalling). The newly assembled and annotated mitochondrial genomes can be used as a reference in environmental DNA studies focusing on bioprospecting and biomonitoring of these and other coastal species experiencing environmental insult. Given the small size of the sequencing device and low cost, we argue that ONT technology has the potential to improve access to high-throughput sequencing technologies in low- and moderate-income countries.

Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection

The development of management strategies for the promotion of sustainable fisheries relies on a deep knowledge of ecological and evolutionary processes driving the diversification and genetic variation of marine organisms. Sustainability strategies are especially relevant for marine species such as the European sardine (Sardina pilchardus), a small pelagic fish with high ecological and socioeconomic importance, especially in Southern Europe, whose stock has declined since 2006, possibly due to environmental factors. Here, we generated sequences for 139 mitochondrial genomes from individuals from 19 different geographical locations across most of the species distribution range, which was used to assess genetic diversity, diversification history and genomic signatures of selection. Our data supported an extensive gene flow in European sardine. However, phylogenetic analyses of mitogenomes revealed diversification patterns related to climate shifts in the late Miocene and Pliocene that may indicate past divergence related to rapid demographic expansion. Tests of selection showed a significant signature of purifying selection, but positive selection was also detected in different sites and specific mitochondrial lineages. Our results showed that European sardine diversification has been strongly driven by climate shifts, and rapid changes in marine environmental conditions are likely to strongly affect the distribution and stock size of this species.

The complete mitogenome of Argentina brasiliensis Kobyliansky, 2004 and a phylogenetic analyses of the order Argentiniformes

The deep sea environment is the largest environment and host some of the most extreme ecosystems on Earth, therefore, possessing a large and unique fish diversity that encompasses about 15% of all known species. Our knowledge about these fishes is still very limited in many biological fields basically due to the complexity to obtain specimens for research. In the present study, we describe the complete mitochondrial genome of Argentina brasiliensis, aiming a species characterization and the study of the phylogenetic relationships in the order Argentiniformes. The mitogenome is composed by 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region (D-loop), as found in other vertebrates. The phylogenetic results show that the order Argentiniformes is composed by two family groups the first formed by Argentinidae and Opisthoproctidae and the second formed by Bathylagidae and Microstomatidae. Additionally, we found that the genus Argentina is not monophyletic, and we suggest additional studies in the family Argentinidae to better investigate this question.

Population genomics of the southern giraffe

Studying wildlife taxonomic diversity and identifying distinct populations has traditionally been largely based on morphology and geographic origin. More recently, this method has been supplemented by genetic data from the mitochondrial genome. However, this is limited as only maternally inherited and may not reflect the true nature of a population's genetics. Within the giraffe (Giraffa spp.), subspecies and unique populations were successfully characterized using both mitochondrial and genomic DNA studies, which led to new insights and, in some cases, unexpected results that required further verification. Here, we sequenced the genomes of 85 southern giraffe (G. giraffa) individuals from ten populations across southern Africa for a detailed investigation into the genetic diversity and history of its two subspecies, the Angolan (G. g. angolensis) and the South African (G. g. giraffa) giraffe. While the overall genotypes show low levels of runs of homozygosity compared to other mammals, the degree of heterozygosity is limited despite the large population size of South African giraffe. The nuclear genotype is largely congruent with the mitochondrial genotype. However, we have identified that the distribution of the Angolan giraffe is not as far east as indicated in an earlier mitochondrial DNA study. Botswana's Central Kalahari Game Reserve giraffe are unique, with a clear admixture of Angolan and South African giraffe populations. However, the enigmatic desert-dwelling giraffe of northwest Namibia is locally distinct from other Angolan giraffe yet exhibits intra-subspecies signs of admixture resulting from a recent introduction of individuals from Namibia's Etosha National Park. Whole genome sequencing is an invaluable and nearly indispensable tool for wildlife management to uncover genetic diversity that is undetectable through mitogenomic, geographical, and morphological means.

A systematic survey of environmental DNA in Palau's lakes and waterfalls reveals an increase in Leptospira levels after flooding

Objective

Leptospirosis is an important bacterial zoonosis which is widespread in tropical and subtropical islands and influences human and animal health which has secondary economic effects. Although leptospirosis is endemic in Palau, an Oceanian Pacific Island country, few systematic surveys of potential risk factors for Leptospira infection, such as weather and host animals, have been conducted in the natural environment. We used environmental DNA metabarcoding to assess the distribution, species diversity, and abundance of pathogenic Leptospira in this endemic region to investigate the potential environmental risks.

Methods

Forty-two paired water samples, representing fine and rainy weather conditions, were collected from four representative waterfalls and lakes on Babeldaob Island, the largest island in Palau. High-throughput sequencing analysis was conducted for polymerase chain reaction products of leptospiral 16S rRNA and vertebrate animal mitochondrial 12S rRNA genes.

Results

We revealed greater Leptospira diversity and abundance in samples collected after continuous rain, particularly in the presence of flooding, compared with samples collected under typhoon, monsoon, or fine weather conditions. From same samples, six mammalian species including cats (Felis catus), mice (Mus musculus), Yap flying fox (Pteropus yapensis), rats (Rattus spp.), and pigs (Sus scrofa) were repeatedly detected. These may be candidates of host animals of Leptospira in Palau; however, their detection was not clearly correlated with that of Leptospira.

Conclusion

We repeatedly detected several species of pathogenic Leptospira from water samples of a wide region of Babeldaob Island. We confirmed that Leptospira contamination in freshwater environments increased under rainy conditions, particularly in the presence of flooding. This information could be used to improve public health control measures in this region.

Insights into the structural features and phylogenetic implications of the complete mitochondrial genome of Fasin rainbow fish (Melanotaenia fasinensis)

The Fasin rainbow fish, scientifically named Melanotaenia fasinensis, is highly prized by aquarium enthusiasts for its vibrant colors and adaptability to artificial aquatic environments. This species is endemic to the karst landscape of the Bird's Head region in Papua, Indonesia, and belongs to the family Melanotaeniidae. Discovered relatively recently in 2010, this species was designated as endangered by the International Union for Conservation of Nature (IUCN) in 2021. However, there is currently insufficient data regarding its phylogenetic position. To address this gap, our study employed next-generation sequencing (NGS) to analyze the entire mitochondrial genome of M. fasinensis. The mitochondrial genome comprises 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with a total length of 16,731 base pairs. The base composition of the mitogenome revealed percentages of 27.76% adenine (A), 27.34% thymine (T), 16.15% guanine (G), and 28.75% cytosine (C) residues. Our phylogenetic analysis based on sequence data indicated that all species of the Melanotaeniidae family clustered together on the same branch. Furthermore, the intergeneric and interspecific taxonomic positions were explicit and clear. Phylogenetically, Melanotaeniidae were more closely related to the family Isonidae than to the family Atherinomorus. The phylogenetic position of M. fasinensis was relatively basal within the genus Melanotaenia. This study provides valuable molecular insights for further exploration of the phylogeography and evolutionary history of M. fasinensis and other members of the genus Melanotaenia.

Genomic insights into fish pathogenic bacteria: A systems biology perspective for sustainable aquaculture

Fish diseases significantly challenge global aquaculture, causing substantial financial losses and impacting sustainability, trade, and socioeconomic conditions. Understanding microbial pathogenesis and virulence at the molecular level is crucial for disease prevention in commercial fish. This review provides genomic insights into fish pathogenic bacteria from a systems biology perspective, aiming to promote sustainable aquaculture. It covers the genomic characteristics of various fish pathogens and their industry impact. The review also explores the systems biology of zebrafish, fish bacterial pathogens, and probiotic bacteria, offering insights into fish production, potential vaccines, and therapeutic drugs. Genome-scale metabolic models aid in studying pathogenic bacteria, contributing to disease management and antimicrobial development. Researchers have also investigated probiotic strains to improve aquaculture health. Additionally, the review highlights bioinformatics resources for fish and fish pathogens, which are essential for researchers. Systems biology approaches enhance understanding of bacterial fish pathogens by revealing virulence factors and host interactions. Despite challenges from the adaptability and pathogenicity of bacterial infections, sustainable alternatives are necessary to meet seafood demand. This review underscores the potential of systems biology in understanding fish pathogen biology, improving production, and promoting sustainable aquaculture.

Complete mitochondrial genome sequence and phylogenetic analysis of the hybrid flat fish Platichthys stellatus (♀) × Platichthys bicoloratus (♂)

We report the complete mitochondrial genome of the hybrid flounder Platichthys stellatus (♀) × Platichthys bicoloratus (♂). The mitochondrial genome contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 control region (D-loop), for a total length of 16,874 bp. The nucleotide composition of the heavy strand was 29.15% C, 26.99% A, 26.14% T, and 17.71% G. A maximum-likelihood phylogenetic analysis showed that the hybrid flat fish was a member of the same clade as P. stellatus (maternal inheritance). Our findings add to the extant data on the subfamily Pleuronecidae and provide insight into their molecular phylogeny and taxonomy.

DNA metabarcoding unveils the hidden species composition in fish surimi: Implications for the management of unlabeled and mixed seafood products

Fish surimi products are traditional foods primarily made from fish meat and may contain a complex species composition. In Taiwan, the abundant fishery resources and diverse fish species lead to local catches being widely used as ingredients in fish surimi products. However, due to growing market demand and increasingly scarce resources, some surimi products contain sensitive species, such as sharks, posing potential threats to the ecological environment and biodiversity. In this study, by applying metabarcoding techniques, we analyzed 120 fish surimi product samples from different brands and types throughout the four seasons in Taiwan's market. The main fish species identified included milkfish (Chanos chanos), dolphinfish (Coryphaena hippurus), Pomfret (Taractes rubescens), swordfish (Istiophorus spp.) and cartilaginous. Moreover, at least 37 species of cartilaginous fish, including 26 endangered species, were found. Through comprehensive and accurate species identification of surimi product ingredients, we unveiled the usage of sensitive species in products on the market. This finding is important for the surimi industry's quality control and market supervision. Furthermore, it can promote the sustainable use of Taiwan's fishery resources and protect biodiversity.

The complete mitochondrial genome of the blackskin catfish (Clarias meladerma: Clariidae) from Rokan River, Riau, Indonesia

Clarias meladerma Bleeker, 1846, a native catfish species in Indonesia belonging to the family Clariidae. The present study the complete mitochondrial genome sequence of C. meladerma from the Rokan River was sequenced by using next-generation sequencing, and its phylogenetic relationship was analyzed. The mitochondrial genome comprises 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, with a total length of 16,808 bp. The mitogenome of C. meladerma exhibits a base composition of 32.49% adenine, 25.75% thymine, 14.51% guanine, and 27.25% cytosine. Phylogenetic analysis indicated that C. meladerma has the same clade with C. macrocephalus, C. batrachus, and C. fucus. In essence, the findings of this study lay down a genetic foundation for future investigations into C. meladerma.

Environmental DNA Reveals the Impact of Submarine Groundwater Discharge on the Spatial Variability of Coastal Fish Diversity

Submarine groundwater discharge (SGD) has recently been recognized as an influential factor in coastal ecosystems; however, little research has been conducted on its effects on coastal fish diversity. To investigate the relationship between SGD and fish diversity, we conducted a survey at the coastal island scale using the environmental DNA (eDNA) method. Our findings indicate that fish species richness and functional richness peak at stations with high SGD. Environmental variables, such as salinity, dissolved inorganic nitrogen (DIN) concentration, and SGD, significantly influence fish diversity. Carnivore fish richness was negatively correlated with salinity, while planktivore fish richness was positively correlated. Additionally, SGD and DIN concentrations were found to be crucial in shaping omnivorous and pelagic communities, respectively. This study highlights the role of SGD in enhancing nutrient conditions favorable for diverse fish communities and demonstrates the effectiveness of eDNA metabarcoding for rapid marine biodiversity assessment. These findings provide valuable insights for coastal ecosystem monitoring and management.

Chromosome-Level Genome Assembly of the Viviparous Eelpout Zoarces viviparus

The viviparous eelpout Zoarces viviparus is a common fish across the North Atlantic and has successfully colonized habitats across environmental gradients. Due to its wide distribution and predictable phenotypic responses to pollution, Z. viviparus is used as an ideal marine bioindicator organism and has been routinely sampled over decades by several countries to monitor marine environmental health. Additionally, this species is a promising model to study adaptive processes related to environmental change, specifically global warming. Here, we report the chromosome-level genome assembly of Z. viviparus, which has a size of 663 Mb and consists of 607 scaffolds (N50 = 26 Mb). The 24 largest represent the 24 chromosomes of the haploid Z. viviparus genome, which harbors 98% of the complete Benchmarking Universal Single-Copy Orthologues defined for ray-finned fish, indicating that the assembly is highly contiguous and complete. Comparative analyses between the Z. viviparus assembly and the chromosome-level genomes of two other eelpout species revealed a high synteny, but also an accumulation of repetitive elements in the Z. viviparus genome. Our reference genome will be an important resource enabling future in-depth genomic analyses of the effects of environmental change on this important bioindicator species.

Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation

Hybridization has been recognized to play important roles in evolution, however studies of the genetic consequence are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the genus Xiphophorus are proposed to have evolved with multiple ancient and ongoing hybridization events. They have served as an informative research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genomic resource including annotations for all described 26 Xiphophorus species and three undescribed taxa and resolve all uncertain phylogenetic relationships. We investigate the molecular evolution of genes related to cancers such as melanoma and for the genetic control of puberty timing, focusing on genes that are predicted to be involved in pre-and postzygotic isolation and thus affect hybridization. We discovered dramatic size-variation of some gene families. These persisted despite reticulate evolution, rapid speciation and short divergence time. Finally, we clarify the hybridization history in the entire genus settling disputed hybridization history of two Southern swordtails. Our comparative genomic analyses revealed hybridization ancestries that are manifested in the mosaic fused genomes and show that hybridization often preceded speciation.

phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases

We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on the uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (i) species or classification of query sequences and (ii) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of nonmitochondrial genes, e.g. ITS or rbcL.

Comparative mitogenomics of marine angelfishes (F: Pomacanthidae)

The targeted capture of ultraconserved elements (UCEs) has substantially increased the amount of genetic data available for phylogenomic reconstructions. These capture datasets frequently contain mitochondrial DNA as a by-product, often in the form of complete mitogenomes. These can be efficiently harvested to expand existing datasets without additional costs. Here, we present new mitochondrial genomes for six marine angelfish species (F: Pomacanthidae), assembled and annotated from off-target UCE reads. We provide the first comparative analysis of all mitochondrial genomes available for the Pomacanthidae. Results showed that the average length of pomacanthid mitogenomes is 16.8 kbp. Total GC and AT content varied between 44.5% and 46.3%, and 53.7% and 55.5%, respectively. The architecture of angelfish mitogenomes was comparable to that seen in other fish species with 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and the control region. All 13 PCGs evolved under purifying selection, highlighting a high level of selection pressure and gene expression to preserve genetic integrity. The ND6 and ATP8 genes had the highest ratio of non-synonymous (dN) to synonymous (dS) substitutions, indicating a relaxation of purifying selection constraints. Finally, these newly assembled mitogenomes will allow further investigations of the population genetics, systematics and evolutionary biology of one of the most prominent reef fish family in the aquarium trade.

Mitochondrial Genome Characteristics Reveal Evolution of Acanthopsetta nadeshnyi (Jordan and Starks, 1904) and Phylogenetic Relationships

In the present study, the mitochondrial genomic characteristics of Acanthopsetta nadeshnyi have been reported and have depicted the phylogenetic relationship among Pleuronectidae. Combined with a comparative analysis of 13 PCGs, the TN93 model was used to review the neutral evolution and habitat evolution catalysis of the mitogenome to verify the distancing and purification selectivity of the mitogenome in Pleuronectidae. At the same time, a species differentiation and classification model based on mitogenome analysis data was established. This study is expected to provide a new perspective on the phylogenetic relationship and taxonomic status of A. nadeshnyi and lay a foundation for further exploration of environmental and biological evolutionary mechanisms.

Exploring microbiome and plankton responses and interactions in the mangrove ecosystem through eDNA and network analysis

The comprehensive analysis of multiple biological communities is essential for assessing diversities within mangrove ecosystems, yet such studies are infrequent. Environmental DNA (eDNA) facilitates the simultaneous exploration of organisms across various levels within a single ecosystem. In this investigation, 16S rRNA, cytochrome C oxidase I (COI), and Mito-fish primers were employed to characterize the microbiome, eukaryotic plankton, and fish communities, along with their intricate interactions, across 24 samples from three Chinese mangrove reservoirs. The resulting dataset encompasses 3779 taxonomic groups (genus level), spanning from the microbiome to vertebrates. Diversity analysis unveiled a higher level of stability in the microbiome community compared to plankton, underscoring the superior site-specificity of plankton. The association analysis revealed that biodiversity was primarily affected by temperature, turbidity, and fluorescent dissolved organic matter (fDOM). Notably, the physicochemical factors, turbidity, and fDOM had a more pronounced impact on the microbiome than on plankton, explaining their distinct sensitivities to site-specific conditions. Network analysis constructed 15 biological interaction subnetworks representing various community connections. The most connected genera in each subnetwork, highly responsive to different environmental factors, could serve as potential indicators of distinct ecosystem states. In summary, our findings represent the first comparison of the response sensitivities of different communities and the construction of their interaction networks in mangrove environments. These results contribute valuable insights into marine ecosystem dynamics and the role of environmental factors in shaping biodiversity.

CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish

Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution. Database URL:  http://210.22.121.250:8888/CoSFISH/home/indexPage.

Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool

The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia. Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost-effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning.

The complete mitochondrial genome of Hypsipetes amaurotis (Passeriformes: Pycnonotidae)

The brown-eared bulbul (Hypsipetes amaurotis) is a medium-sized songbird native to East Asia and characterized by its prominent reddish-brown ear-coverts. Previous studies on it have primarily been from the taxonomic and morphological aspects, with limited research in the realm of molecular biology. In this study, we sequenced and annotated the complete mitochondrial genome of H. amaurotis, which was the first reported complete mitogenome of the genus Hypsipetes. The mitogenome of H. amaurotis is 17,871 bp in length and was predicted to encode 37 typical mitochondrial genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs). Specifically, this mitogenome contains two D-loop control regions that are of similar length and sequencing pattern. A total of 8 Pycnonotidae and six outgroup taxa were used to determine the phylogenetic placement with two methods: Maximum Likelihood Approximation (IQ-TREE) and Bayesian inference (MrBayes). Our findings reveal that H. amaurotis is phylogenetically closely related to Ixos mcclellandii. The outcomes are generally consistent with the phylogenetic trees constructed in previous studies. The data gathered from this research provides valuable insights for future genomic investigations into the evolution, ecology, and conservation of this species.

New species of redbait from the Philippines (Teleostei, Emmelichthyidae, Emmelichthys)

We describe a new species of redbait in the genus Emmelichthys collected from fish markets on Panay and Cebu islands in the Visayas region of the Philippines. The species is externally similar to E.struhsakeri but is diagnosable by two prominent fleshy papillae associated with the cleithrum and fewer pectoral-fin rays (18-19 vs. 19-21) and gill rakers (30-33 vs. 34-41). Additionally, mitochondrial DNA differentiates this taxon from other species of Emmelichthys. We generate mitochondrial genomes for two of the three type specimens and several other emmelichthyids to place the new taxon in a phylogenetic context. Analysis of the protein-coding mitochondrial loci calls into question the monophyly of two emmelichthyid genera (Emmelichthys and Erythrocles) and highlights the need for subsequent analyses targeting the intrarelationships of the Emmelichthyidae.

Comparative evaluation for the performance of environmental DNA and RNA analyses targeting mitochondrial and nuclear genes from ayu (Plecoglossus altivelis)

Environmental DNA and RNA (eDNA and eRNA; collectively eNA) analyses have the potential for non-invasive and cost-efficient biomonitoring compared with traditional capture-based surveys. Although various types of eNA particles, including not only mitochondrial eDNA but also nuclear eDNA and their transcripts, are present in the water, performances of eNA detection and quantification have not yet been evaluated sufficiently across multiple mitochondrial and nuclear genes. We conducted a tank experiment with ayu (Plecoglossus altivelis) to compare the detection sensitivity, yields per water sample, and quantification variability between replicates of each type of eNAs. The assay targeting the multi-copy nuclear gene exhibited a higher sensitivity than the assay targeting the mitochondrial gene, and both the target eDNA and eRNA concentrations per water sample were higher for the nuclear gene. On the contrary, variation in eRNA quantifications per sample does not necessarily correspond to that in eDNA, and the intra-sample quantification variability (represented as the CVs between PCR replicates) tended to be larger for eRNA than eDNA. Our results suggested that, even if suitable to the sensitive detection of species occurrence, the use of eRNA particularly derived from multi-copy nuclear gene may not be necessarily appropriate for the reliable assessment of species abundance. The findings in this study would help optimize eNA analyses for making biomonitoring and stock assessment in aquatic environments more efficient and reliable.

Complete mitogenome of Lepidopygopsis typus, an evolutionarily-distinct, endangered cyprinid fish from the Western Ghats Biodiversity Hotspot: Phylogenetic relationships and implications for conservation

The mitogenome of Lepidopygopsis typus, an evolutionarily distinct, endangered, cyprinid fish from the Western Ghats Biodiversity Hotspot, was characterized. Total length of the mitogenome was 16,729 bp, and comprised of 13 protein coding, 22 tRNA and two rRNA genes. Thirteen protein coding genes contributed a total nucleotide length of 11,408 bp, which coded for a total of 3794 amino acids and accounting for 68.2 % of the mitogenome. A maximum likelihood phylogenetic tree based on mitogenomes of members of cyprinid subfamilies Torinae, Schizothoracinae and Schizopygopsinae, recovered L. typus in a well-resolved clade of Torinae with members of the Western Ghats endemic genus Hypselobarbus as sister taxa. Selection analysis suggested that the branch of L. typus and Hypselobarbus spp. was under intensified selection with reference to other members of Torinae. There were 19 codons under diversifying selection in L. typus, which could be the result of positive selection for adapting to high-altitude, upstream tributaries of Periyar River, where the species has a restricted distribution. With respect to Hypselobarbus spp., L. typus was under relaxed selection with about 68 % of codons experiencing neutral evolution. Restricted distribution, low population size and relaxation in selection can likely trigger extinction in L. typus, and therefore urgent conservation and monitoring plans are required to secure the future of this evolutionary distinct, and globally endangered species.

Assessing the impact of river connectivity on fish biodiversity in the Yangtze River Basin using a multi-index evaluation framework

The Yangtze River Basin, the world's third-largest river basin and a hot spot for global biodiversity conservation, is facing biodiversity crisis caused by reduced river connectivity. The deterioration arises from four dimensions: longitudinal, lateral, vertical and temporal. However, limited research has quantified the spatiotemporal connectivity of the Yangtze River Basin and further evaluated the consequent impact on fish biodiversity. In our study, a multi-index evaluation framework was developed to assess the variations in the four-dimensional connectivity of the Yangtze River Basin from 1980 to 2020, and fish biodiversity affected by reduced connectivity was detected by environmental DNA metabarcoding. Our results showed that the Yangtze River Basin suffers from a pronounced connectivity reduction, with 67% of assessed rivers experiencing deteriorated connectivity in recent years. The lost fish biodiversity along the river reaches with the worst connectivity was likely attributed to the construction of hydropower plants. The headwaters and the downstreams of most hydropower plants had a higher fish biodiversity compared with reservoirs. The free-flowing reaches in the downstream of the lowest hydropower station, had higher lotic fish abundance compared with that in the upstream. As for the entire Yangtze River Basin, 67% of threatened fish species, with 70% endemic species, were threatened by reduced river connectivity. Our result indicates that the massive loss of river connectivity changes the spatiotemporal patterns of fish community and threatens protected fish. More effective measures to restore the populations of affected fish in rivers with reduced river connectivity are required.

Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae)

Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.

Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus ) highlights hybridization precedes speciation

Hybridization has been recognized as an important driving force for evolution, however studies of the genetic consequence and its cause are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the central American genus Xiphophorus were proposed to have evolved with multiple ancient and ongoing hybridization events, and served as a valuable research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genome resource and its annotation of all 26 Xiphophorus species. On this dataset we resolved the so far conflicting phylogeny. Through comparative genomic analyses we investigated the molecular evolution of genes related to melanoma, for a main sexually selected trait and for the genetic control of puberty timing, which are predicted to be involved in pre-and postzygotic isolation and thus to influence the probability of interspecific hybridization in Xiphophorus . We demonstrate dramatic size-variation of some gene families across species, despite the reticulate evolution and short divergence time. Finally, we clarify the hybridization history in the genus Xiphophorus genus, settle the long dispute on the hybridization origin of two Southern swordtails, highlight hybridizations precedes speciation, and reveal the distribution of hybridization ancestry remaining in the fused genome.

rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R

The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.

Complete mitochondrial genome of golden variant of freshwater fish Labeo rajasthanicus (Cypriniformes: Cyprinidae): endemic to India

The complete mitochondrial genome of the freshwater fish species Labeo rajasthanicus was obtained, using Illumina NovaSeq 6000 with 2 × 150 bp paired-end sequencing. The mitogenome of L. rajasthanicus is 16,738 bp in length (GenBank accession no.: OQ834146), comprised of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, i.e. D-loop. The arrangement of genes was found to be identical to other Cypriniformes fish mitogenome, available in the NCBI database. The taxonomic status of L. rajasthanicus as a valid species was debated by some researchers and it was considered a synonym of L. boggut. However, phylogenetic analysis in the present study supports the species validity of L. rajasthanicus, as it showed a distinct node well separated from L. boggut and supported by a high bootstrap value. Furtherly, the pairwise genetic divergence among studied species showed the divergence between L. rajasthanicus and L. boggut as 1.6% whereas the minimum divergence was found to be 0.13% with L. dussumieri followed by L. fimbriatus (0.58%) and L. gonius (0.63%). The complete mitogenome of L. rajasthanicus will also be useful as a baseline reference genome for the reconstruction and annotation of the mitogenome of other Labeo species.

Description of eight new mitochondrial genomes for the genus Neoarius and phylogenetic considerations for the family Ariidae (Siluriformes)

The genus Neoarius, known as marine catfish, is a group of the family Ariidae, composed of 10 species found in Oceania. None of the species in this genus have their mitochondrial genome described, which is highly valuable in phylogenetic and molecular evolution studies. For the present work, eight species from the Neoarius genus were selected: Neoarius utarus, Neoarius midgleyi, Neoarius graeffei, Neoarius leptaspis, Neoarius berenyi, Neoarius paucus, Neoarius pectoralis, and Neoarius aff. graeffei. DNA sequences of the eight species were obtained through the NCBI Sequence Read Archive (SRA) database, and the mitochondrial genomes were assembled using the NOVOplasty tool on the Galaxy platform, subsequently annotated with the MitoAnnotator tool. We then utilized the protein-coding genes from the mitogenomes to estimate the phylogenetic relationships within the group, including seven additional mitogenomes available in the NCBI. In all species, the mitochondrial genomes presented 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 D-loop.

The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses

Hemiculterella wui is an endemic small freshwater fish, distributed in the Pearl River system and Qiantang River, China. In this study, we identified and annotated the complete mitochondrial genome sequence of H. wui. The mitochondrial genome was 16,619 bp in length and contained 13 protein coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. The nucleotide composition of the mitochondrial genome was 29.9% A, 25.3% T, 27.4% C, and 17.5% G, respectively. Most PCGs used the ATG start codon, except COI and ATPase 8 started with the GTG start codon. Five PCGs used the TAA termination codon and ATPase 8 ended with the TAG stop codon, and the remaining seven genes used two incomplete stop codons (T and TA). Most of the tRNA genes showed classical cloverleaf secondary structures, except that tRNASer(AGY) lacked the dihydrouracil loop. The average Ka/Ks value of the ATPase 8 gene was the highest, while the average Ka/Ks value of the COI gene was the lowest. Phylogenetic analyses showed that H. wui has a very close relationship with Pseudohemiculter dispar and H. sauvagei. This study will provide a valuable basis for further studies of taxonomy and phylogenetic analyses in H. wui and Xenocyprididae.

The Mitochondrial Genome of Linichthys laticeps (Cypriniformes: Cyprinidae): Characterization and Phylogeny

Mitochondrial genomes (mitogenomes) have been widely used in phylogenetic analysis and evolutionary biology. The Labeoninae is the largest subfamily of Cypriniformes and has great economic importance and ecological value. In this study, we sequenced, annotated, and characterized the complete mitogenome of Linichthys laticeps and then constructed the phylogenetic tree with previously published Labeoninae mitogenomes. The mitogenome of L. laticeps was 16,593 bp in length, with an A + T content of 57.1%. The mitogenome contained a standard set of 37 genes and a control region with the same order and orientation of genes as most fish mitogenomes. Each protein-coding gene (PCG) was initiated by an initial ATG codon, excluding COI, that began with a GTG codon. Furthermore, most of the PCGs were terminated by a conventional stop codon (TAA/TAG), while an incomplete termination codon (TA/T) was detected in 7 of the 13 PCGs. Most tRNA genes in L. laticeps were predicted to fold into the typical cloverleaf secondary structures. The Ka/Ks (ω) values for all PCGs were below one. The phylogenetic relationships of 96 Labeoninae mitogenomes indicated that Labeoninae was not a monophyletic group and L. laticeps was closely related to the genera Discogobio and Discocheilus. Overall, our study provided the first complete annotated mitogenome of L. laticeps, which filled a knowledge gap in Labeoninae and extended the understanding of the taxonomy and mitogenomic phylogeny of the subfamily Labeoninae.

Characteristics and phylogenetic analysis of the complete mitochondrial genome of Glyptothorax pallozonus (Siluriformes, Sisoridae)

Glyptothorax pallozonus Lin, 1934 is a small benthic fish belonging to the Sisoridae family that is distributed in the Dongjiang and Rongjiang Rivers of China. In the present study, we sequenced and characterized the complete mitochondrial genome of G. pallozonus for the first time. The complete mitogenome of G. pallozonus is 16,542 bp in length and includes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNA (rRNAs), and a control region (CR). The mitogenome architecture was identical to that of other teleosts. Maximum likelihood (ML) phylogenetic analysis strongly supported the monophyly of Glyptothorax, which contains two clades. These results advance our understanding of the molecular phylogeny of the genus Glyptothorax.

The complete mitochondrial genomes of two imperiled species endemic to the Southwestern United States: Peppered Chub (Macrhybopsis tetranema) and Gila Trout (Oncorhynchus gilae)

Macrhybopsis tetranema and Oncorhynchus gilae are fish species endemic to the Southwestern United States. We present the complete mitochondrial genomes for these species. Each genome consisted of 13 protein-coding genes, two ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and the control region (D-loop). Mitogenome lengths were 16,916 base pairs (bp) for M. tetranema, and 16,976 bp for O. gilae. The GC content was 41% for M. tetranema and 46% for O. gilae. The relationships of M. tetranema and O. gilae were consistent with previous phylogenetic analyses.

rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R

Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa to meet taxonomic classification goals then are currently curated by professional staff. Thus, there is a growing need for an easy to implement tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire seed sequences containing a user-defined primer set. Next these seeds are used to iteratively blast search seed sequences against a local NCBI formatted database using a taxonomic rank based stratified random sampling approach (blast_seeds()) that results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer specific reference barcode sequences from NCBI. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, and fungal ITS locus than CRABS, METACURATOR, RESCRIPt, and ECOPCR reference databases. We then further demonstrate the utility of rCRUX by generating 16 reference databases for metabarcoding loci that lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.