MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

Integrative evidence reveals a new species of Hysterothylacium (Nematoda: Ascaridoidea), with the characterization of its complete mitochondrial genome

The genus Hysterothylacium (Ascaridida: Raphidascarididae) is among the commonest groups of parasitic nematodes occurring in the digestive tract of marine fishes. In the present study, a new species of Hysterothylacium, H. hainanense sp. n. collected from Uranoscopus tosae (Jordan & Hubbs) and U. japonicus Houttuyn (Perciformes: Uranoscopidae) in the Chinese waters was described using integrative methods, including light and scanning electron microscopy, and ASAP and BI analyses based on the ITS sequence data. The complete mitochondrial genome of the new species was sequenced and annotated, which represents the first mitogenomic data for the genus Hysterothylacium, and also for the family Raphidascarididae. The mitogenome of H. hainanense sp. n. is 14059 bp in length, including 12 protein coding genes (missing atp8), 22 tRNA genes, 2 rRNA genes and 2 non-coding regions, which has 67.0% of overall A + T content, and represents the lowest level of A + T content in the ascaridoid mitogenomes reported so far. Molecular phylogenetic results suggested a close affinity between H. hainanense sp. n. and H. fabri in the genus Hysterothylacium.

Mitogenome data sequence of a mangrove oyster of interest for cultivation in Ecuador: Crassostrea sp. (Bivalvia: Ostreidae)

Ostreids are one of the most exploited groups in aquaculture worldwide. In Ecuador, where aquaculture is dominated by Penaeus (Litopenaeus) vannamei, the introduction of the Pacific oyster Crassostrea gigas in 1990 aimed to diversify the industry. Initially, the Pacific oyster showed promising growth rates in both marine and estuarine environments. Unfortunately, the temperature and salinity variability along the Ecuadorian coast is a challenge for the species, causing massive mortalities, especially during the rainy months that last from December to April in Ecuador. This has motivated research into the possibility of domesticating native species. The mangrove oyster, an estuarine species, not only supports local livelihoods through its harvest but also plays a crucial role in maintaining the ecosystem. Previous trials have shown successful spat production under controlled conditions, highlighting the mangrove oyster's adaptability to captivity and its robust growth in the field. Consequently, efforts are underway to reduce the overexploitation of this species and protect the ecosystem through aquaculture trials. Despite these advancements, genomic studies of Ecuadorian oyster species remain limited. The Crassostrea mitogenome presented here, consisting of 18,937 bp and 40 genes (including 13 protein-coding genes, 25 transfer RNA genes, and two ribosomal RNA genes) contributes to the taxonomic-molecular identification of Ecuadorian mangrove oysters and supports extractive traceability. This analysis not only enhances our understanding of natural populations but also provides a basis for conservation efforts.

The first complete mitochondrial genome and phylogenetic analysis of the ornate flying snake Chrysopelea ornata (Shaw 1802) Colubridae

The first complete mitochondrial genome sequencing of ornate flying snake (Chrysopelea ornata_Shaw 1802) was conducted utilizing Next-generation sequencing technologies. The complete mitochondrial genome of flying tree snake is 17,252 bp long with a base composition of A-36%, T-27%, G-12%, C-25% with a GC content of 38%. Chrysopelea ornata also shows mitogenome organization of 37 genes including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and two non-coding regions. Nine genes including eight tRNAs and NAD6 were encoded. Phylogenetic investigations, utilizing the entire mitochondrial genome of chrysopelea ornata, reveal the strongest association with the genus Ptyas.

Integrated evidence reveals a new subspecies of the genus Seuratascaris (Nematoda: Ascaridomorpha), with characterization of the complete mitochondrial genome

Species of Seuratascaris Sprent, 1985 are a rarely reported group of ascaridoid nematodes, parasitising various frogs and toads. In the present study, a new subspecies of Seuratascaris, S. physalis bazhaiensis n. subsp. was described using integrated taxonomic methods, based on specimens collected from Odorrana graminea (Anura: Ranidae) in Guangxi Zhuang Autonomous Region, China. Results of the Assemble Species by Automatic Partitioning (ASAP) and Bayesian inference based on the mitochondrial cox1, cox2 and rrnS data all supported S. physalis bazhaiensis representing a distinct taxon from the nominate subspecies S. physalis physalis. Supplementary morphometric and genetic data of S. phy. physalis are presented based on newly collected material from Odorrana tiannanensis (Anura: Ranidae) and Rhacophorus sp. (Anura: Rhacophoridae) in Yunnan Province, China. A key to species of Seuratascaris is provided. The complete mitochondrial genome of S. physalis bazhaiensis was sequenced and annotated, and represents the first mitogenomic data for the genus Seuratascaris. This mitogenome has only 13,628 bp (including 12 protein-coding genes, 22 tRNA genes, 2 ribosomal RNAs, and only 1 non-coding region), and is the smallest of the reported ascaridoid mitogenomes so far.

Draft genome of the endangered visayan spotted deer (Rusa alfredi), a Philippine endemic species

The Visayan Spotted Deer (VSD), or Rusa alfredi, is an endangered and endemic species in the Philippines. Despite its status, genomic information on R. alfredi, and the genus Rusa in general, is missing. This study presents the first draft genome assembly of the VSD using the Illumina short-read sequencing technology. The resulting RusAlf_1.1 assembly has a 2.52 Gb total length, with a contig N50 of 46 Kb and scaffold N50 size of 75 Mb. The assembly has a BUSCO complete score of 95.5%, demonstrating the genome's completeness, and includes the annotation of 24,531 genes. Our phylogenetic analysis based on single-copy orthologs revealed a close evolutionary relationship between R. alfredi and the genus Cervus. RusAlf_1.1 represents a significant advancement in our understanding of the VSD. It opens opportunities for further research in population genetics and evolutionary biology, potentially contributing to more effective conservation and management strategies for this endangered species.

Phylogenetic relationships and divergence times of Odonata inferred from mitochondrial genome

Understanding the origin and evolutionary history of Odonata are crucial, as they represent central members of the first winged lineages. Here, we assembled the largest mitogenome dataset to date, comprising 143 mitogenomes representing three suborders, 18 families, of which 53 mitogenomes were newly sequenced. Phylogenetic inferences demonstrate that the mitogenome is a powerful tool for resolving lower-level divergence within Odonata, and it falls short in addressing higher-level relationships like suborder, superfamily, and interfamily classifications. The evolutionary history of Odonata was reconstructed by incorporating 11 fossil records, estimating the origin of Odonata occurred in the Jurassic, with the Cretaceous emerging as a critical period for the initial radiation of main Odonata lineages. Furthermore, we employed fossil calibration strategies from various studies to calibrate our analyses, enabling the investigation of mito-nuclear discordance patterns in divergence time inferences. Our results revealed significant differences in divergence time estimates inferred solely from mitochondrial or nuclear data within Odonata, particularly pronounced when using older upper bounds values for fossils.

The complete mitochondrial genome of the Toxopneustes pileolus Lamarck, 1816 (Echinoidea: Camarodonta: Toxopneustidae) and phylogenetic analysis

In this study, we report the complete mitochondrial genome sequence of Toxopneustes pileolus (Lamarck, 1816), which is the first complete mitochondrial genome of this genus Toxopneustes. The mitochondrial genome is 15,711 bp in length and includes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one non-coding control region (D-loop). Phylogenetic analysis based on mitochondrial genomes suggested a potential close relationship between the genus Toxopneustes and the genus Lytechinus. This study provided valuable genetic data for T. pileolus and contributed to the exploration of the phylogenetic relationships within the family Toxopneustidae.

An Integrative Phylogenetic Analysis of the Genus Rhynchium Spinola (Hymenoptera: Vespidae: Eumeninae) from China Based on Morphology, Genomic Data and Geographical Distribution

The species of the genus Rhynchium Spinola are important natural insect control resources and widespread in the Old World. Due to the various color patterns of several species in China, it is difficulty to accurately classify and identify the genus. We combined their morphology with population genetic differentiation, phylogenetic relationship and geographical distribution to delimitate the species of Rhynchium from China. Within the genus, more than 600 pinned specimens were examined and a total of 37 whole genomes were analyzed, of which 35 were newly sequenced. Firstly, COI sequences, 13 PCGs and 2 rRNAs sequences of the mitochondrial genomes, USCO nucleotide matrix of 90% completeness (USCO90_fna), and USCO amino acid matrix of 90% completeness (USCO90_faa) were extracted from the whole-genome data. Then, genetic distances were calculated using the COI sequences, and ABGD species delimitation analysis identified three valid species. By integrating the four phylogenetic trees inferred from the four datasets and morphological analysis, the specimens of Rhynchium from China were recognized as R. carnaticum (newly recorded), R. quinquecinctum, and R. brunneum; the last is the most widely distributed in China, while the remaining two only occur in Hainan and Yunnan, respectively, markedly different from previous records. Finally, it is interesting that color patterns of the species R. brunneum seem to closely relate to the geographical distribution, embodying two different modes in the South and the North of China, as well as a transitional state in the middle. The roles of the color patterns are still not resolved and their underlying evolutionary mechanisms need further exploration.

Comparative mitogenomics of Cheiracanthium species (Araneae: Cheiracanthiidae) with phylogenetic implication and evolutionary insights

The genus Cheiracanthium C. L. Koch, 1839 is the most species-rich genus of the family Cheiracanthiidae. Given the unavailability of information on the evolutionary biology and molecular taxonomy of this genus, here we sequenced nine mitochondrial genomes (mitogenomes) of Cheiracanthium species, four of which were fully annotated, and conducted comparative analyses with other well-characterized Araneae mitogenomes. We also provide phylogenetic insights on the genus Cheiracanthium. The circular mitogenomes of the Cheiracanthium contain 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and one putative control region (CR). All genes show a high A+T bias, characterized by a negative AT skew and positive GC skew, along with numerous overlapped regions and intergenic spacers. Approximately half of the tRNAs lack TΨC and/or dihydrouracil (DHU) arm and are characterized with unpaired amino acid acceptor arms. Most PCGs used the standard ATN start codons and TAR termination codons. The mitochondrial gene order of Cheiracanthium differs significantly from the putative ancestral gene order (Limulus polyphemus). Our novel phylogenetic analyses infer Cheiracanthiidae to be the sister group of Salticidae in BI analysis, but as sister to the node with Miturgidae, Viridasiidae, Corinnidae, Selenopidae, Salticidae, and Philodromidae in ML analysis. We confirm that Cheiracanthium is paraphyletic, for the first time using molecular phylogenetic approaches, with the earliest divergence estimated at 67 Ma. Our findings enhance our understanding of Cheiracanthium taxonomy and evolution.

Characterization of the complete mitochondrial genomes of Corynosoma bullosum (von Linstow, 1892) and C. evae Zdzitowiecki, 1984 (Acanthocephala: Polymorphida), and the phylogenetic implications

Species of the genus Corynosoma (Acanthocephala: Polymorphida) mainly parasitize marine mammals and rarely marine birds, and are of veterinary and medical importance due to causing corynosomiasis in wildlife and humans. However, the current knowledge of the mitochondrial genomes and mitogenomic phylogeny of this group remains very insufficient. In the present study, the complete mitochondrial genomes of C. bullosum (von Linstow, 1892) and C. evae Zdzitowiecki, 1984 were sequenced and annotated for the first time. Both mitogenomes comprise 12 protein-coding genes (missing atp8), 22 tRNA genes, and 2 ribosomal RNAs (rrnS and rrnL), plus 2 non-coding regions (NCR1 and NCR2). Corynosoma bullosum has the largest mitogenome (14,879 bp) of any polymorphid species reported so far, while C. evae has the smallest (13,947 bp), except for Sphaerirostris lanceoides (Petrochenko, 1949). Comparative mitogenomic analysis also revealed the presence of distinct discrepancies in A + T content and gene rearrangement across the families Polymorphidae, Centrorhynchidae, and Plagiorhynchidae. Moreover, phylogenetic analyses based on the concatenated amino acid sequences of 12 protein-coding genes strongly supported the monophyly of the order Polymorphida and a close affinity between the families Polymorphidae and Centrorhynchidae in Polymorphida. The present mitogenomic phylogeny provides additional evidence for a sister relationship between the genera Corynosoma and Bolbosoma and demonstrated that C. evae has a closer relationship with C. villosum than C. bullosum in the genus Corynosoma.

Genome assembly of Hawaiian flower thrips Thrips hawaiiensis (Thysanoptera: Thripidae)

The Hawaiian flower thrips, Thrips hawaiiensis, is a common flower inhabiting pest of various horticultural plant species. It damages flowers and fruits by puncturing. T. hawaiiensis shows a rapidly developed resistance to chemical control. The lack of a high-quality reference genome limits our understanding of the genetics of T. hawaiiensis. Here, we sequenced the genome of T. hawaiiensis using Oxford Nanopore sequencing technology, Illumina, and Hi-C technology, yielding a genome assembly of 287.59 Mb with scaffold N50 of 13.84 Mb. BUSCO analysis demonstrated the T. hawaiiensis genome assembly has a high-level completeness of 98.7%. In total, 18,289 protein-coding genes were annotated and 26.69% of the genome were annotated as repeats. Our study presents the first high-quality genome assembly of T. hawaiiensis and lays the foundation for further studies on thrips genetic characteristics and pest management.

The complete mitochondrial genome and phylogenetic analyses of Cathartes melambrotus (Wetmore 1964) (Aves: Cathartidae)

Cathartes melambrotus is the largest member of the genus Cathartes, and soars over the forested areas of Amazonia in search of carrion. The complete mitochondrial genome of C. melambrotus was reported in this study. The 19,232 base pair genome consisted of 16 protein coding genes, 25 tRNAs, two rRNAs, and two control regions. The mitochondrial genome contained the avian ancestral duplicated gene region, with the same rearrangements previously reported in Accipitriformes, Cathartiformes, and Stigiformes. With the publishing of the C. melambrotus genome all seven Cathartiformes species mitochondrial genomes are available and can be included in subsequent phylogenetic and genomic analyses.

The complete mitochondrial genomes and phylogenetic analysis of two Chinese endemic cave fishes, Sinocyclocheilus guilinensis and S. huangtianensis (Cypriniformes: Cyprinidae)

Sinocyclocheilus is a group of cyprinid fishes endemic to China distributed in the karst region of southwest China. In this study, the complete mitogenomes of Sinocyclocheilus guilinensis Ji, 1985 and Sinocyclocheilus huangtianensis Zhu et al. 2011 are reported and characterized. Both genomes contain 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a non-coding control region, with lengths of 16,576 bp and 16,578 bp, respectively. Phylogenetic analysis shows that S. guilinensis is the earliest branching species in the S. jii group, while S. huangtianensis and S. jii are sister groups. These mitochondrial genomes are valuable for studying systematics of Sinocyclocheilus.

A Review of the Psyllid Genus Epipsylla (Hemiptera, Psyllidae) from the Chinese Mainland with Phylogenetic Considerations and the Description of a New Species

Epipsylla Kuwayama, 1908, constitutes an Old World genus of psyllids with 15 described species. Based on characters of immatures, Epipsylla was recently assigned to Ciriacreminae (Psyllidae). The genus is morphologically well circumscribed but species are currently difficult to identify as many descriptions lack detail and precision. Eight species are reported from the Chinese mainland. Here, we provide diagnoses for the adults of these species and, as far as known, the fifth-instar immatures. Figures are provided of taxonomically relevant adult characters. A new species, Epipsylla suni sp. nov., is described from Yunnan (China). We provide illustrations of its habitus and morphological features, and list the host plant. Furthermore, we sequenced the mitochondrial genome of the new species and constructed a phylogenetic tree using thirteen protein-coding genes and two rRNA genes. The results of the molecular phylogenetic analysis using the maximum likelihood method support the assignment to Ciriacreminae.

Mitochondrial Gene Expression of Three Different Dragonflies Under the Stress of Chlorpyrifos

Chlorpyrifos (CPF) is an organophosphate insecticide that is extensively utilized globally due to its effectiveness against over 200 pest species. CPF exhibits its toxicity primarily through the inhibition of the acetylcholinesterase (AChE) enzyme, while mitochondrial damage and dysfunction have also been observed. The present study quantified the transcript levels of mitochondria protein-coding genes (mtPCGs) using quantitative real-time polymerase chain reaction (RT-qPCR) in samples of larvae of three dragonfly species (A. parthenope, E. elegans, and G. confluens) under different levels of CPF stress. By exposing larvae from uncontaminated populations to 0.05 μg/L CPF for 24 h, the transcript levels of seven mtPCGs in A. parthenope were significantly increased (p < 0.05) by 1.89 ± 0.42-fold for COI, 4.30 ± 0.24-fold for COIII, 5.94 ± 0.17-fold for ND1, 4.69 ± 0.56-fold for ND2, 3.44 ± 0.48-fold for ND4, 2.19 ± 0.53-fold for ND4L, and 5.05 ± 0.36-fold for Cytb, respectively. In E. elegans, the transcript levels of ND1, ND2, and ND4 increased by 1.23 ± 0.15, 1.48 ± 0.31, and 1.98 ± 0.25-fold, respectively (p < 0.05). In G. confluens, the transcript levels of COI, COIII, and ND4 increased by 1.56 ± 0.13, 1.50 ± 0.26, and 3.74 ± 0.40-fold, respectively (p < 0.01). It was demonstrated that the transcript levels of different mtPCGs showed significant up-regulation in the three different dragonfly larvae under CPF stress in the absence of mortality. ND4 was significantly increased in all three species, indicating that it is an important target gene. The present study underscores the response of mitochondrial gene expression in larvae of three different species in response to CPF pollutants, indicating that pesticide influences can potentially alter mitochondrial gene expression and potentially act as a method for assessing aquatic ecosystem health.

Characterization of the complete mitochondrial genomes of four tarantulas (Arachnida: Theraphosidae) with phylogenetic analysis

To better understand the evolution of mitochondrial genomes (mitogenomes) within the family Theraphosidae, we characterized mitogenomes of four tarantulas (Grammostola pulchripes, Phormictopus atrichomatus, Pterinochilus murinus and Pterinopelma sazimai) for the first time. The mitogenomes were all classical circular structures, with lengths ranging from 13,822 bp to 14,011 bp. The constitutive genes and the orientation of the coding strand observed in the four mitogenomes were consistent with those found in other species belonging to the Theraphosidae family. The four mitogenomes were compacted and exhibited a preference for A and T, with the rRNA sequences showing a higher A+T content. Ka/Ks and p-distances analyses showed the ND6 gene had highest evolutionary rate, while the COⅠ gene displayed relatively slower evolution. In contrast to previous phylogenetic studies, our phylogenetic analysis based on mitogenomes provides new phylogenetic relationships among subfamilies. Subfamily Theraphosinae is most closely related to Ornithoctoninae, slightly distant from Harpactirinae, and farthest from Selenocosmiinae. The new data we acquired regarding these mitogenomes will aid in understanding the complex interrelationships among species within the Theraphosidae family.

Identification and characterization of a novel Pavlovskyella (Acari: Argasidae) from Chile, parasite of the culpeo fox (Lycalopex culpaeus)

Soft ticks (Argasidae) of the subgenus Pavlovskyella Pospelova-Shtrom are worldwide distributed parasites of medical importance. However, the systematics of the subgenus are currently under debate because genetic data shows that the group is paraphyletic. Meanwhile, species of Pavlovskyella continue to be discovered. In this study a novel species of the subgenus is described from specimens collected on a fox in central Chile. The larva of this new species differentiates from other Pavlovskyella spp. by having the following combination of characters: subpyriform dorsal plate; 15 pairs of setae, 7 anterolateral, 3 central, and 5 posterolateral, and hypostome with denticles in the distal third. Nymphs and adults of the species lack cheeks, eyes or bulging structures on the flank, but exhibit dorsoventral grooves, and humps on tarsi I, II, and III. Moreover, a patch of glabrous integument appears on the distal portion of coxal folds. A phylogenetic analysis using the mitogenome indicates a monophyletic group composed by Ornithodoros (Pavlovskyella) brasiliensis Aragão, Ornithodoros (Pavlovskyella) furcosus Neumann, Ornithodoros (Pavlovskyella) improvisus Muñoz-Leal & Venzal, and Ornithodoros (Pavlovskyella) rostratus Aragão. Interestingly, a phylogeny using 18S-28S rDNA sequences shows that South American Pavlovskyella spp. are paraphyletic, as depicted in previous studies. Adding species of the subgenus from the Neotropical region to phylogenetic analyses could aid to solve this paraphyly. Furthermore, this is the fifth species of Pavlovskyella described in South America, and the second in Chile.

Successful Traceability of Wildlife Samples Contributes to Wildlife Conservation: A Case Study of Tracing the Snub-Nosed Monkey (Rhinopithecus spp.)

Rapid and effective methods for tracing the geographic origin of wildlife samples are essential for tackling the illegal wildlife trade. Traditional morphological categorization methods are often inadequate as relying on the mitochondrial COXI barcode is insufficient for determining geographic populations. To address these limitations, we developed a bioinformatics-based pipeline for the rapid identification of traceable nuclear genome loci. This pipeline has been applied to the whole-genome sequence (WGS) data of China's flagship species, the snub-nosed monkey (Rhinopithecus spp.). These species are known for sex-biased dispersal and hybrid speciation, which complicates genealogy tracing. Using phylogenetic principles, we employed the Robinson and Foulds (RF) distance and scanned over 1,850,726 population-specific loci, identifying five pairs that can trace genealogy origins rapidly and cost-effectively using PCR. Additionally, we found that relying only on mitochondrial genetic information is insufficient for rapid and accurate traceability to subspecies-level geographic populations. Our pipeline efficiently identifies loci and traces the geographic origin of snub-nosed monkey individuals, providing a valuable tool for species preservation and combating the wildlife trade. This approach can be extended to other species, aiding in the conservation of endangered wildlife and tracing criminal evidence.

The complete mitochondrial genome of Neobythites sivicola (Jordan & Snyder, 1901) (Ophidiiformes: Ophidiidae)

The genus Neobythites is the most diverse group in the family Ophidiidae. In this study, we assembled and reported the complete mitochondrial genome of N. sivicola for the first time. The mitochondrial genome is 17,316 bp in length and contains 13 PCGs, 2 rRNAs, and 22 tRNAs. Phylogenetic analysis revealed that N. sivicola was the sister species to N. unimaculatus, and Neobythites was closer to Sirembo. This study significantly contributes to the genomic resources available for the family Ophidiidae and the genus Neobythites, providing a valuable molecular resource for further research on the taxonomy and phylogenetics of this family.

A Genomic-Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi

Environmental DNA (eDNA) analysis has become a popular conservation tool for detecting rare and elusive species. eDNA assays typically target mitochondrial DNA (mtDNA) due to its high copy number per cell and its ability to persist in the environment longer than nuclear DNA. Consequently, the development of eDNA assays has relied on mitochondrial reference sequences available in online databases, or in cases where such data are unavailable, de novo DNA extraction and sequencing of mtDNA. In this study, we designed eDNA primers for the critically endangered Bellinger River turtle (Myuchelys georgesi) using a bioinformatically assembled mitochondrial genome (mitogenome) derived from a reference genome. We confirmed the accuracy of this assembled mitogenome by comparing it to a Sanger-sequenced mitogenome of the same species, and no base pair mismatches were detected. Using the bioinformatically extracted mitogenome, we designed two 20 bp primers that target a 152-base-pair-long fragment of the cytochrome oxidase 1 (CO1) gene and a 186-base-pair-long fragment of the cytochrome B (CytB) gene. Both primers were successfully validated in silico, in vitro, and in situ.

Evolutionary dynamics of repetitive elements and their relationship with genome size in Acrididae

It is widely accepted that repetitive elements (REs) represent the primary mechanism driving genome size variation across eukaryotes. The observed genome sizes and REs of 59 species within the Acrididae were obtained and characterized. The genome sizes observed ranged from 6.60 pg to 19.35 pg, while the proportion of REs varied from 57.92 % to 83.58 %. The primary contributors were identified as LTR (2.34 % ∼ 20.98 %) and LINEs (6.70 % ∼ 16.33 %). The results of ancestral reconstruction indicated that the proportion of REs in ancestral nodes was 69.53 %, which suggests that they have undergone extensive genome expansion or contraction. A significant positive correlation was identified between the proportion of REs and genome size. Transposable elements were found to account for approximately 41 % of the observed variation in genome size. Moreover, the LTR was identified as the most significant RE type in relation to genome size expansion within the Acrididae.

Phylogenomic analyses of hamsters (Cricetinae) inferred from GBS data and mitochondrial genomes

Accurate species delimitation and identification is crucial for species conservation, providing a foundation for studies on evolutionary biology, ecology, and essentially all biological disciplines. The subfamily Cricetinae (Cricetidae, Rodentia), known as hamsters, is widely distributed in the Palearctic region. At present, there are nine genera and 18 species of hamsters are recognized worldwide, although the taxonomic status of certain taxa remains unclear. In this study, we collected 146 hamster specimens representing 14 species and generated new mitochondrial genomes and nuclear genome-wide single nucleotide polymorphisms (SNPs) to explore their relationships among these hamsters using multiple species delimitation approaches. Results showed: (1) strong phylogenetic support for the classification of Urocricetus, Nothocricetulus, and Cansumys as separate genera; (2) Urocricetus contained two separate species, U. kamensis and U. lama, with U. alticola and U. tibetanus considered synonyms of U. lama; (3) U. kamensis and U. lama are separated by the Nujiang River, with the matching divergence time suggesting that the formation of the river was the primary evolutionary factor driving the species differentiation, and (4) genetic differentiation occurred within the Tscherskia genus, which included two cryptic species.

A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections

Low coverage 'genome-skims' are often used to assemble organelle genomes and ribosomal gene sequences for cost-effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet poor preservation resulting in degraded DNA often hinders polymerase chain reaction-based analyses. However, it is possible to generate libraries and sequence the short fragments typical of degraded DNA to generate genome-skims from museum collections. Here we introduce a snakemake toolkit comprised of three pipelines skim2mito, skim2rrna and gene2phylo, designed to unlock the genomic potential of historical museum specimens using genome skimming. Specifically, skim2mito and skim2rrna perform the batch assembly, annotation and phylogenetic analysis of mitochondrial genomes and nuclear ribosomal genes, respectively, from low-coverage genome skims. The third pipeline gene2phylo takes a set of gene alignments and performs phylogenetic analysis of individual genes, partitioned analysis of concatenated alignments and a phylogenetic analysis based on gene trees. We benchmark our pipelines with simulated data, followed by testing with a novel genome skimming dataset from both recent and historical solariellid gastropod samples. We show that the toolkit can recover mitochondrial and ribosomal genes from poorly preserved museum specimens of the gastropod family Solariellidae, and the phylogenetic analysis is consistent with our current understanding of taxonomic relationships. The generation of bioinformatic pipelines that facilitate processing large quantities of sequence data from the vast repository of specimens held in natural history museum collections will greatly aid species discovery and exploration of biodiversity over time, ultimately aiding conservation efforts in the face of a changing planet.

Comparative Analysis of Seventeen Mitochondrial Genomes of Mileewinae Leafhoppers, Including the Unique Species Mileewa digitata (Hemiptera: Cicadellidae: Mileewinae) From Xizang, China, and New Insights Into Phylogenetic Relationships Within Mileewini

The subfamily Mileewinae in China comprises one tribe (Mileewini), four genera (Ujna, Mileewa, Processina, Anzihelus), and 71 species, yet only 11 mitochondrial genomes have been published. This study aimed to elucidate ambiguous diagnostic traits in traditional taxonomy and examined phylogenetic relationships among genera by sequencing mitochondrial genomes from 16 species. The lengths of the mitochondrial genomes ranged from 14,532 to 15,280 bp, exhibiting an AT content of 77.2%-80.7%, indicative of AT bias. Each genome contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). Notably, the genome of the Xizang endemic Mileewa digitata measures 15,280 bp, with an AT content of 80.7%, 10,941 bp of PCGs, and a 949 bp control region (CR) followed by a 19 bp poly-A tail. Gene arrangement among the 17 genomes mirrors that of other Mileewinae species. Analyses of nucleotide diversity and evolutionary rates indicate purifying selection on PCGs, with atp8 exhibiting the greatest variability and evolutionary rate, whereas cox1 shows the least. Genetic distance studies display minimal separation among Mileewa species, specifically Mileewa nii with Mileewa margheritae and Mileewa rufivena with Mileewa ussurica, as well as the two morphs of Mileewa digitata. Phylogenetic analyses using Bayesian Inference (BI) and Maximum Likelihood (ML) generated six trees, further questioning the monophyly of the genera Mileewa, Ujna, and Processina. The reconstructed ancestral state based on the forewing patch position suggests that the common ancestor of Chinese Mileewini species was situated exclusively on the costal margin, prompting a proposed division of the tribe's species into two categories (genera). This research enriches the understanding of phylogenetic relationships within Mileewinae and contributes to the mitochondrial genome database for this group, paving the way for future taxonomic studies in China.

Molecular Phylogenetic Relationships Based on Mitogenomes of Spider: Insights Into Evolution and Adaptation to Extreme Environments

In this study, we performed a comparative analysis based on a total of 255 spider mitogenomes and four outgroups, of which the mitogenomes of 39 species were assembled de novo, to explore the phylogenetic relationships and the adaptive evolution of mitogenomes. Results showed that Argyroneta aquatica had the longest mitochondrial length and the most pronounced codon preference to be UUA, followed by CCU. Codon usage frequencies were similar between families and codon usage in the mitogenome of spiders was mainly influenced by natural selection pressures rather than G/C mutation bias. Our phylogenetic topology clearly explained the evolutionary relationships among the spiders, and divergence time estimates indicated that the spiders originated in the early Devonian, and that the two clades of Mesothelae and Opisthothelae separated in the late Carboniferous. Ancestral range and trait reconstruction results supported the ancestral origin of spiders to the Devonian Nearctic realm, with the trapdoor being the original trait. Selection analysis detected positive selection signals in the ATP8 gene in Desis jiaxiangi. The ND5 gene is a convergent evolutionary gene between D. jiaxiangi and A. aquatica. Positive selection signals in the ATP8 gene and convergent selection sites in the ND5 gene may facilitate metabolic adaptation to the aquatic environment in two aquatic spiders. In conclusion, our analysis contributes to a better understanding of the taxonomic status, species diversity, mitochondrial characteristics, and environmental adaptations of these spiders.

Study of Mitogenomes Provides Implications for the Phylogenetics and Evolution of the Infraorder Muscomorpha in Diptera

The Muscomorpha is one of the most species-rich brachyceran groups in Diptera, with many species serving as important disease vectors; however, its high-level phylogenetic relationships have long been controversial and unsolved. This study comparatively analyzed the characteristics of mitogenomes of 131 species that represent 18 superfamilies in Muscomorpha, in which mitogenomes of 16 species have been newly sequenced and annotated, demonstrating that their gene composition, order, AT bias, length variation, and codon usage are consistent with documented dipteran mitogenomes. The phylogenetic topologies demonstrated that the robustness of Muscomorpha and major clades within Muscomorpha are monophyletic: Cyclorrhapha, Schizophora, and Calyptratae. A clade of Empidoidea were recovered as the sister group to Cyclorrhapha. Within Cyclorrhapha, Platypezoidea and Syrphoidea were sequentially placed as basal groups of the Cyclorrhapha. The remaining cyclorrhaph superfamilies gathered as two main clades. Ephydroidea were, in most cases, placed as the sister group to Calyptratae. Within Calyptratae, Hippoboscoidea were sister to an assemblage of lineages composed of an Oestroid grade and Muscoidea. The Muscomorpha was proposed to originate in the early Jurassic, and the main clade diversified near the Cretaceous-Paleogene extinction event, estimated using the MCMCtree and six fossil calibration points. The ancestral area of origin and geographic range of Muscomorpha was deduced to be the Palaearctic region with 56.9% probability using the RASP software based on a dated tree.

Integrative taxonomy of the genus Pseudoacanthocephalus (Acanthocephala: Echinorhynchida) in China, with the description of two new species and the characterization of the mitochondrial genomes of Pseudoacanthocephalus sichuanensis sp. n. and Pseudoacanthocephalus nguyenthileae

BACKGROUND

Acanthocephalans (thorny headed worms) of the genus Pseudoacanthocephalus mainly parasitize amphibians and reptiles across the globe. Some species of the genus Pseudoacanthocephalus also can accidentally infect human and cause human acanthocephaliasis. Current knowledge of the species composition of the genus Pseudoacanthocephalus from amphibians and reptiles in China is incomplete. An insufficiency of genetic data on species of the genus Pseudoacanthocephalus, including the complete mitochondrial genomes, has limited the use of molecular-based methods to better define the taxonomy and phylogeny of the genus Pseudoacanthocephalus. A more rigorous molecular phylogeny with broader representatives of the genus Pseudoacanthocephalus is required to further clarify the systematic status of the family Pseudoacanthocephalidae.

METHODS

Many specimens of the genus Pseudoacanthocephalus collected from toads and frogs in China were identified to species level using integrated morphological methods (light and scanning electron microscopy) and molecular approaches (sequencing different nuclear and mitochondrial genetic markers). The Assemble Species by Automatic Partitioning (ASAP) and Bayesian inference (BI) methods were applied for species delimitation. The complete mitochondrial genomes of two Pseudoacanthocephalus species were also sequenced and annotated to enrich the body of mitogenomic data on acanthocephalans. Additionally, phylogenetic analyses based on the amino acid sequences of 12 protein-coding genes (PCGs) of mitochondrial genomes of acanthocephalans using maximum likelihood (ML) and BI were performed to further investigate the phylogenetic position of the family Pseudoacanthocephalidae in the order Echinorhynchida.

RESULTS

Three Pseudoacanthocephalus species, including P. sichuanensis sp. n., P. previatesticulus sp. n. and P. nguyenthileae were described. The results of ASAP and BI analyses based on the cytochrome c oxidase subunit 1 and subunit 2 (cox1, cox2) and 12S ribosomal RNA (12S) sequences supported the separation of P. sichuanensis and P. previatesticulus from the congeneric species. The results of BI inference using the internal transcribed spacer (ITS), cox1, cox2 and 12S sequence data indicated that P. sichuanensis and P. nguyenthileae have a closer relationship than P. previatesticulus and P. bufonis in Pseudoacanthocephalus. The complete mitogenomes of P. sichuanensis and P. nguyenthileae have 15,812 and 13,701 bp, respectively, with both including 36 genes and two non-coding regions. Phylogenetic results based on mitogenomic data demonstrated that the two families Pseudoacanthocephalidae and Arhythmacanthidae have a sister relationship in the order Echinorhynchida.

CONCLUSIONS

Two new species of the genus Pseudoacanthocephalus, namely P. sichuanensis sp. n. and P. previatesticulus sp. n., were identified based on integrated evidence. This is the first report of P. nguyenthileae in China. A revised key for the species of the genus Pseudoacanthocephalus was provided. Molecular analyses revealed that the mitochondrial cox1, cox2 and 12S genes as genetic markers seem to be more suitable for species delimitation of Pseudoacanthocephalus than the nuclear ITS region. BI results suggested a close affinity between P. sichuanensis and P. nguyenthileae. The mitochondrial genomic data of P. sichuanensis and P. nguyenthileae are provided for the first time. Mitogenomic phylogenetic results further confirmed the validity of the family Pseudoacanthocephalidae.

The complete mitochondrial genome of Leptopilina myrica (Hymenoptera: Figitidae)

The complete mitochondrial genome of Leptopilina myrica Chen, 2023 has been sequenced and analyzed for the first time. The total length we assembled is 15,448 bp, which comprises 13 PCGs, 22 tRNAs, 2 rRNAs, and a CR. The overall nucleotide composition consists of 41.1% A, 37.7% T, 14.7% C, and 6.5% G, respectively. The nucleotide sequences of 13 PCGs and 2 rRNAs from L. myrica and another 10 Drosophila parasitoid species were used for phylogenetic analysis by MrBayes, with one species from Drosophilidae as an outgroup. The result shows that L. myrica is closely related to L. syphax.

Response strategies to acute and chronic environmental stress in the arctic breeding Lapland longspur (Calcarius lapponicus)

The potentially devastating effects of climate change have raised awareness of the need to understand how the biology of wild animals is influenced by extreme-weather events. We investigate how a wild arctic-breeding bird, the Lapland longspur (Calcarius lapponicus), responds to different environmental perturbations and its coping strategies. We explore the transcriptomic response to environmental adversity during the transition from arrival at the breeding grounds to incubation on the Arctic tundra. The effects of an extremely cold spring on arrival and a severe storm during incubation are examined through RNA-seq analysis of pertinent tissues sampled across the breeding cycle. The stress response, circadian rhythms, reproduction, and metabolism are all affected. A key gene of the Hypothalamic-Pituitary-Adrenal axis, FKBP5, was significantly up-regulated in hypothalamus. The genome assembly and gene expression profiles provide comprehensive resources for future studies. Our findings on different coping strategies to chronic and acute stressors will contribute to understanding the interplay between changing environments and genomic regulation.

Museomics Sheds Light on Evolutionary Diversity in a Critically Endangered Cockatoo Species From Wallacea

Accurate identification of evolutionarily significant units of rare and threatened organisms provides a foundation for effective management and conservation. Up to seven subspecies of the critically endangered Yellow-crested Cockatoo (Cacatua sulphurea) have been described, four of which were commonly recognised pre-2014. In the absence of genotypic data, C. sulphurea subspecies delimitation has been based on morphology, behaviour and biogeography. To clarify genetic relationships and shed light on the diversification of this parrot radiation, whole genomes were sequenced for 16 museum specimens, covering the geographic range of the proposed seven subspecies as well as one C. galerita galerita. Combined with four museum-derived wild Cacatua sequences from NCBI, the results indicate there are three distinct C. sulphurea subspecies clusters centred in different biogeographic subregions of Wallacea (Timor; Sumba; as well as the Sulawesi Region and the main Lesser Sunda chain), separated by shallow genetic distances (da < 0.148%). The results raise questions about the recent species-level elevation of the phenotypically most distinct subspecies, C. s. citrinocristata, and about the origins of C. s. abbotti, the only subspecies west of Wallace's Line. Our analyses suggest C. s. abbotti is unlikely to be embedded within C. sulphurea, suggesting its origin on the remote Masalembu islands may be due to human translocation via historical trade routes. These genomic results inform the prioritisation and streamlining of conservation measures for the critically endangered C. sulphurea by identifying and delimiting likely conservation units.

Phylogeny and divergence time estimation of the subfamily Amphipsyllinae based on the Frontopsylla diqingensis mitogenome

Fleas are primarily parasites of small mammals and serve as essential vectors of the transmission of plague. The subfamily Amphipsyllinae (Siphonaptera: Leptopsyllidae) consists of 182 species across 13 genera, widely distributed worldwide. Only two species of Amphipsyllinae have been sequenced for complete mitogenomes to date. It hinders the taxonomy and evolutionary history studies of fleas. In this study, we first sequenced the Frontopsylla diqingensis mitogenome and performed comparative mitogenomic analyses with the two other species (Frontopsylla spadix and Paradoxopsyllus custodis) in Amphipsyllinae available in the NCBI database. The evolutionary process of Amphipsyllinae was comprehensively analyzed in terms of nucleotide composition, codon usage, nucleotide diversity, tRNA secondary structure, nucleotide skew, phylogeny tree, and divergence time. Nucleotide diversity and tRNAs of three species of fleas of Amphipsyllinae have differences among different species. The effective number of codon (ENC)-plot, neutrality curve, PR2, and correspondence analysis (COA) showed that the codon preference of Amphipsyllinae was influenced mainly by natural selection. For phylogenetic trees and divergence time of the order Siphonaptera, our results showed two concatenated data matrices, namely, PCG: (((Ceratophyllidae + Leptopsyllidae) + ((Vermipsyllidae + Hystrichopsyllidae) + Ctenophthalmidae)) + (Pulicidae + Pygiopsyllidae)); PCGRNA: ((((Ceratophyllidae + Leptopsyllidae) + ((Vermipsyllidae + Hystrichopsyllidae) + Ctenophthalmidae)) + Pulicidae) + Pygiopsyllidae). We concluded that P. custodis and Macrostylophora euteles from GenBank are the same species by phylogenetic trees and sequence alignment, and supported the monophyly of Amphipsyllinae. Amphipsyllinae diverged in the Cenozoic, approximately 73.37-40.32 million years ago (Mya). The majority of the species within the intraordinal divergence into extant lineages occurred after the K-Pg boundary. The common ancestor of the extant order Siphonaptera diverged during the Cretaceous. Our findings supported those of Zhu et al. (1). This study provides new insights into the evolutionary history and taxonomy of the order Siphonaptera.

When paleontology meets genomics: complete mitochondrial genomes of two saber-toothed cats' species (Felidae: Machairodontinae)

Within the Machairodontinae subfamily, commonly referred to as saber-toothed cats, it is worth noting that only two species, namely Homotherium latidens, recognized as the scimitar-toothed cat, and Smilodon populator, renowned as the saber-toothed tiger, possess partial mitochondrial genomes accessible in the NCBI database. These sequences, however, do not include the mitogenome control region (mtDNA control region) and have several gaps in their genes, including protein-coding genes (PCGs) that are widely used in phylogenetic analysis. In this study, we aimed to obtain a complete assembly of the mitogenomes of these two species from next-generation sequencing data available at NCBI's SRA. The de novo assemblies showed complete mitogenomes with 17,323bp (H. latidens) and 16,769 bp (S. populator), both with 13 PCGs, 22tRNAs, two rRNAs and the mtDNA control region, with all genes following the standard order and position of most vertebrate mitogenomes. Despite being generally very similar to previous studies, our phylogeny and molecular dating reveals an earliest divergence between North American and North Sea H. latidens specimens which may be related to an Early Pleistocene migration across Beringia.

Saltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group

Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of study. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no "true" species tree could be inferred, and applied our new test (called 2A2B) to whole genome data and to individual loci. We used four strategies, two based on our new assemblies using either conserved genes or ≥50 kb-long syntenic blocks with conserved collinearity across Neotropical Sophophora, and two consisted of windows from pseudo-reference genomes aligned to either an ingroup or outgroup species. Evidence for reticulation varied among the strategies, being lowest in the synteny-based approach, where it did not exceed ∼7% of the blocks in the most conflicting species quartets. High incidences of reticulation were restricted to three nodes on the tree that coincided with major paleogeographical events in South America. Our results identify possible technical biases in quantifying reticulate evolution and indicate that episodic rapid radiations have played a major role in the evolution of a largely understudied Neotropical clade.

Comparative Genomics Provides Insights into Adaptive Evolution and Demographics of Bats

Bats possess a range of distinctive characteristics, including flight, echolocation, impressive longevity, and the ability to harbor various zoonotic pathogens. Additionally, they account for the second-highest species diversity among mammalian orders, yet their phylogenetic relationships and demographic history remain underexplored. Here, we generated de novo assembled genomes for 17 bat species and 2 of their mammalian relatives (the Amur hedgehog and Chinese mole shrew), with 12 genomes reaching chromosome-level assembly. Comparative genomics and ChIP-seq assays identified newly gained genomic regions in bats potentially linked to the regulation of gene activity and expression. Notably, some antiviral infection-related gene under positive selection exhibited the activity of suppressing cancer, evidencing the linkage between virus tolerance and cancer resistance in bats. By integrating published bat genome assemblies, phylogenetic reconstruction established the proximity of noctilionoid bats to vesper bats. Interestingly, we found 2 distinct patterns of ancient population dynamics in bats and population changes since the last glacial maximum does not reflect species phylogenetic relationships. These findings enriched our understanding of adaptive mechanisms and demographic history of bats.

Establishment of Real-Time PCR Method to Differentiate Phlebotomus sichuanensis (Diptera, Psychodidae) from P. chinensis s.s. Based on Whole Mitochondrial Genome Analysis

Phlebotomus sichuanensis, considered a potential vector for visceral leishmaniasis (VL), is distributed in the southern Gansu and northern Sichuan regions in China. However, the high similarity in the morphology of P. sichuanensis and P. chinensis s.s. poses unresolved taxonomic challenges. In this study, phlebotomine sand flies were collected from three locations in the southern Gansu and northern Sichuan regions (SCB group) and three locations that are the dominant distribution areas of P. chinensis s.s. (ZHB group). Their whole mitochondrial genomes were sequenced and analyzed. The differential analysis revealed that there were 339 fixed differential sites in the mitochondrial genome-coding region of P. chinensis s.s. and P. sichuanensis, among which the COI gene had the most differential sites (57), followed by ND5 (46), ND4 (38), and CYTB (37), while ATP8 had the least differential sites (4). The molecular genetic p-distance was calculated based on 13 protein-coding regions, and the genetic distance ranged from 0.001 to 0.018 in the ZHB group and from 0.001 to 0.006 in the SCB group, while the interspecies molecular genetic distance was 0.464-0.466 between the two groups. A phylogenetic maximum likelihood tree was constructed from 16 samples via tandem sequence of 13 protein-coding regions, and the topology showed that the ZHB and SCB groups formed separate clusters. A real-time PCR method was established based on the differences in the COI fragment, which can identify P. sichuanensis from P. chinensis s.s. effectively. This study presents objective evidence of the genetic differentiation between P. sichuanensis and P. chinensis s.s., and provides a method for identifying these two morphologically highly similar VL-transmitting sandflies.

Exploring mitogenomic data to enhance the understanding of Seirinae (Collembola: Entomobryidae) evolution, distribution and taxonomy

The subfamily Seirinae (Collembola: Entomobryidae) is among the most diverse suprageneric taxa of epedaphic springtails and is particularly abundant and species-rich in tropical and subtropical regions. Numerous studies have investigated its internal and external phylogenetic relationships, enhancing our understanding on Seirinae systematics. Recent taxonomic efforts have also advanced our knowledge on the subfamily morphology and diversity. In this study, we reevaluate the phylogeny of Seirinae using the mitogenomes of 26 samples from different continents, aiming to discuss recent findings regarding the group systematics, to identify cases of alien species introduced in China and Thailand, and propose new synonyms for Seira spp. Additionally, we describe a new species from Thailand and provide a redescription of Seira brasiliana (Arlé) based on the study of Brazilian and Chinese specimens. Through these efforts, we provide further ground for understanding the evolution, systematics, distribution and taxonomy of the group, contributing to future studies on Seirinae and Entomobryidae.

Morphometric and phylogenetic analysis of a commercial fish Leiognathusequula (Teleostei, Leiognathidae)

The complete mitochondrial genome and phylogenetic analysis for Leiognathusequula from the South China Sea was performed using shallow genome skimming. For accurate species identification and redescription, morphometric and meristic characters were examined and compared with previous descriptions. To facilitate the identification of species and to enable comparison with the mitochondrial genome phylogeny, molecular comparisons were conducted using three mitochondrial genes: large ribosomal RNA (16S rRNA), cytochrome c oxidase subunit 1 (COX1), and NADH dehydrogenase (ND5). The mitogenome (16 398 bp) comprised 38 mitochondrial genes, similar to most bony fishes: 13 protein-coding genes (PCGs), 2 rRNA and 22 transfer RNA genes, and 1 non-coding region. The complete mitogenome comprised 30.7% A, 24.2% T, 15.0% G, and 30.1% C. The A+T content (54.9%) was higher than the G+C content (45.1%). All PCGs started with the typical ATG codon, except COX1, which started with GTG. Seven PCGs ended with incomplete stop codons (TA or T). The Ka/Ks ratios of all PCGs were < 1, indicating purifying selection. The phylogenies of Leiognathidae, both based on the amino acid sequences of the 13 PCGs and the single genes 16S RNA and COX1, were monophyletic with high nodal support (> 75%). L.brevirostris (NC 026232) is believed to be a Nuchequula species, whereas L.ruconius (NC 057225) is not classified under Leiognathus in the NCBI database. The phylogenetic trees divided the Leiognathidae family into three clades. The mitogenome phylogeny suggested that the Leiognathidae and Chaetodontidae clades are sister groups. These findings provide important genetic data for population genetics research and a phylogenetic analysis of Leiognathidae.

Mitochondrial Genomes of Mammals from the Brazilian Cerrado and Phylogenetic Considerations for the Orders Artiodactyla, Carnivora, and Chiroptera (Chordata: Mammalia)

We assembled and annotated the complete mitochondrial genomes of Lycalopex vetulus (hoary fox), Cerdocyon thous (bush dog), Tayassu pecari (white-lipped peccary), and Tadarida brasiliensis (Brazilian free-tailed bat). The mitogenomes exhibited typical vertebrate structures, containing 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and a D-loop region. Phylogenetic reconstruction using the 13 protein-coding genes revealed robust relationships among species within Carnivora, Chiroptera, and Artiodactyla, corroborating previous studies. Secondary structure analysis of tRNAs and ribosomal genes showed slight variations among species of the same order. This research highlights the importance of mitochondrial genomics in understanding the evolutionary relationships and genetic diversity of Cerrado mammals, contributing to conservation efforts for this unique ecosystem.

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.

Genomic and transcriptomic perspectives on the origin and evolution of NUMTs in Orthoptera

Nuclear mitochondrial pseudogenes (NUMTs) result from the transfer of mitochondrial DNA (mtDNA) to the nuclear genome. NUMTs, as "frozen" snapshots of mitochondria, can provide insights into diversification patterns. In this study, we analyzed the origins and insertion frequency of NUMTs using genome assembly data from ten species in Orthoptera. We found divergences between NUMTs and contemporary mtDNA in Orthoptera ranging from 0 % to 23.78 %. The results showed that the number of NUMT insertions was significantly positively correlated with the content of transposable elements in the genome. We found that 39.09 %-68.65 % of the NUMTs flanking regions (2,000 bp) contained retrotransposons, and more NUMTs originated from mitochondrial rDNA regions. Based on the analysis of the mitochondrial transcriptome, we found a potential mechanism of NUMT integration: mitochondrial transcripts are reverse transcribed into double-stranded DNA and then integrated into the genome. The probability of this mechanism occurring accounts for 0.30 %-1.02 % of total mitochondrial nuclear transfer events. Finally, based on the phylogenetic tree constructed using NUMTs and contemporary mtDNA, we provide insights into ancient evolutionary events such as species-specific "autaponumts" and "synaponumts" shared among different species, as well as post-integration duplication events.

The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs

Pigs play a central role in human livelihoods in China, but a lack of systematic large-scale whole-genome sequencing of Chinese domestic pigs has hindered genetic studies. Here, we present the 1000 Chinese Indigenous Pig Genomes Project sequencing dataset, comprising 1011 indigenous individuals from 50 pig populations covering approximately two-thirds of China's administrative divisions. Based on the deep sequencing (~25.95×) of these pigs, we identify 63.62 million genomic variants, and provide a population-specific reference panel to improve the imputation performance of Chinese domestic pig populations. Using a combination of methods, we detect an ancient admixture event related to a human immigration climax in the 13th century, which may have contributed to the formation of southeast-central Chinese pig populations. Analyzing the haplotypes of the Y chromosome shows that the indigenous populations residing around the Taihu Lake Basin exhibit a unique haplotype. Furthermore, we find a 13 kb region in the THSD7A gene that may relate to high-altitude adaptation, and a 0.47 Mb region on chromosome 7 that is significantly associated with body size traits. These results highlight the value of our genomic resource in facilitating genomic architecture and complex traits studies in pigs.

Complete mitochondrial genomes of Notropis oxyrhynchus and Notropis buccula (Cypriniformes: Leuciscidae)

The Leuciscidae (minnows, shiners and relatives) is a diverse family of freshwater fishes with many species endangered due to anthropogenic stressors. Notropis oxyrhynchus and Notropis buccula are two shiners found only in the upper Brazos River basin in Texas, USA and listed as endangered due to contracted habitat. The complete mitochondrial genome was sequenced for two vouchered specimens for each species; Notropis oxyrhynchus having a total mitogenome length of 16,711 bp and N. buccula having a total mitogenome length 16685-16686 bp, with both including 13 protein-coding genes, 22 transfer RNAs genes, and 2 ribosomal RNA genes. Phylogenetic analysis supports previous hypotheses regarding placement of these species.

A new species of giant gecko of the genus Rhacodactylus from New Caledonia (Squamata, Gekkota, Diplodactylidae)

We describe a new species of giant gecko, Rhacodactylus willihenkeli sp. nov. from New Caledonia. The new species is most similar in external appearance and molecular data (16S and ND2 sequences) with R. leachianus from which it differs in coloration as well as having a genetic distance of 5.0% in the 16S gene fragment and 8.5% in the ND2 fragment, respectively.

A Whole-Genome Survey and the Mitochondrial Genome of Acanthocepola indica Provide Insights into Its Phylogenetic Relationships in Priacanthiformes

Acanthocepola indica, a deep-sea snake fish, is primarily found in the Indo-west Pacific region, including India, Korea, Japan, and the South China Sea. The taxonomic classification of A. indica based on morphological characteristics remains inaccurate and unclear. In this study, we utilized next-generation sequencing to generate comprehensive genomic data for A. indica. The estimated genome size of A. indica was 422.95 Mb, with a heterozygosity ratio of 1.02% and a sequence repeat ratio of 22.43%. Our analysis suggested that A. indica is diploid, and the draft genome assembly consists of 1,059,784 contigs with a contig N50 of 1942 bp. We identified a total of 444,728 simple sequence repeats in the genome of A. indica. Furthermore, we successfully assembled the complete mitochondrial genome (16,439 bp) of A. indica, which included 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. Phylogenetic analysis based on mitochondrial genomes revealed that A. indica is closely related to Acanthocepola krusensternii and Cepola schlegelii, providing evidence that the family Cepolidae belongs to the order Priacanthiformes. Population size dynamics analysis indicated that A. indica experienced a bottleneck effect during the Pleistocene Glacial Epoch, likely due to the changes in glacial cycles and sea level fluctuations since ~800 Kya.

The complete mitochondrial genome of Epicauta sibirica Pallas, 1773 (Coleoptera: Meloidae)

Epicauta sibirica is both an important pest and an important economic insect. The mitogenome is 15,717 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The nucleotide composition of E. sibirica is 37.0% of A, 18.3% of C, 11.3% of G, and 33.4% of T. The genus Epicauta was detected as a monophyletic group and more closely related to the genus Lytta than other genera within Meloidae. This study supplemented additional genetic data for future research on the phylogeny and evolution of Meloidae species.

OGU: A Toolbox for Better Utilising Organelle Genomic Data

Organelle genomes serve as crucial datasets for investigating the genetics and evolution of plants and animals, genome diversity, and species identification. To enhance the collection, analysis, and visualisation of such data, we have developed a novel open-source software tool named Organelle Genome Utilities (OGU). The software encompasses three modules designed to streamline the handling of organelle genome data. The data collection module is dedicated to retrieving, validating and organising sequence information. The evaluation module assesses sequence variance using a range of methods, including novel metrics termed stem and terminal phylogenetic diversity. The primer module designs universal primers for downstream applications. Finally, a visualisation pipeline has been developed to present comprehensive insights into organelle genomes across different lineages rather than focusing solely on individual species. The performance, compatibility and stability of OGU have been rigorously evaluated through benchmarking with four datasets, including one million mixed GenBank records, plastid genomic data from the Lamiaceae family, mitochondrial data from rodents, and 308 plastid genomes sourced from various angiosperm families. Based on software capabilities, we identified 30 plastid intergenic spacers. These spacers exhibit a moderate evolutionary rate and offer practical utility comparable to coding regions, highlighting the potential applications of intergenic spacers in organelle genomes. We anticipate that OGU will substantially enhance the efficient utilisation of organelle genomic data and broaden the prospects for related research endeavours.

Insights into Mitochondrial Rearrangements and Selection in Accipitrid Mitogenomes, with New Data on Haliastur indus and Accipiter badius poliopsis

BACKGROUND/OBJECTIVES

Accipitridae mitogenomes exhibit unique structural variations, including duplicated control regions (CRs) that undergo gradual degeneration into pseudo-CRs, revealing a complex evolutionary landscape. However, annotation of this characteristic in a subset of accipitrid genomes is lacking. Due to the taxonomic diversity of Accipitridae and the presence of understudied species, comprehensive mitogenomic studies are essential. This study sought to expand and investigate the evolutionary characteristics of Accipitridae mitogenomes.

METHODS

A comparative analysis was conducted using the newly acquired complete mitogenomes of Haliastur indus and Accipiter badius poliopsis along with 22 available accipitrid mitogenomes. Codon usage, selective pressure, phylogenetic relationships, and structural variations were comparatively analyzed.

RESULTS

Accipitrid mitogenomes showed a strong AT bias with adenine preference. Most protein-coding genes (PCGs) were under purifying selection except for ND3, which underwent positive selection. The ATP8 gene exhibited relaxed purifying selection on codon usage patterns and showed high genetic variation. Selection for ATP8 and ND3 genes was specific to certain clades of accipitrids. Gene order re-examination revealed both non-degenerate CRs and highly degenerate CR2 fragments in the Accipitridae family. Non-degenerate CRs were found in early diverging species, such as Elanus caeruleus and Pernis ptilorhynchus orientalis, while more recent lineages had highly degenerate CR2 fragments with missing conserved element. Repeat motifs and sequence variations were observed in the functional CR.

CONCLUSIONS

These findings suggest that ATP8 and ND3 genes reflect metabolic adaptations, while CRs indicate potential diversification of these accipitrid species. This study provides valuable insights into mitochondrial genome evolution within the Accipitridae family.

Insight into the Phylogenetic Relationships of Phasmatodea and Selection Pressure Analysis of Phraortes liaoningensis Chen & He, 1991 (Phasmatodea: Lonchodidae) Using Mitogenomes

Stick and leaf insects are a group among the Insecta that are famous for their extraordinary mimicry ability. Since the establishment of the Phasmatodea, their internal classification has been constantly revised. Mitochondrial genes as molecular markers have been widely used for species classification, but the phylogenetic relationships within the Phasmatodea remain to be thoroughly discussed. In the present study, five mitogenomes of Phasmatodea ranging from 15,746 bp to 16,747 bp in length were sequenced. Bayesian inference (BI) and maximum likelihood (ML) analyses were carried out based on a 13 PCGs data matrix (nt123) and a combined matrix of 13 PCGs and two rRNA genes (nt123_rRNA). The present study supports the conclusion that Phylliidae was the basal group of Neophasmatodea and confirms the monophyly of Lonchodinae and Necrosciinae, but it shows that Lonchodidae was polyphyletic. A sister group of Bacillidae and Pseudophasmatidae was also recovered. The phylogenetic tree based on the nt_123 dataset showed higher node support values. The construction of a divergent time tree in this study supported the conclusion that extant Phasmatodea originated in the Jurassic (170 Mya) and most lineages diverged after the Cretaceous-Paleogene extinction event. To explore whether the mitochondrial genes of Phraortes liaoningensis collected from high latitudes where low temperatures occur for eight months of the year are under selection pressure, this study used the branch-site model and the branch model to analyze the selection pressure on the 13 mitochondria protein-coding genes (PCGs). We found that both ND2 and ND4L of Ph. liaoningensis exhibited positive selection sites using the branch-site model. This study shows that a low-temperature environment causes mitochondrial genes to be selected to meet the energy requirements for survival.

Comparative mitogenomic analysis and phylogeny of Veneridae with doubly uniparental inheritance

Doubly uniparental inheritance (DUI) is an atypical animal mtDNA inheritance system, reported so far only in bivalve species, in which two mitochondrial lineages exist: one transmitted through the egg (F-type) and the other through the sperm (M-type). Although numerous species exhibit this unusual organelle inheritance, it is primarily documented in marine and freshwater mussels. The distribution, function and molecular evolutionary implications of DUI in the family Veneridae, however, remain unclear. Here, we investigated 17 species of Veneridae, compared mitochondrial genomes of DUI species and reconstructed their phylogenetic framework. Different sex-linked mitochondrial genomes have been identified in the male gonads and adductor muscles of 7 venerids, indicating the presence of DUI in these species. Analysis of the unassigned regions (URs) of the mitochondrial genome in DUI species revealed that 13 out of 44 URs contained repetitive sequences, with nine being long unassigned regions (LURs). All LURs were capable of forming secondary structures, and most of them exhibited patterns of significant sequence similarity to elements known to have specific functions in the control regions of sea urchins and mammals. The F/M phylogeny showed that DUI venerids exhibit both taxon-specific patterns and gender-specific patterns, with Gafrarium dispar experiencing masculinization events.

The first complete mitochondrial genome of Mylabris sibirica (Coleoptera: Meloidae) and its phylogenetic analysis

The complete mitochondrial genome of Mylabris sibirica Fischer von Waldheim, 1823 was sequenced and characterized. The mitogenome is 15,794 bp long with 37 annotated genes, comprising 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The phylogenetic analysis based on the mitochondrial genome sequences revealed that M. sibirica clustered with M. quadripunctata. This study presents the complete mitochondrial genome of M. sibirica for the first time, which could be beneficial for systematic studies on Mylabrini.