Mitogenomic Data Research Articles

Mitogenome architecture supports the non-monophyly of the cosmopolitan parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) recovered by nuclear and mitochondrial phylogenomics.

Mitochondrial DNA gene organisation is an important source of phylogenetic information for various metazoan taxa at different evolutionary timescales, though this has not been broadly tested for all insect groups nor within a phylogenetic context. The cosmopolitan subfamily Doryctinae is a highly diverse group of braconid wasps mainly represented by ectoparasitoids of xylophagous beetle larvae. Previous molecular studies based on Sanger and genome-wide (ultraconserved elements, UCE; and mitochondrial genomes) sequence data have recovered a non-monophyletic Doryctinae, though the relationships involved have always been weakly supported. We characterised doryctine mitogenomes and conducted separate phylogenetic analyses based on mitogenome and UCE sequence data of ~100 representative doryctine genera to assess the monophyly and higher-level classification of the subfamily. We identified rearrangements of mitochondrial transfer RNAs (tRNAs) that support a non-monophyletic Doryctinae consisting of two separate non-related clades with strong geographic structure ('New World' and 'Old World' clades). This geographic structure was also consistently supported by the phylogenetic analyses preformed with mitogenome and UCE sequence data. These results highlight the utility of the mitogenome gene rearrangements as a potential source of phylogenetic information at different evolutionary timescales.

Genomic insights on conservation priorities for North Sea houting and European lake whitefish (Coregonus spp.).

Population genomics analysis holds great potential for informing conservation of endangered populations. We focused on a controversial case of European whitefish (Coregonus spp.) populations. The endangered North Sea houting is the only coregonid fish that tolerates oceanic salinities and was previously considered a species (C. oxyrhinchus) distinct from European lake whitefish (C. lavaretus). However, no firm evidence for genetic-based salinity adaptation has been available. Also, studies based on microsatellite and mitogenome data suggested surprisingly recent divergence (c. 2500 years bp) between houting and lake whitefish. These data types furthermore have provided no evidence for possible inbreeding. Finally, a controversial taxonomic revision recently classified all whitefish in the region as C. maraena, calling conservation priorities of houting into question. We used whole-genome and ddRAD sequencing to analyse six lake whitefish populations and the only extant indigenous houting population. Demographic inference indicated post-glacial expansion and divergence between lake whitefish and houting occurring not long after the Last Glaciation, implying deeper population histories than previous analyses. Runs of homozygosity analysis suggested not only high inbreeding (FROH up to 30.6%) in some freshwater populations but also FROH up to 10.6% in the houting prompting conservation concerns. Finally, outlier scans provided evidence for adaptation to high salinities in the houting. Applying a framework for defining conservation units based on current and historical reproductive isolation and adaptive divergence led us to recommend that the houting be treated as a separate conservation unit regardless of species status. In total, the results underscore the potential of genomics to inform conservation practices, in this case clarifying conservation units and highlighting populations of concern.

The phylogeny of ceutorhynchine weevils (Ceutorhynchinae, Curculionidae): Mitogenome data improve the resolution of tribal relationships

AbstractCeutorhynchinae Gistel are a diverse weevil subfamily of almost worldwide distribution and considerable economic importance. Nevertheless, the classification of Ceutorhynchinae and their phylogenetic relationships are not yet fully resolved. Here, we sequenced the mitogenomes of 54 ceutorhynchine species. Phylogenetic analyses by maximum likelihood and Bayesian inference were performed on a dataset of 13 protein‐coding and two ribosomal genes. All analyses recovered three well supported clades A–C. A principal component analysis shows that codon usage differs considerably between these clades, indicating a compositional asymmetry in ceutorhynchine mitogenomes. This increased the challenge of resolving the early relationships among the three clades. The resolution of the later diversification was more robust, and the resulting topologies were largely compatible with each other and with the current taxonomic classification. Exceptions are the genera Micrelus Thomson, which is transferred from the tribe Ceutorhynchini to Egriini Pajni and Kohli (new position) and Amalus Schoenherr, which is transferred to Phytobiini Gistel (new position). Amalini Wagner 1936 is a junior synonym of Phytobiini Gistel 1848 (syn. n.). Coeliodini Lacordaire (new status), a tribe previously regarded as junior synonym of Ceutorhynchini, is re‐established. Our analyses also clarified the difficult assignments of taxa to the tribes Scleropterini Schultze and Phytobiini. All taxa with the ability to jump as adult beetles belong to clade B, which comprises the tribes Cnemogonini Colonnelli, Hypurini Schultze, Mecysmoderini Wagner and Phytobiini. With dense taxon sampling and appropriate analytical methods, mitogenome data provide a phylogeny well suited to improve the traditional classification of this neglected and species‐rich taxon.

Complete Mitogenome sequencing of the fish louse Argulus japonicus (Crustacea: Branchiura): Comparative analyses and phylogenetic implications.

The fish louse Argulus japonicus, a branchiuran crustacean of the Argulidae family, is attracting increasing attention because of its parasitic tendencies and significant health threats to global fish farming. The mitogenomes can yield a foundation for studying epidemiology, genetic diversity, and molecular ecology and therefore may be used to assist in the surveillance and control of A. japonicus. In this study, we sequenced and assembled the complete mitogenome of A. japonicus to shed light on its genetic and evolutionary blueprint. Our investigation indicated that the 15,045-bp circular genome of A. japonicus encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs) with significant AT and GC skews. Comparative genomics provided an evolutionary scenario for the genetic diversity of 13 PCGs: all were under purifying selection, with cox1 and nad6 having the lowest and highest evolutionary rates, respectively. Genome-wide phylogenetic trees established a close relationship between species of the families Argulidae (Arguloida) and Armilliferidae (Porocephalida) within Crustacea, and further, A. japonicus and Argulus americanus were determined to be more closely related to each other than to others within the family Argulidae. Single PCG-based phylogenies supported nad1 and nad6 as the best genetic markers for evolutionary and phylogenetic studies for branchiuran crustaceans due to their similar phylogenetic topologies with those of genome-based phylogenetic analyses. To sum up, these comprehensive mitogenomic data of A. japonicus and related species refine valuable marker resources and should contribute to molecular diagnostic methods, epidemiological investigations, and ecological studies of the fish ectoparasites in Crustacea.

Phylogeography and demographic history of macaques, fascicularis species group, in East Asia: Inferred from multiple genomic markers

Climate changes at larger scales have influenced dispersal and range shifts of many taxa in East Asia. The fascicularis species group of macaques is composed of four species and is widely distributed in Southeast and East Asia. However, its phylogeography and demographic histories are currently poorly understood. Herein, we assembled autosomal, mitogenome, and Y-chromosome data for 106 individuals, and combined them with 174 mtDNA dloop haplotypes of this species group, with particular focus on the demographic histories and dispersal routes of Macaca fuscata, M. cyclopis, and M. mulatta. The results showed: (1) three monophyletic clades for M. fuscata, M. cyclopis, and M. mulatta based on the multiple genomics analyses; (2) the disparate demographic trajectories of the three species after their split ∼1.0 Ma revealed that M. cyclopis and M. fuscata were derived from an ancestral M. mulatta population; (3) the speciation time of M. cyclopis was later than that of M. fuscata, and their divergence time occurred at the beginning of “Ryukyu Coral Sea Stage” (1.0–0.2 Ma) when the East China Sea land bridge was completely submerged by the sea level rose; and (4) the three parallel rivers (Nujiang, Lancangjiang, and Jinshajiang) of Southwestern China divided M. mulatta into Indian and Chinese genetic populations ∼200 kya. These results shed light on understanding not only the evolutionary history of the fascicularis species group but also the formation mechanism of faunal diversity in East Asia during the Pleistocene.

Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial

Anthropogenic factors have impacted the diversity and evolutionary trajectory of various species. This can be through factors such as pressure on population size or range, habitat fragmentation, or extensive manipulation and translocation. Here we use time-calibrated data to better understand the pattern and processes of evolution in the heavily manipulated European fallow deer (Dama dama). During the Pleistocene, fallow deer had a broad distribution across Europe and were found as far north as Britain during the Eemian interglacial. The last glacial period saw fallow deer retreat to southern refugia and they did not disperse north afterwards. Their recolonisation was mediated by people and, from northern Europe and the British Isles, fallow deer were transported around the world. We use ancient and modern mitochondrial DNA (mtDNA) and mitogenomic data from Eemian Britain to assess the pattern of change in distribution and lineage structure across Europe over time. We find founder effects and mixed lineages in the northern populations, and stability over time for populations in southern Europe. The Eemian sample was most similar to a lineage currently in Italy, suggesting an early establishment of the relevant refuge. We consider the implications for the integration of anthropogenic and natural processes towards a better understanding of the evolution of fallow deer in Europe.

Two new species of Erythroneurini (Hemiptera, Cicadellidae, Typhlocybinae) from southern China based on morphology and complete mitogenomes.

Erythroneurine leafhoppers (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) are utilized to resolve the relationship between the four erythroneurine leafhopper (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini): Arboridia (Arboridia) rongchangensis sp. nov., Thaia (Thaia) jiulongensis sp. nov., Mitjaevia bifurcata Luo, Song & Song, 2021 and Mitjaevia diana Luo, Song & Song, 2021, the two new species are described and illustrated. The mitochondrial gene sequences of these four species were determined to update the mitochondrial genome database of Erythroneurini. The mitochondrial genomes of four species shared high parallelism in nucleotide composition, base composition and gene order, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and an AT control region, which was consistent with majority of species in Cicadellidae; all genes revealed common trait of a positive AT skew and negative GC skew. The mitogenomes of four species were ultra-conservative in structure, and which isanalogous to that of others in size and A + T content. Phylogenetic trees based on the mitogenome data of these species and another 24 species were built employing the maximum likelihood and Bayesian inference methods. The results indicated that the four species belong to the tribe Erythroneurini, M. diana is the sister-group relationship of M. protuberanta + M. bifurcata. The two species Arboridia (Arboridia) rongchangensis sp. nov. and Thaia (Thaia) jiulongensis sp. nov. also have a relatively close genetic relationship with the genus Mitjaevia.

Characterization of the Complete Mitochondrial Genome of Wintersweet (Chimonanthus praecox) and Comparative Analysis within Magnoliids.

Mitochondrial genome sequencing is a valuable tool for investigating mitogenome evolution, species phylogeny, and population genetics. Chimonanthus praecox (L.) Link, also known as "La Mei" in Chinese, is a famous ornamental and medical shrub belonging to the order Laurales of the Calycanthaceae family. Although the nuclear genomes and chloroplast genomes of certain Laurales representatives, such as Lindera glauca, Laurus nobilis, and Piper nigrum, have been sequenced, the mitochondrial genome of Laurales members remains unknown. Here, we reported the first complete mitogenome of C. praecox. The mitogenome was 972,347 bp in length and comprised 60 unique coding genes, including 40 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. The skewness of the PCGs showed that the AT skew (-0.0096233) was negative, while the GC skew (0.031656) was positive, indicating higher contents of T's and G's in the mitochondrial genome of C. praecox. The Ka/Ks ratio analysis showed that the Ka/Ks values of most genes were less than one, suggesting that these genes were under purifying selection. Furthermore, there is a substantial abundance of dispersed repeats in C. praecox, constituting 16.98% of the total mitochondrial genome. A total of 731 SSR repeats were identified in the mitogenome, the highest number among the eleven available magnoliids mitogenomes. The mitochondrial phylogenetic analysis based on 29 conserved PCGs placed the C. praecox in Lauraceae, and supported the sister relationship of Laurales with Magnoliales, which was congruent with the nuclear genome evidence. The present study enriches the mitogenome data of C. praecox and promotes further studies on phylogeny and plastid evolution.

Four new complete mitochondrial genomes of Gobioninae fishes (Teleostei: Cyprinidae) and their phylogenetic implications.

The subfamily Gobioninae is one of the most diverse fish groups within Cyprinidae. Their taxonomy and phylogenetic relationships are not completely resolved. In this study, the complete mitochondrial genomes (mitogenome) of four Gobioninae species (Microphysogobio elongatus, Microphysogobio chinssuensis, Gobio rivuloides and Rhinogobio nasutus) were sequenced and compared. The mitogenomes of four species ranges from 16603 bp to 16609 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Most PCGs had significant codon usage bias. Except for the tRNASer (GCT), all the nucleotide substitutions of tRNA loops higher than the stems could fold into a stable secondary structure. The nucleotide compositions of Gobioninae mitogenome were biased toward A/T, and NAD4 was subjected to low purification selection and had a faster evolution rate among 13 PCGs. Bayesian inference and maximum likelihood phylogenetic analyses showed the consistent results. The four sequenced species clustered together with their congener species. However, more samples and mitogenome data are needed to untangle the phylogenetic relationships among genera Microphysogobio, Romanogobio, Hugobio, Biwia and Platysmacheilus.

Revisiting the genus Pseudocuneopsis (Bivalvia, Unionidae): Morphology, mitochondrial phylogenomics, and the description of a new species

AbstractSpecies diversity can be underestimated due to a lack of regional studies and limitations in research methods. China is widely recognized as one of the primary hotspots for the biodiversity of freshwater mussels as it harbours a wealth of endemic species. Pseudocuneopsis was recently established to belong to the Unioninae subfamily within Unionidae and is endemic to China. Recent research has expanded the diversity and range of distribution of this genus. However, sufficient data is required to precisely determine the phylogenetic relationships within Pseudocuneopsis. This study conducted an integrative taxonomy using morphological, COI barcode, and complete maternal mitogenome data to clarify the taxonomy of Pseudocuneopsis. Both morphological and COI barcode data supported the validity of all Pseudocuneopsis species. Furthermore, a new species, Pseudocuneopsis yemaoi sp. n. was described from a tributary of the Man River in Hubei, China. Mitochondrial phylogenomic analyses showed that P. yemaoi was closely related to P. sichuanensis and resolved phylogenetic relationship as (P. capitata + (P. yangshuoensis + (P. sichuanensis + P. yemaoi))). Our results highlight the significance of utilizing integrative classification methods. Moreover, we propose enhancing the research and preservation measures of minor streams in China, as these streams may house distinctive species.

Museomics allows comparative analyses of mitochondrial genomes in the family Gryllidae (Insecta, Orthoptera) and confirms its phylogenetic relationships.

Next-generation sequencing technology can now be used to sequence historical specimens from natural history collections, an approach referred to as museomics. The museomics allows obtaining molecular data from old museum-preserved specimens, a resource of biomolecules largely underexploited despite the fact that these specimens are often unique samples of nomenclatural types that can be crucial for resolving scientific questions. Despite recent technical progress, cricket mitogenomes are still scarce in the databases, with only a handful of new ones generated each year from freshly collected material. In this study, we used the genome skimming method to sequence and assemble three new complete mitogenomes representing two tribes of the cricket subfamily Eneopterinae: two were obtained from old, historical type material of Xenogryllus lamottei (68 years old) and X. maniema (80 years old), the third one from a freshly collected specimen of Nisitrus vittatus. We compared their genome organization and base composition, and reconstructed the molecular phylogeny of the family Gryllidae. Our study not only confirmed that the genome skimming method used by next generation sequencing allows us to efficiently obtain the whole mitogenome from dry-pinned historical specimens, but we also confirmed how promising it is for large-scale comparative studies of mitogenomes using resources from natural history collections. Used in a phylogenetic context the new mitogenomes attest that the mitogenomic data contain valuable information and also strongly support phylogenetic relationships at multiple time scales.

Novel gene arrangement in the mitochondrial genome of Aspersentis megarhynchus (Acanthocephala, Echinorhynchida, Heteracanthocephalidae), and its phylogenetic implications.

The Heteracanthocephalidae Petrochenko, 1956 is a rare family of acanthocephalans mainly parasitic in fishes. The pattern of mitogenomic evolution of the Heteracanthocephalidae is still unknown, and the phylogenetic relationships of the Heteracanthocephalidae with the other 14 families within the order Echinorhynchida remain unclear. In the present study, the complete mitochondrial genome of Aspersentis megarhynchus (von Linstow, 1892) Golvan, 1960 was sequenced and annotated for the first time, which represents the first mitogenomic data for the genus Aspersentis and also for the family Heteracanthocephalidae. The mitogenome of A. megarhynchus has 14,661 bp and includes 36 genes, containing 12 protein-coding genes (PCGs) (missing atp8), 22 tRNA genes, and 2 ribosomal RNAs (rrnS and rrnL), plus two non-coding regions. Comparative mitochondrial genomic analysis revealed that the presence of translocations of several tRNA genes (trnV, trnE, and trnT) and the gene arrangement in the mitogenome of A. megarhynchus represents a new type in Acanthocephala. Moreover, the mitogenomic phylogenetic results based on concatenated amino acid sequences of 12 protein-coding genes strongly supported the validity of the Heteracanthocephalidae and suggested close affinity between the Heteracanthocephalidae and Echinorhynchidae in the order Echinorhynchida.

Limits of mitochondrial genes in delimiting species within a Carbula species complex (Hemiptera: Pentatomidae).

Molecular data has become a powerful tool for species delimitation, particularly among those that present limited morphological differences; while the mitochondrial genome, with its moderate length, low cost of sequencing and fast lineage sorting, has emerged as a practical data set. Due to the limited morphological differences among the closely related species of Carbula Stål 1865, the species boundaries between Carbula abbreviata (Motschulsky, 1866), Carbula humerigera (Uhler, 1860), and Carbula putoni (Jakovlev, 1876) have remained particularly unclear. In this study, we applied two phylogenetic reconstruction methods to two data sets (mitogenome and COI) to assess the phylogeny of Carbula distributed in Asia, and five species delimitation methods to determine the boundaries between East Asian Carbula species. Our phylogenetic analyses showed Carbula to be paraphyletic; the seven known species distributed within East Asia to form a single monophyletic group, and within this, C. abbreviata, C. humerigera, C. putoni and middle-type to comprise a C. humerigera species complex. Our results show that mitogenome data alone, while effective in the differentiation of more distantly related Carbula species, is not sufficient to accurately delimit the species within this newly described complex.

Unusual rearrangements of mitogenomes in Diptera revealed by comparative analysis of 135 tachinid species (Insecta, Diptera, Tachinidae)

The Tachinidae is one of the most speciose families in Diptera, and the exclusively parasitoid species play an important role in regulating populations of many herbivorous insects in ecosystems, including many agricultural pests. To better comprehend the characteristics and evolution of the mitochondrial genome for the Tachinidae, we are adding a massive amount of new molecular data by assembling the mitogenomes for 71 genera and 135 species from all four tachinid subfamilies through next-generation sequencing, and we are presenting the most comprehensive mitogenomic phylogenetic analysis of this family so far. Extensive rearrangements observed in the mitogenome of Admontia podomyia (Exoristinae) are unique for the entire suborder Cyclorrhapha. The rearrangement pattern suggests that the process involved a tandem duplication of the complete mitogenome, followed by both random and nonrandom loss of one copy of each gene. Additionally, five minor mitogenome rearrangements are discovered and described in three subfamilies. We present the largest species-level phylogenetic hypothesis for Tachinidae to date, based on mitogenomes of 152 species of Tachinidae, representing all four subfamilies and with five non-tachinid outgroups. Our analyses support the monophyly of the Tachinidae and most tribes and genera were recovered with good support, but the higher-level phylogenetic relationships within Tachinidae were poorly resolved, indicating that mitogenome data alone are not enough to unambiguously resolve the deeper phylogenetic relationships within Tachinidae.

Characterization of the Cambaroides wladiwostokiensis Birstein & Vinogradov, 1934 (Decapoda: Astacidea) Mitochondrial Genome Using Genome Skimming and the Phylogenetic Implications within the Astacidea Infraorder.

The mitochondrial genome is a powerful tool for exploring and confirming species identity and understanding evolutionary trajectories. The genus Cambaroides, which consists of freshwater crayfish, is recognized for its evolutionary and morphological complexities. However, comprehensive genetic and mitogenomic data on species within this genus, such as C. wladiwostokiensis, remain scarce, thereby necessitating an in-depth mitogenomic exploration to decipher its evolutionary position and validate its species identity. The mitochondrial genome of C. wladiwostokiensis was obtained through shallow Illumina paired-end sequencing of total DNA, followed by hybrid assembly using both de novo and reference-based techniques. Comparative analysis was performed using available Cambaroides mitochondrial genomes obtained from National Center for Biotechnology Information (NCBI). Additionally, phylogenetic analyses of 23 representatives from three families within the Astacidea infraorder were employed using the PhyloSuite platform for sequence management and phylogenetic preparation, to elucidate phylogenetic relationships via Bayesian Inference (BI), based on concatenated mitochondrial fragments. The resulting genome, which spans 16,391 base pairs was investigated, revealing 13 protein-coding genes, rRNAs (12S and 16S), 19 tRNAs, and a putative control region. Comparative analysis together with five other Cambaroides mitogenomes retrieved from GenBank unveiled regions that remained unread due to challenges associated with the genome skimming technique. Protein-coding genes varied in size and typically exhibited common start (ATG) and stop (TAA) codons. However, exceptions were noted in ND5 (start codon: GTG) and ND1 (stop codon: TAG). Landscape analysis was used to explore sequence variation across the five available mitochondrial genomes of Cambaroides. Collectively, these findings reveal variable sites and contribute to a deeper understanding of the genetic diversity in this genus alongside the further development of species-specific primers for noninvasive monitoring techniques. The partitioned phylogenetic analysis of Astacidea revealed a paraphyletic origin of Asian cambarids, which confirms the data in recent studies based on both multilocus analyses and integrative approaches.

In Search of the Elusive North: Evolutionary History of the Arctic Fox (Vulpes lagopus) in the Palearctic from the Late Pleistocene to the Recent Inferred from Mitogenomic Data.

Despite the high level of interest, the population history of arctic foxes during the Late Pleistocene and Holocene remains poorly understood. Here we aimed to fill gaps in the demographic and colonization history of the arctic fox by analyzing new ancient DNA data from fossil specimens aged from 50 to 1 thousand years from the Northern and Polar Urals, historic DNA from museum specimens from the Novaya Zemlya Archipelago and the Taymyr Peninsula and supplementing these data by previously published sequences of recent and extinct arctic foxes from other regions. This dataset was used for reconstruction of a time-calibrated phylogeny and a temporal haplotype network covering four time intervals: Late Pleistocene (ranging from 30 to 13 thousand years bp), Holocene (ranging from 4 to 1 thousand years bp), historical (approximately 150 years), and modern. Our results revealed that Late Pleistocene specimens showed no genetic similarity to either modern or historical specimens, thus supporting the earlier hypothesis on local extinction rather than habitat tracking.

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis.

Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome. In the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated. The P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.

The complete mitochondrial genome of Erinaceus concolor (Mammalia: Eulipotyphla) from Türkiye with phylogenetic implications

As a reference mitogenome, the complete mitochondrial genome of the white-breasted hedgehog, Erinaceus concolor, was firstly presented in this study by employing Long-Range PCR and Next-Generation Sequencing. The total lengths of the mitogenomes were 17.451 bp and 17.455 bp. A total of 37 genes, namely two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and a non-coding D-loop were encoded in the mitogenome, compatible with the previously reported mitogenomes belonging to representatives of the family Erinaceidae (Mammalia: Eulipotyphla). Maximum Likelihood and Bayesian Inference phylogenetic analyses of Eulipotyphla and Erinaceidae based on the complete mitogenomes revealed a conventional relationship for the relevant organism's groups. Divergence time analyses based on complete mitogenome data revealed that evolutionary divergence events within Erinaceidae began about 58.87 Myr ago corresponding to the early Eocene, and the basal split of Erinaceus dates back to approximately 11.01 Myr ago in the late Miocene. Single cytochrome b-based analyses can be considered weaker, as they produce phylogenies that are relatively inconsistent with the natural classification of Eulipotyphla and put the onset of evolutionary divergence events earlier. The genetic information obtained as a result of this study can be used as a genetic resource for conservation biology studies; it will also undoubtedly contribute to the understanding of molecular evolution of E. concolor and closely related taxa.

First record of the complete mitochondrial genome of Botyodes diniasalis (Walker, 1859) (Lepidoptera: Crambidae)

We performed the first sequencing of the complete mitogenome of Botyodes diniasalis by high-throughput sequencing. A circular DNA molecule of 15,219 bp in size, encoding 2 rRNAs, 22 tRNAs, and 13 PCGs, contains a non-coding AT-rich region. The overall nucleotide composition of the genome is A (39.5%), T (41.3%), C (11.3%), and G (7.8%). Phylogenetic analysis based on mitogenomic data suggest that the species B. diniasalis has a close evolutionary relationship with B. principalis in Margaroniini. The complete mitogenome of B. diniasalis will serve as a valuable resource for future studies on evolution, taxonomy, genetic conservation, and utilization of Botyodes.

Phylogenomic analyses reveal a single deep-water colonisation in Patellogastropoda

Patellogastropoda, the true limpets, is a major group of gastropods widely distributed in marine habitats from the intertidal to deep sea. Though important for understanding their evolutionary radiation, the phylogenetic relationships among the patellogastropod families have always been challenging to reconstruct, with contradictory results likely due to insufficient sampling. Here, we obtained mitogenomic and phylogenomic data (transcriptomic or genomic) from six species representing the three predominantly deep-water patellogastropod families: Lepetidae, Neolepetopsidae, and Pectinodontidae. By using various phylogenetic methods, we show that mitogenome phylogeny recovers monophyly of eight families in most of the trees, though the relationships among families remain contentious. Meanwhile, a more robust family-level topology consistent with morphology was achieved by phylogenomics. This also reveals that these mainly deep-water families are monophyletic, suggesting a single colonisation of the deep water around the Jurassic. We also found a lack of significant correlation between genome size and habitat depth, despite some deep-water species exhibiting larger genome sizes. Our phylogenomic tree provides a stable phylogenetic backbone for Patellogastropoda that includes seven of the nine recognized families and paves the way for future evolutionary analyses in this major group of molluscs.