Mitogenomic Analysis Research Articles

Mitochondrial Genomes from Fungal the Entomopathogenic Moelleriella Genus Reveals Evolutionary History, Intron Dynamics and Phylogeny

Members of the genus Moelleriella (Hypocreales, Clavicipitaceae) are insect pathogens with specificity for scale insects and whiteflies. However, no mitochondrial genomes are available for these fungi. Here, we assembled seven mitogenomes from M. zhongdongii, M. libera, M. raciborskii, M. gracilispora, M. oxystoma, Moelleriella sp. CGMCC 3.18909, and Moelleriella sp. CGMCC 3.18913, which varied in size from 40.8 to 95.7 Kb. Synteny and codon usage bias was relatively conserved, with the mitochondrial gene arrangement being completely homologous to the gene order of 21 other species within the Hypocreales. Nevertheless, significant intron polymorphism was observed between Moelleriella species. Evolutionary analyses revealed that all 15 core protein–coding genes had ka/ks < 1, indicating purifying selection pressure. Sequence variation within the mitochondrial ATP synthase F0 subunit 6 (atp6) gene showed the largest genetic distance, with the ATP synthase F0 subunit 9 (atp9) gene showing the smallest. Comparative analyses of mitogenomes revealed that introns were the primary factor contributing to the size variation in Moelleriella and, more broadly, within Hypocreales mitogenomes. Phylogenetic analyses indicated that the seven Moelleriella species examined form a well–supported clade, most closely related to Metarhizium. These data present the first mitogenomes from Moelleriella and further advance research into the taxonomy, origin, evolution, and genomics of Moelleriella.

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

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

Assembly and comparative analysis of the complete mitogenome of Rubus chingii var. suavissimus, an exceptional berry plant possessing sweet leaves

Rubus chingii var. suavissimus is a special berry plant of Rubus in the Rosaceae family. Its leaves contain high-sweetness, low-calorie, and non-toxic sweet ingredients, known as rubusoside. As a medicine and food biofunctional plant, it is a combination of “tea, sugar, and medicine.” In this study, the complete mitogenome of R. chingii var. suavissimus was successfully assembled and annotated based on PacBio HiFi sequencing technology. The mitogenome of R. chingii var. suavissimus was a typical master circle structure, spanning 432,483 bp and containing 34 unique protein-coding genes (PCGs), 20 tRNAs, and 3 rRNAs. The majority of these PCGs was subjected to purifying selection, and only one gene (ccmB) showed sign of positive selection. The mitogenome of R. chingii var. suavissimus contained a large number of repeats, and the homogeneous fragments transferring between plastid genome and mitogenome, with a total of 55 pairs of mitochondrial plastid sequences (MTPTs), and the total size was 56,913 bp. Comparative analysis showed that the non-coding region in the mitogenome of R. chingii var. suavissimus had undergone frequent rearrangements during evolution, but the coding region was still highly conserved. Furthermore, the maximum likelihood and Bayesian inference phylogenetic trees were reconstructed of 10 shared PCGs in 36 plant species. The topological structures of two phylogenetic trees were consistent with the APG IV classification system and had high support rates. In general, this study clarifies the mitogenome of R. chingii var. suavissimus and provides valuable insights into the genetic evolution of the Rosaceae family.

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.

Redescription and validity of Formosania gilberti Oshima, 1919 (Cypriniformes: Balitoridae), an endemic hillstream loach from Taiwan

For over a century, only one species of Formosania has been recognised in Taiwanese waters. However, through the use of mitogenomic analyses and the identification of morphological differences, an endemic balitorid loach was revalidated and redescribed based on specimens herein of northern Taiwan. Formosania gilberti Oshima, 1919 was previously mistreated as a junior synonym of F. lacustris (Steindachner, 1908), but the two can be clearly differentiated by their vertebral counts (26+11 vs. 26+12) and body marking patterns (intensely mottled with vermicular markings vs. cloud-like blotches or brown and blotchless). Furthermore, mitogenomic analyses also showed high intra-specific diversity among Formosania loaches in Taiwan, which not only supports F. gilberti as a valid species but also hints the presence of a species complex distributed in western Taiwan.

Characterization of the Complete Mitogenome of the Ring-Necked Pheasant Phasianus colchicus (Galliformes: Phasianidae) and Systematic Implications for Phasianinae Phylogenetics.

Phasianidae mitogenomes exhibit significant structural variations critical for understanding evolution and subspecies divergence. However, annotations of these features in some pheasant species remain limited. This study aimed to enhance understanding of Phasianidae mitogenomes and their evolutionary patterns. A comparative analysis of complete mitogenomes from Phasianus colchicus, Phasianus versicolor, and 22 other accipitrids was conducted, examining codon usage, rRNA structures, selective pressures, phylogenetics, and structural variations. The mitogenome of P. colchicus is 16,696 bp, comprising 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, with a base composition of A: 30.61%, T: 25.26%, C: 30.85%, and G: 13.28%. Phylogenetic analysis revealed P. colchicus and P. versicolor are closely related, with the following relationship: ((Phasianus + Chrysolophus) + (Crossoptilon + Lophura)). Divergence timing aligns with the Tibetan Plateau uplift during the Tertiary Pliocene. Ka/Ks analysis suggests the CO I, CO II, CO III, ND1, ND4L, and ND6 genes in Phasianus underwent strong selective pressure for plateau adaptation. The study confirms Phasianus monophyly and its close relationship with Chrysolophus. Adaptation-related selective pressures on the CO I, CO II, CO III, ND1, ND4L, and ND6 genes highlight its role in plateau environments, offering valuable insights into pheasant phylogeny.

Comprehensive analysis of the first complete mitogenome and plastome of a traditional Chinese medicine Viola diffusa

BackgroundViola diffusa is used in the formulation of various Traditional Chinese Medicines (TCMs), including antiviral, antimicrobial, antitussive, and anti-inflammatory drugs, due to its richness in flavonoids and triterpenoids. The biosynthesis of these compounds is largely mediated by cytochrome P450 enzymes, which are primarily located in the membranes of mitochondria and the endoplasmic reticulum.ResultsThis study presents the complete assembly of the mitogenome and plastome of Viola diffusa. The circular mitogenome spans 474,721 bp with a GC content of 44.17% and encodes 36 unique protein-coding genes, 21 tRNA, and 3 rRNA. Except for the RSCU values of 1 observed for the start codon (AUG) and tryptophan (UGG), the mitochondrial protein-coding genes exhibited a codon usage bias, with most estimates deviating from 1, similar to patterns observed in closely related species. Analysis of repetitive sequences in the mitogenome demonstrated potential homologous recombination mediated by these repeats. Sequence transfer analysis revealed 24 homologous sequences shared between the mitogenome and plastome, including nine full-length genes. Collinearity was observed among Viola diffusa species within the other members of Malpighiales order, indicated by the presence of homologous fragments. The length and arrangement of collinear blocks varied, and the mitogenome exhibited a high frequency of gene rearrangement.ConclusionsWe present the first complete assembly of the mitogenome and plastome of Viola diffusa, highlighting its implications for pharmacological, evolutionary, and taxonomic studies. Our research underscores the multifaceted importance of comprehensive mitogenome analysis.

A Comparative Analysis of Mitogenomes in Species of the Tapinoma nigerrimum Complex and Other Species of the Genus Tapinoma (Formicidae, Dolichoderinae).

Using next-generation sequencing data, the complete mitogenomes of six species from the genus Tapinoma were assembled. This study explores the mitochondrial genomes of Tapinoma species, among them the five species from the Tapinoma nigerrimum complex, comparing them with each other and with other species from Dolichoderinae subfamily to understand their evolutionary relationships and evolution. Tapinoma mitochondrial genomes contain the typical set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and the A + T-rich control region. A phylogenetic analysis using the protein-coding gene sequences from available Dolichoderinae mitogenomes supports the monophyletic nature of the genus Tapinoma, with the T. nigerrimum complex forming a well-supported clade. Key findings include genetic traits unique to the T. nigerrimum complex, such as a start codon in the atp8 gene and a complete stop codon in cox1, distinguishing them from other Tapinoma species. Additionally, a gene rearrangement involving tRNA-Trp, tRNA-Cys, and tRNA-Tyr was found exclusively in the Tapinoma species, suggesting a potential phylogenetic marker for the genus.

Mitogenome based adaptations and phylogeny of Beetal goats in India

Beetal goats, the second largest Indian goat breed, are known for their adaptation to hot arid tropical climates. Beyond their phylogenetic significance, recent evidence suggests that mitogenome modifications play a crucial role in the adaptation of animals to environmental stress factors. This study aims to characterize the mitogenome of Beetal goats at the molecular level, elucidate their mitogenomic adaptations and determine the maternal phylogenetic status of Indian Beetal goats. Whole genome sequencing of pooled DNA samples from five unrelated Beetal goats was carried out to obtain mitogenome sequence. The Beetal goat mitogenome comprised of a coding region with 37 genes: 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and two ribosomal RNAs (rRNAs), as well as a non-coding hypervariable displacement loop (D-loop) region. We identified nine SNPs inclusive of seven synonymous and two nonsynonymous ones located in PCGs that too in respiratory complex I subunit genes, five of which were novel. Two nonsynonymous SNPs (10,229 A > G in ND4 and 13,964 G > A in ND6) were homoplasmic ones with marked influence on their mRNA and protein structures. Synonymous SNPs influenced the minimum free energy (MFE) and topology of predicted mRNA secondary structures, thereby affecting mRNA stability and translation efficiency. Phylogenetic analysis of the D-loop region classified Beetal goats into haplogroup B. Mitogenome analysis of Beetal goats, in comparison with other goat populations revealed the greatest genetic similarity to Southeast Asian goats. The comprehensive analysis of mitochondrial DNA in Beetal goats reveals significant genetic adaptations crucial for their survival in hot, arid environments. This study also highlights the complex matrilineal origins of Beetal goats.

Assembly, Annotation, and Comparative Analysis of Mitochondrial Genomes in Trichoderma.

Trichoderma is a widely studied ascomycete fungal genus, including more than 400 species. However, genetic information on Trichoderma is limited, with most species reporting only DNA barcodes. Mitochondria possess their own distinct DNA that plays a pivotal role in molecular function and evolution. Here, we report 42 novel mitochondrial genomes (mitogenomes) combined with 18 published mitogenomes of Trichoderma. These circular mitogenomes exhibit sizes of 26,276-94,608 bp, typically comprising 15 core protein-coding genes (PCGs), 2 rRNAs, and 16-30 tRNAs; however, the number of endonucleases and hypothetical proteins encoded in the introns of PCGs increases with genome size enlargement. According to the result of phylogenetic analysis of the whole mitogenome, these strains diverged into six distinct evolutionary branches, supported by the phylogeny based on 2830 single-copy nuclear genes. Comparative analysis revealed that dynamic Trichoderma mitogenomes exhibited variations in genome size, gene number, GC content, tRNA copy, and intron across different branches. We identified three mutation hotspots near the regions encoding nad3, cox2, and nad5 that caused major changes in the mitogenomes. Evolutionary analysis revealed that atp9, cob, nad4L, nad5, and rps3 have been influenced by positive selection during evolution. This study provides a valuable resource for exploring the important roles of the genetic and evolutionary dynamics of Trichoderma mitogenome in the adaptive evolution of biocontrol fungi.

Assembly and comparative analysis of the first complete mitochondrial genome of Astragalus membranaceus (Fisch.) Bunge: an invaluable traditional Chinese medicine

BackgroundAstragalus membranaceus (Fisch.) Bunge is one of the most well-known tonic herbs in traditional Chinese medicine, renowned for its remarkable medicinal value in various clinical contexts. The corresponding chloroplast (cp) and nuclear genomes have since been accordingly sequenced, providing valuable information for breeding and phylogeny studies. However, the mitochondrial genome (mitogenome) of A. membranaceus remains unexplored, which hinders comprehensively understanding the evolution of its genome.ResultsFor this study, we de novo assembled the mitogenome of A. membranaceus (Fisch.) Bunge var. mongholicus (Bunge) P. K. Hsiao using a strategy integrating Illumina and Nanopore sequencing technology and subsequently performed comparative analysis with its close relatives. The mitogenome has a multi-chromosome structure, consisting of two circular chromosomes with a total length of 398,048 bp and an overall GC content of 45.3%. It encodes 54 annotated functional genes, comprising 33 protein-coding genes (PCGs), 18 tRNA genes, and 3 rRNA genes. An investigation of codon usage in the PCGs revealed an obvious preference for codons ending in A or U (T) bases, given their high frequency. RNA editing identified 500 sites in the coding regions of mt PCGs that exhibit a perfect conversion of the base C to U, a process that tends to lead to the conversion of hydrophilic amino acids into hydrophobic amino acids. From the mitogenome analysis, a total of 399 SSRs, 4 tandem repeats, and 77 dispersed repeats were found, indicating that A. membranaceus possesses fewer repeats compared to its close relatives with similarly sized mitogenomes. Selection pressure analysis indicated that most mt PCGs were purifying selection genes, while only five PCGs (ccmB, ccmFc, ccmFn, nad3, and nad9) were positive selection genes. Notably, positive selection emerged as a critical factor in the evolution of ccmB and nad9 in all the pairwise species comparisons, suggesting the extremely critical role of these genes in the evolution of A. membranaceus. Moreover, we inferred that 22 homologous fragments have been transferred from cp to mitochondria (mt), in which 5 cp-derived tRNA genes remain intact in the mitogenome. Further comparative analysis revealed that the syntenic region and mt gene organization are relatively conserved within the provided legumes. The comparison of gene content indicated that the gene composition of Fabaceae mitogenomes differed. Finally, the phylogenetic tree established from analysis is largely congruent with the taxonomic relationships of Fabaceae species and highlights the close relationship between Astragalus and Oxytropis.ConclusionsWe provide the first report of the assembled and annotated A. membranaceus mitogenome, which enriches the genetic resources available for the Astragalus genus and lays the foundation for comprehensive exploration of this invaluable medicinal plant.

Comparative Analyses of the Complete Mitogenomes of Two Oxyria Species (Polygonaceae) Provide Insights into Understanding the Mitogenome Evolution Within the Family.

Oxyria (Polygonaceae) is a small genus only comprising two species, Oxyria digyna and O. sinensis. Both species have well-documented usage in Chinese herbal medicine. We sequenced and assembled the complete mitogenomes of these two species and conducted a comparative analysis of the mitogenomes within Polygonaceae. Both O. digyna and O. sinensis displayed distinctive multi-branched conformations, consisting of one linear and one circular molecule. These two species shared similar gene compositions and exhibited distinct codon preferences, with mononucleotides as the most abundant type of simple sequence repeats. In the mitogenome of O. sinensis, a pair of long forward repeat sequences can mediate the division of molecule 1 into two sub-genomic circular molecules. Homologous sequence analysis revealed the occurrence of gene transfer between the chloroplast and mitochondrial genomes within Oxyria species. Additionally, a substantial number of homologous collinear blocks with varied arrangements were observed across different Polygonaceae species. Phylogenetic analysis suggested that mitogenome genes can serve as reliable markers for constructing phylogenetic relationships within Polygonaceae. Comparative analysis of eight species revealed Polygonaceae mitogenomes exhibited variability in gene presence, and most protein-coding genes (PCGs) have undergone negative selection. Overall, our study provided a comprehensive overview of the structural, functional, and evolutionary characteristics of the Polygonaceae mitogenomes.

Mitogenomic analysis of the position of the Azygiidae and constituent genera, with a new species of Azygia

The Azygiidae Looss, 1899 is a family of digeneans with a Holarctic distribution in which members of some genera mature in marine elasmobranchs while others occur only in freshwater teleosts. Some have questioned whether the marine genus Otodistomum Stafford, 1904 indeed belongs to the same family as the freshwater azygiid genera, namely Azygia Looss, 1899, Proterometra Horsfall, 1933, and Leuceruthrus Marshall and Gilbert, 1905. We present phylogenetic analyses based on mitochondrial genomes, rDNA operons, and partial cytochrome c oxidase I (Cox1) sequences from North American and Asian species that support the monophyly of Azygiidae, and placement of Azygioidea in the suborder Hemiurata, in contrast to recently published mitochondrial genome phylogenies. All phylogenies indicate that Azygia includes Leuceruthrus, which we therefore propose to be a junior synonym, together with suppression of the Leuceruthrinae. The status of Proterometra was equivocal, with support in some but not all analyses of 28S, but not in other markers. We describe a new species of Azygia from northeastern North America. Our results confirm the morphological variability of adults in Azygia, with worm size positively correlated with host size in Azygia angusticauda. Phylogenies suggest a marine origin for the Azygiidae, and a Palearctic origin for freshwater azygiids, with a single trans-Atlantic radiation to the Nearctic.

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.

New mitochondrial gene order arrangements and evolutionary implications in the class Octocorallia.

The complete mitochondrial genomes of octocorals typically range from 18.5 kb to 20.5 kb in length and include 14 protein-coding genes (PCGs), two ribosomal RNA genes and one tRNA. To date, seven different gene orders (A-G) have been described, yet comprehensive investigations of the actual number of arrangements, as well as comparative analyses and evolutionary reconstructions of mitochondrial genome evolution within the whole class Octocorallia, have been often overlooked. Here, we considered the complete mitochondrial genomes available for octocorals and explored their structure and gene order variability. Our results updated the actual number of mitochondrial gene order arrangements so far known for octocorals from 7 to 14 and allowed us to explore and preliminarily discuss the role of some of the structural and functional factors in the mitogenomes. We performed comparative mitogenomic analyses on the existing and novel octocoral gene orders, considering different mitogenomic structural features such as genome size, GC percentage, AT and GC skewness. The mitochondrial gene order history mapped on a recently published nuclear loci phylogeny showed that the most common rearrangement events in octocorals are inversions, inverted transpositions and transpositions. Furthermore, gene order rearrangement events were restricted only to some regions of the tree. Overall, different rearrangement events arose independently and from the ancestral and most common gene order, instead of being derived from other rearranged orders. Finally, our data demonstrate how the study of mitochondrial gene orders can be used to explore the evolution of octocorals and in some cases can be used to assess the phylogenetic placement of certain taxa.

Comparative characterization and phylogenetic analysis of complete mitogenome of three taxonomic confused groupers and the insight to the novel gene tandem duplication in Epinephelus

Epinephelus bilobatus, Epinephelus maculatus and Epinephelus longispinis are three groupers that share common morphological characteristics and coloration patterns and have been morphologically confused and misidentified with each other for a long time. Complete mitochondrial genomes of the three groupers were determined and analyzed in this study. Mitogenomes of E. bilobatus, E. maculatus and E. longispinis were 17, 354 bp, 17, 066 bp and 17, 221 bp in size respectively and consisted of 13 protein-coding genes, two ribosomal RNA genes and one control region. However, different from most teleosts, which contain canonical 22 tRNAs, more numbers of tRNAs were identified in the three groupers with 27 tRNAs in E. bilobatus and E. longispinis and 25 tRNAs in E. maculatus. The increased number of tRNAs was due to the presence of tandemly duplicated tRNA-Asp genes that were located between tRNA-Ser and COII genes (six duplications in E. bilobatus and E. longispinis, four duplications in E. maculatus). Intact gene tandem duplication was an uncommon feature that was found in the typical teleost mitogenomes. The phylogenetic trees of the 32 groupers (genus Epinephelus) that were constructed based on 12 protein-coding genes revealed that Epinephelus species with tandemly duplicated tRNA-Asp genes were clustered into one monophyletic group, distinct from other Epinephelus species without any duplication features, which indicated that tandemly duplicated tRNA-Asp genes may be the particular linage-specific characteristics that evolve from a common ancestor and have the ability to distinguish them from other Epinephelus species. The results of the mitogenomes comparative analyses of the three groupers revealed the genetic distance of mitogenomes between each two species to be 0.062 (E. bilobatus vs E. maculatus), 0.091 (E. bilobatus vs E. longispinis) and 0.087 (E. maculatus vs E. longispinis). All values were far greater than the minimum value of 0.020 for species identification, which shows that they were three independent species at molecular level. Regarding the relationships between the three groupers, E. bilobatus was found to be more closely related to E. maculatus in comparison to E. longispinis. The results provide valuable molecular data for the species identification and phylogenetic analyses on E. bilobatus, E. maculatus and E. longispinis, and also provided a new insight into the tandem gene duplication features of Epinephelus mitogenomes.

Sturnidae sensu lato Mitogenomics: Novel Insights into Codon Aversion, Selection, and Phylogeny.

The Sturnidae family comprises 123 recognized species in 35 genera. The taxa Mimidae and Buphagidae were formerly treated as subfamilies within Sturnidae. The phylogenetic relationships among the Sturnidae and related taxa (Sturnidae sensu lato) remain unresolved due to high rates of morphological change and concomitant morphological homoplasy. This study presents five new mitogenomes of Sturnidae sensu lato and comprehensive mitogenomic analyses. The investigated mitogenomes exhibit an identical gene composition of 37 genes-including 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes-and one control region (CR). The most important finding of this study is drawn from CAM analyses. The surprisingly unique motifs for each species provide a new direction for the molecular species identification of avian. Furthermore, the pervasiveness of the natural selection of PCGs is found in all examined species when analyzing their nucleotide composition and codon usage. We also determine the structures of mt-tRNA, mt-rRNA, and CR structures of Sturnidae sensu lato. Lastly, our phylogenetic analyses not only well support the monophyly of Sturnidae, Mimidae, and Buphagidae, but also define nine stable subclades. Taken together, our findings will enable the further elucidation of the evolutionary relationships within Sturnidae sensu lato.

The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata.

Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multi-branched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species.

Comprehensive analysis of the Lycopodium japonicum mitogenome reveals abundant tRNA genes and cis-spliced introns in Lycopodiaceae species.

Lycophytes and ferns represent one of the earliest-diverging lineages of vascular plants, with the Lycopodiaceae family constituting the basal clade among lycophytes. In this research, we successfully assembled and annotated the complete Lycopodium japonicum Thunb. (L. japonicum) mitochondrial genome (mitogenome) utilizing PacBio HiFi sequencing data, resulting in a single circular molecule with a size of 454,458 bp. 64 unique genes were annotated altogether, including 34 protein-coding genes, 27 tRNAs and 3 rRNAs. It also contains 32 group II introns, all of which undergo cis-splicing. We identified 195 simple sequence repeats, 1,948 dispersed repeats, and 92 tandem repeats in the L. japonicum mitogenome. Collinear analysis indicated that the mitogenomes of Lycopodiaceae are remarkably conserved compared to those of other vascular plants. We totally identified 326 RNA editing sites in 31 unique protein-coding genes with 299 sites converting cytosine to uracil and 27 sites the reverse. Notably, the L. japonicum mitogenome has small amounts foreign DNA from plastid or nuclear origin, accounting for only 2.81% of the mitogenome. The maximum likelihood phylogenetic analysis based on 23 diverse land plant mitogenomes and plastid genomes supports the basal position of lycophytes within vascular plants and they form a sister clade to all other vascular lineages, which is consistent with the PPG I classification system. As the first reported mitogenome of Lycopodioideae subfamily, this study enriches our understanding of Lycopodium mitogenomes, and sets the stage for future research on mitochondrial diversity and evolution within the lycophytes and ferns.

Elucidating Scarab Divergence in an Evolutionary-Ecological Context through the Comprehensive Analysis of the Complete Mitogenome of Anomala.

Anomala Samouelle, 1819 is one of the specious genera of Coleoptera, with over 1000 known species, and includes some of the most destructive pests of crops or forests. Morphological convergence is a common phenomenon within this genus, making the identification of closely related species very difficult. To explore the phylogenetic placement of Anomalini and provide a basis for the classification and identification of Anomala, we comparatively analyzed the complete mitogenome of three Anomala species (A. exoleta, A. perplexa diana, and A. praecoxalis). Based on all accessible mitogenome data, we performed comparative mitochondrial genomics analysis of this genus and reconstructed the phylogenetic relationships of Scarabaeidae based on two datasets (protein-coding genes and amino acids) and two methods (Bayesian approach and maximum likelihood). The phylogenetic relationships found in this study highly support that the groups of Aphodiinae, Cetoniinae, Dynastinae, Rutelinae and Scarabaeinae are monophyletic. Interestingly, the phylogenetic clustering relationship was highly consistent with the Scarabaeidae diet, indicating that the herbivorous species and dung-eating species are clustered separately. The phylogenetic tree showed that the subfamily Melolonthinae and the genus Anomala are not monophyletic, suggesting that these two groups should be further revised with more data.