Complete Mitochondrial Genome Research Articles

Detailed characterization of the complete mitochondrial genome of the oceanic whitetip shark Carcharhinus longimanus (Poey, 1861)

BackgroundThe oceanic whitetip shark Carcharhinus longimanus (family Carcharhinidae) is one of the largest sharks inhabiting all tropical and subtropical oceanic regions. Due to their life history traits and mortality attributed to pelagic longline fishing practices, this species is experiencing substantial population decline. Currently, C. longimanus is considered by the IUCN Red List of Threatened Species as “vulnerable” throughout its range and “critically endangered” in the western north Atlantic. This study sequences and describes the complete mitochondrial genome of C. longimanus in detail.Methods and resultsThe mitochondrial genome of C. longimanus was assembled through next-generation sequencing and then analyzed using specialized bioinformatics tools. The circular, double-stranded AT-rich mitogenome of C. longimanus is 16,704 bp long and contains 22 tRNA genes, 2 rRNA genes, 13 protein coding genes and a 1,065 bp long control region (CR). Out of the 22 tRNA genes, only one (tRNA-Ser1) lacked a typical ‘cloverleaf’ secondary structure. The prevalence of TTA (Leu), ATT (Ile) and CTA (Leu) codons in the PCGs likely contributes to the AT-rich nature of this mitogenome. In the CR, ten microsatellites were detected but no tandem repeats were found. Stem-and-loop secondary structures were common along the entire length of the CR. Ka/Ks values estimated for all PCGs were < 1, indicating that all the PCGs experience purifying selection. A phylomitogenomic analysis based on translated PCGs confirms the sister relationship between C. longimanus and C. obscurus. The analysis did not support the monophyly of the genus Carcharhinus.ConclusionsThe assembled mitochondrial genome of this pelagic shark can provide insight into the phylogenetic relationships in the genus Carcharhinus and aid conservation and management efforts in the Central Pacific Ocean.

Assembly and comparative analysis of the complete mitochondrial genome of Vaccinium carlesii Dunn

Vaccinium L. is an important fruit tree with nutritional, medicinal, and ornamental values. However, the mitochondrial (mt) genome of Vaccinium L. remains largely unexplored. Vaccinium carlesii Dunn is an endemic wild resource in China, which is crucial for blueberry breeding. The V. carlesii mt genomes were sequenced using Illumina and Nanopore, which total length was 636,904 bp with 37 protein coding genes, 20 tRNA genes, and three rRNA genes. We found four pairs of long repeat fragments homologous recombination mediated the generation of substructures in the V. carlesii mt genome. We predicted 383 RNA editing sites, all converting cytosine (C) to uracil (U). According to the phylogenetic analysis, V. carlesii and V. macrocarpon of the Ericaceae exhibited the closest genetic relationship. This study provides a theoretical basis for understanding the evolution of higher plants, species classification and identification, and will also be useful for further utilization of Vaccinium germplasm resources.

Comparative mitochondrial genome analysis provides new insights into the classification of Modiolinae.

Mitochondrial genomes have become a powerful tool for studying molecular genetics and phylogeny of mollusks. Currently, the position of Modiolinae within Mytilidae and the taxonomic and phylogenetic relationships within Modiolinae were still controversial. This study focuses on the complete mitochondrial genomes of two species: Modiolus modulaides (Röding, 1798) and Modiolus auriculatus Krauss, 1848, which have not been sequenced before. We assembled and characterized the mitochondrial genomes of M. modulaides and M. auriculatus and then analyzed the phylogenetic relationships. The mitochondrial genomes of M. modulaides and M. auriculatus were 15,422bp and 16,027bp, respectively. Both of them were composed of 36 functional genes, including 12 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. All protein-coding genes showed A + T bias, positive GC skews, and negative AT skews in nucleotide composition. Phylogenetic analysis based on the mitochondrial genomes showed that Modiolinae and Bathymodiolinae clustered together to form a sister relationship. Seven Modiolinae species were divided into two clades: L1 (M. modulaides, M. auriculatus and Modiolus philippinarum Hanley, 1843) and L2 [Modiolus modiolus (Linnaeus, 1758), Modiolus kurilensis Bernard, 1983, Modiolus nipponicus (Oyama, 1950), and Modiolus comptus (Sowerby III, 1915)]. The divergence time of the two clades was approximately 105.75Ma. Furthermore, the transfer RNA gene rearrangement, longer genetic distance, and greater genetic differentiation were confirmed between the L1 and L2 clades, as well as differences in the external characteristics of the shells of the two clades. Based on the molecular data, it was speculated that species from the L1 clade might belong to other genera or new genera. This study provides molecular information for further taxonomic and phylogenetic studies of Mytilidae.

The first complete mitochondrial genome of the genus Laelaps with novel gene arrangement reveals extensive rearrangement and phylogenetics in the superfamily Dermanyssoidea.

We collected 56 specimens ofLaelaps chini from the endemic Hengduan Mountain rat species (Eothenomys miletus) and obtained the first complete mitochondrial genome of L. chini by next-generation sequencing (NGS). The L. chini mitogenome is 16,507bp in size and contains 37 genes and a control region of 2380bp in length. The L. chini mitogenome has a high AT content and a compact arrangement with four overlapping regions ranging from 1 to 2bp and 16 spacer regions ranging from 1 to 48bp. We analyzed 13 protein-coding genes of L. chini mitogenome andfound that protein-coding genes in the L. chini mitogenome preferred codons ending in A/U and codon usage pattern was mainly influenced by natural selection. Cox1 has the slowest evolution rate and cox3 has the fastest evolution rate. We combined the mitochondrial genome of eight species ofgamasid mites in the superfamily Dermanyssoidea from Genbank and theL. chini mitochondrial genometo analyze its rearrangement patterns and breakpoint numbers. We found that the L. chini mitogenome showed a novel arrangement pattern and nine species ofgamasid mites in the superfamily Dermanyssoidea, which have been sequenced complete mitochondrial genomes to date, all showed different degrees of rearrangement. Laelaps chini, Echinolaelaps echidninus and Echinolaelaps fukinenensis were closely related species based on genetic distance and phylogenetic analyses. Notably they are clustered with Varroa destructor of the family Varroidae, suggesting that the family Varroidae is more closely related to the family Laelapidae, but more data are needed to test whether Varroa can be classified under the family Laelapidae. The L. chini mitogenome is the first complete mitochondrial genome for the genus Laelaps, and contributes to further exploration of the mitochondrial gene rearrangements and phylogeny for the superfamily Dermanyssoidea.

DNA barcodes are ineffective for species identification of Acropora corals from the aquarium trade.

Species identification of stony corals (Scleractinia), which are regulated under the Convention on International Trade in Endangered Species of Wild Fauna and Flora, is critical for effective control of harvest quotas, enforcement of trade regulations and species conservation in general. DNA barcoding has the potential to enhance species identification success, depending on the specific taxon concerned and genetic markers used. For Acropora, DNA barcoding, based on the mitochondrial putative control region (mtCR) and the nuclear PaxC intron (PaxC), has been commonly used for species identification and delimitation, but the reliability and robustness of these loci remain contentious. Therefore, we sought to verify the applicability of this approach. In this study, we obtained 127 Acropora colonies from the aquarium trade to test the effectiveness of barcoding mtCR and PaxC for species identification. We were able to recover sequences for both loci in over half of the samples (n = 68), while gene amplification and sequencing of mtCR (n = 125) outperformed PaxC (n = 70). Amongst the 68 samples with both loci recovered, just a single sample could be unambiguously identified to species. Preliminary identities, based on only one gene, were assigned for 40 and 65 samples with mtCR and PaxC, respectively. Further analyses of 110 complete mitochondrial genomes obtained from GenBank showed that, despite the full length of the sequences, only eight species were delimited, of which only three species were correspondingly monophyletic. Therefore, we conclude that the commonly used DNA barcoding markers for Acropora are ineffective for accurate species assignments due to limited variability in both markers and even across the entire mitochondrial genome. Therefore, we propose that barcoding markers should generally not be the only means for identifying corals.

A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis

BackgroundThe holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis.ResultsThe mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers.ConclusionsThese findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.

Complete Mitochondrial Genomes of the Leptocircini Species Iphiclides podalirius and I. podalirinus (Lepidoptera: Papilionidae)

The complete mitochondrial genomes of two Iphiclides species, namely I. podalirius and I. podalirinus, were sequenced, assembled, and reported in this article. Both genomes comprise 37 genes, with 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The gene orders and alignments agree with the reported mitogenomes of Leptocircini butterflies, while the start codon for the COX1 gene in I. podalirinus is CGA instead of the commonly seen ATN type. Codon preference shows that methionine and tryptophan are the poorest, while arginine, leucine, and serine are the richest. Phylogenetic analysis using Bayesian Inference shows both Iphiclides species are sister to the genus Lamproptera and are basal to all remaining Leptocircini species. The Kimura 2-parameter (K2P) distances of I. podalirinus from I. podalirius exceed 5%, demonstrating its solid species status. The K2P distance between the North African feisthamelii and podalirius exceeds 2%, indicating the reasonable elevation of I. feisthamelii to the full specific level as its type locality is Algeria. Future research is required to tackle the relationship between the Iberian feisthamelii and podalirius using more evidence.

Complete Mitochondrial Genomes of the Leptocircini Species Iphiclides podalirius and I. podalirinus (Lepidoptera: Papilionidae)

The complete mitochondrial genomes of two Iphiclides species, namely I. podalirius and I. podalirinus, were sequenced, assembled, and reported in this article. Both genomes comprise 37 genes, with 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The gene orders and alignments agree with the reported mitogenomes of Leptocircini butterflies, while the start codon for the COX1 gene in I. podalirinus is CGA instead of the commonly seen ATN type. Codon preference shows that methionine and tryptophan are the poorest, while arginine, leucine, and serine are the richest. Phylogenetic analysis using Bayesian Inference shows both Iphiclides species are sister to the genus Lamproptera and are basal to all remaining Leptocircini species. The Kimura 2-parameter (K2P) distances of I. podalirinus from I. podalirius exceed 5%, demonstrating its solid species status. The K2P distance between the North African feisthamelii and podalirius exceeds 2%, indicating the reasonable elevation of I. feisthamelii to the full specific level as its type locality is Algeria. Future research is required to tackle the relationship between the Iberian feisthamelii and podalirius using more evidence.

Molecular phylogenetic position and description of a new genus and species of freshwater Chaetonotidae (Gastrotricha: Chaetonotida: Paucitubulatina), and the annotation of its mitochondrial genome.

Chaetonotidae is the most diversified family of the entire phylum Gastrotricha; it comprises ~430 species distributed across 16 genera. The current classification, established mainly on morphological traits, has been challenged in recent years by phylogenetic studies, indicating that the cuticular ornamentations used to discriminate among species may be misleading when used to identify groupings, which has been the practice until now. Therefore, a consensus is developing toward implementing novel approaches to better define species identity and affiliation at a higher taxonomic ranking. Using an integrative morphological and molecular approach, including annotation of the mitogenome, we report on some freshwater gastrotrichs characterised by a mixture of two types of cuticular scales diagnostic of the genera Aspidiophorus and Heterolepidoderma . Our specimens' overall anatomical characteristics find no correspondence in the taxa of these two genera, calling for their affiliation to a new species. Phylogenetic analyses based on the sequence of the ribosomal RNA genes of 96 taxa consistently found the new species unrelated to Aspidiophorus or Heterolepidoderma but allied with Chaetonotus aff. subtilis, as a subset of a larger clade, including mostly planktonic species. Morphological uniqueness and position along the non-monophyletic Chaetonotidae branch advocate erecting a new genus to accommodate the current specimens; consequently, the name Litigonotus ghinii gen. nov., sp. nov. is proposed. The complete mitochondrial genome of the new taxon resulted in a single circular molecule 14,384 bp long, including 13 protein-coding genes, 17 tRNA genes and 2 rRNAs genes, showing a perfect synteny and collinearity with the only other gastrotrich mitogenome available, a possible hint of a high level of conservation in the mitochondria of Chaetonotidae. ZooBank: urn:lsid:zoobank.org:pub:9803F659-306F-4EC3-A73B-8C704069F24A.

Complete mitochondrial genome of Melia azedarach L., reveals two conformations generated by the repeat sequence mediated recombination

Melia azedarach is a species of enormous value of pharmaceutical industries. Although the chloroplast genome of M. azedarach has been explored, the information of mitochondrial genome (Mt genome) remains surprisingly limited. In this study, we used a hybrid assembly strategy of BGI short-reads and Nanopore long-reads to assemble the Mt genome of M. azedarach. The Mt genome of M. azedarach is characterized by two circular chromosomes with 350,142 bp and 290,387 bp in length, respectively, which encodes 35 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes. A pair of direct repeats (R1 and R2) were associated with genome recombination, resulting in two conformations based on the Sanger sequencing and Oxford Nanopore sequencing. Comparative analysis identified 19 homologous fragments between Mt and chloroplast genome, with the longest fragment of 12,142 bp. The phylogenetic analysis based on PCGs were consist with the latest classification of the Angiosperm Phylogeny Group. Notably, a total of 356 potential RNA editing sites were predicted based on 35 PCGs, and the editing events lead to the formation of the stop codon in the rps10 gene and the start codons in the nad4L and atp9 genes, which were verified by PCR amplification and Sanger sequencing. Taken together, the exploration of M. azedarach gap-free Mt genome provides a new insight into the evolution research and complex mitogenome architecture.

Graph-based mitochondrial genomes of three foundation species in the Saccharum genus.

We reported the graph-based mitochondrial genomes of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) for the first time. The results revealed pan-structural variation and evolutionary processes in the mitochondrial genomes within Saccharum. Saccharum belongs to the Andropogoneae, and cultivars species in Saccharum contribute nearly 80% of sugar production in the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes, including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short-repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenomes of three Saccharum species, and a systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitogenomes revealed the differential features of the Saccharum mitogenomes.

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

BackgroundCyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes.ResultsWe assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection.ConclusionWe assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.

First complete mitochondrial genome of Pselliophora (Diptera, Tipulidae): genome description and phylogenetic implications

Pselliophora is widely distributed in Eurasia and China. To explore the characteristics of the mitogenome of Pselliophora and reveal phylogenetic relationships, the mitogenome of Pselliophora bifascipennis Brunetti, 1911 was sequenced and annotated. This is the first complete mitochondrial genome in this genus. Its mitogenome is 15821 bp in length, containing 13 protein-coding genes, 22 tRNA and 2 rRNA genes. Nucleotide compositions of its whole mitogenome are 39.09% for A, 38.49% for T, 13.42% for C, and 9.01% for G. Consistent with previous observations of Tipulidae species, the mitogenome of Pselliophora bifascipennis is highly conserved in gene size, organization and codon usage, and secondary structures of tRNAs. Most tRNAs have the typical clover-leaf structure. The control region is 1006 bp long with an A + T content of 92.7%. Phylogenetic tree analysis using the sequences of the mitochondrial genomes of Pselliophora bifascipennis and other Tipulidae species showed that Pselliophora bifascipennis is closely related to Tanyptera hebeiensis. These two species are grouped on the same branch, which is in accordance with the traditional morphological classification. The results of this study lay a foundation for screening molecular markers of mitochondrion for molecular identification and genetic structure research in Tipulidae species.

The complete mitochondrial genome and phylogenetic analysis of Pealius mori (Hemiptera: Aleyrodidae)

The complete mitochondrial genome of Pealius mori (Hemiptera: Aleyrodidae) was determined in this study. The mitogenome was 15,654 bp long with 37 typical Insecta mitochondrial genes and one non-coding control region. Its gene content and order were different to other Hemiptera mitochondrial genomes. The overall nucleotide composition of the mitogenome was 42.62% A, 32.73% T, 11.12% G and 13.54% C, with an A + T bias of 75.34%. Phylogenetic analyses of 14 species in Aleyrodidae, 2 species in Lepidoptera and 1 species in Thysanoptera by Maximum Likelihood showed that P. mori China had been more closely related to P. mori France, closely related to Pealius machili. This result well supported the taxonomic position of Aleyrodidae and their close relationship with the Pealius category.

Complete mitochondrial genome and phylogenetic analysis of Cirriformia tentaculata (Annelida, Polychaeta, Cirratulidae) from Weihai, Shandong, China

Cirriformia species usually inhabit intertidal zones and deep-sea sediments. Their accurate identification has proven to be challenging. Here, we present the complete mitochondrial genome of one Cirriformia tentaculata_Montagu 1808 specimen collected from China. The total length of the complete mitochondrial sequence of C. tentaculata is 15,516 bp and consists of 13 protein-coding genes (PCGs), 23 tRNA genes, two rRNA genes, and an A + T rich region (64.20%). All PCGs begin with the typical ATN start codon, except for cox1, which uses TTG. TAA or TAG serve as termination codons for twelve PCGs, while nad5 terminates with an incomplete codon, T. The phylogenetic tree revealed a close relationship between C. tentaculata in this study, and Cirriformia cf. tentaculata and Timarete posteria from Korea. The information will assist in the future identification and understanding of this species and offers a novel point of reference for identifying Cirriformia species, and phylogenetic studies.

Characterization of two complete mitochondrial genomes of Aromia bungii Faldermann, 1835 (Coleoptera: Chrysomeloidea: Cerambycidae)

The red-necked longhorn beetle Aromia bungii (Coleoptera: Chrysomeloidea: Cerambycidae) is a wood-boring pest of Prunus spp. We analyzed two complete mitochondrial genomes of A. bungii collected in South Korea. The complete mitochondrial genomes were 15,759 bp and 15,760 bp long, including a typical set of genes (13 protein-coding, 22 transfer RNA, and two ribosomal RNA genes) and one non-coding region. Phylogenetic analysis revealed that the two mitochondrial genomes of A. bungie clustered with previously reported three mitochondrial genomes from China in one clade and was a sister group to Closteromerus belonging to the tribe Callichromatini.

Four-toed sengi (Petrodromus tetradactylus, Afrotheria, Mammalia) museomics reveals a crucial role of East African forests in macroscelidean diversification

Abstract Sengis (Macroscelidea) are members of the Afroinsectivora, a group of mammals belonging to the supercohort Afrotheria. Sengis’ low population densities and their distribution, which includes politically unstable regions with ongoing armed conflicts, hinder contemporary sampling of comprehensive datasets. We overcome this obstacle for the species Petrodromus tetradactylus, one of the most widely distributed sengi species, by utilizing 44 historical museum samples from multiple natural history museums. These historical samples were combined with newly generated or published data of 11 modern samples, thus creating a dataset of 55 P. tetradactylus individuals covering most of the species’ distribution. Phylogenetic reconstruction with 11 nuclear loci in conjunction with mostly complete mitochondrial genomes reveals multiple deeply divergent and formerly unknown lineages within this monotypic genus, highlighting the need for a taxonomic revision. Furthermore, we can show that the assumed allopatric distribution of P. tetradactylus in Central Africa most likely represents a sampling artifact. Biogeographic character mapping indicates that the African forest system and its dynamics through climate fluctuations shaped the evolutionary and biogeographic history of this taxon. We show that lineages within Petrodromus that were able to adapt to dryer woodland ecosystems are much more widely distributed than lineages restricted to moist forest systems. The evolution and radiation of the four-toed sengi (P. tetradactylus) mirrors the patterns of its distant relative, the giant sengis (Rhynchocyon) in both ecotype variation and overall distribution, implying a significant influence of climate and landscape features in shaping diversification.

Exploring the mitogenomes of Batracomorphus (Hemiptera: Cicadellidae: Iassinae): new insights from structural diversity and phylogenomic analyses

Abstract Comparisons of mitogenomes are widely used for species identification and to explore the phylogenetic relationship among insect taxa. Batracomorphus is the third most diverse and widely distributed genus in the Cicadellidae (Hemiptera). However, there have been no analyses of genome structure and phylogenetic relationships within the genus. To compensate for the paucity of genomic information in this genus, we sequenced novel complete mitochondrial genomes of 11 Batracomorphus species and combined these with 23 previously sequenced mitochondrial genomes to perform structural comparisons and phylogenomic studies. Our results reveal generally conserved mitogenome organization, with one case of tRNA gene rearrangement, with trnI-trnQ reversed to trnQ-trnI when compared with the ancestral arrangement. Analysis of the ratio of nonsynonymous (Ka) to synonymous substitutions (Ks) showed ATP8 is the fastest and COI is the slowest evolving gene. ND2 and ND6 have highly variable nucleotide diversity, whereas COI and ND1 exhibit the lowest diversity. Phylogenetic analysis of nucleotide sequences grouped Batracomorphus species into a clade within the subfamily Iassinae. Within Batracomorphus, 3 clades were reconstructed consistent with the observed gene rearrangement, indicating that such rearrangements can serve as reliable molecular markers supporting phylogenetic hypotheses. These clades also correspond to clusters of species recovered by morphometric analysis of aedeagal shape, suggesting that characters of the male genitalia traditionally used for species delimitation are phylogenetically informative. Molecular divergence time estimates indicate that most speciation events within Batracomorphus occurred between the Paleogene and Neogene. This study provides insight into the population genetics, molecular biology, phylogeny, and morphological evolution of the leafhopper subfamily Iassinae and its largest genus, Batracomorphus.

Assemble and comparative analysis of the mitochondrial genome of Rhododendron delavayi: Insights into phylogenetic relationships and genomic variations

Rhododendron delavayi, a notable ornamental plant primarily found in regions of China like Yunnan and Guizhou provinces, holds substantial horticultural value. To elucidate the systematic phylogenetic relationships and organelle genomic differences within R. delavayi and related Rhododendron species, we conducted sequencing and assembly of the complete mitochondrial genome of R. delavayi. The full-length mitochondrial genome of it was a singular circular molecule spanning 1,009,263 bp, comprising 53 protein-coding genes, including 18 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 32 protein-coding genes. A total of 1,182 simple sequence repeats (SSRs) loci were identified in the R. delavayi mitochondrial genome, primarily consisting of single nucleotide, dinucleotide, and trinucleotide repeats. Nucleotide diversity analysis highlighted five genes (atp6, atp9, cox2, nad1, and rpl10) with the highest diversity within the mitochondrial genomes of Rhododendron genus. Comparative analysis of the mitochondrial genome of R. delavayi with those of four other Rhododendron species indicated complex rearrangements in 21 genes, including rps4, nad6, rps3, atp6, cob, atp9, nad7, among others. The mitochondrial phylogenetic tree revealed a close relationship between R. delavayi and R. decorum, forming a sister clade to R. × pulchrum and R. simsii. Furthermore, 126 plastid-to-mitochondrial gene transfers in R. delavayi were identified, ranging from 30 bp to 19,385 bp. These fragments collectively constituted 47.54 % and 9.52 % of the chloroplast and mitochondrial genomes (202,169 bp), respectively. Complex mitochondrial-to-mitochondrial transfers were also observed, with 843 identified fragments totaling 312,036 bp (30.92 % of the mitochondrial genome). Segments exceeding 10 kb may mediate homologous recombination within the mitochondrial molecules. Remarkably, our study underscores that the mitochondrial genome of R. delavayi was the largest reported within the Rhododendron genus to date. The intricate rearrangements observed in the mitochondrial genomes of Rhododendron species, alone with the identification of five potential molecular marker sites, provided valuable insights for species classification and parentage identification within the Rhododendron genus.

Characterization of the organellar genomes of Mazzaella laminarioides and Mazzaella membranacea (Gigartinaceae, Rhodophyta)

AbstractMazzaella, a genus with no genomic resources available, has extensive distribution in the cold waters of the Pacific, where they represent ecologically and economically important species. In this study, we aimed to sequence, assemble, and annotate the complete mitochondrial and chloroplast genomes from two Mazzaella spp. and characterize the intraspecific variation among them. We report for the first time seven whole organellar genomes (mitochondria: OR915856, OR947465, OR947466, OR947467, OR947468, OR947469, OR947470; chloroplast: OR881974, OR909680, OR909681, OR909682, OR909683, OR909684, OR909685) obtained through high‐throughput sequencing for six M. laminarioides sampled from three Chilean regions and one M. membranacea. Sequenced Mazzaella mitogenomes have identical gene number, gene order, and genome structure. The same results were observed for assembled plastomes. A total of 52 genes were identified in mitogenomes, and a total of 235 genes were identified in plastomes. Although the M. membranacea plastome included a full‐length pbsA gene, in all M. laminarioides samples, the pbsA gene was split in three open reading frames (ORFs). Within M. laminarioides, we observed important plastome lineage‐specific variations, such as the pseudogenization of the two hypothetical protein‐coding genes, ycf23 and ycf45. Nonsense mutations in the ycf23 and ycf45 genes were only detected in the northern lineage. These results are consistent with phylogenetic reconstructions and divergence time estimation using concatenated coding sequences that not only support the monophyly of M. laminarioides but also underscore that the three M. laminarioides lineages are in an advanced stage of divergence. These new results open the question of the existence of still undisclosed species in M. laminarioides.