NOVOPlasty: de novo assembly of organelle genomes from whole genome data

The complete mitochondrial genome of Vaccinium oldhamii Miquel, a plant of the Ericaceae family

Vaccinium oldhamii Miquel 1866 is a deciduous shrub native to Northeast Asia, including Korea, China, and Japan. Its polyphenol-rich edible berries may aid in managing chronic diseases. Despite its importance, the mitogenome of this species remains understudied. This study assembled the complete mitogenome, consisting of 626,941 bp with 45.34% GC content, using NOVOPlasty and Illumina sequencing. The genome includes 38 protein-coding genes, 24 tRNA genes, and three rRNA genes. Phylogenetic analysis revealed a close relationship with V. macrocarpon. This mitogenome provides a valuable resource for phylogenomic studies and insights into evolutionary relationships within the Vaccinium genus and the Ericales order. Vaccinium oldhamii Miquel 1866 is a deciduous shrub in the Ericales and the Ericaceae and is native to Northeast Asia including Korea, China, and Japan. Particular emphasis has been placed on the edible berries of Vaccinium species and their use as dietary supplements. Specifically, the edible berries of V. oldhamii contain high levels of polyphenols, which may aid in preventing and managing chronic diseases. However, the mitogenome sequence of this species, a valuable resource for studying evolutionary relationships and genetic diversity within the Vaccinium genus, has not been thoroughly investigated. In this study, the complete mitochondrial genome sequence of V. oldhamii was assembled into 626,941 bp circular nucleotides with a GC content of 45.34% using NOVOPlasty and Illumina sequencing data. The comprehensive annotation for mitogenome of V. oldhamii revealed that the mitogenome comprises 38 known protein-coding genes, 24 tRNA genes, and three rRNA genes. Phylogenetic analysis using ML method showed that this species is closely related to the V. macrocarpon. This newly sequenced mitochondrial genome offers a valuable resource for phylogenomic analysis and will enhance our understanding of evolutionary relationships within the Ericales order and/or the Vaccinium genus.

The complete chloroplast genome of Illicium verum and comparative analysis with related species from Magnoliaceae and Illiciaceae

Illicium verum (Illiciaceae), an ecologically significant endemic plant, predominantly grows in Guangxi, China, which is the primary region for its cultivation. This area accounts for more than 80% of the total cultivation and yield in China. Despite its importance, comprehensive studies on the chloroplast (cp) genome of I. verum are limited. In our research, we sequenced and analyzed the complete cp genome of I. verum and conducted a comparative analysis with nine related species from the families Magnoliaceae, Schisandraceae, and Illiciaceae. The cp genome of I. verum spans 143,187 base pairs (bp), comprising a large single copy (LSC) region of 100,868 bp, a small single copy (SSC) region of 20,235 bp, and two inverted repeats (IR) regions, each 11,042 bp in length. We identified 81 simple sequence repeats (SSRs) within this genome. The chloroplast genome contains 78 protein-coding genes, 8 ribosomal RNA (rRNA) genes, and 35 transfer RNA (tRNA) genes. Structurally, the IR regions exhibit greater similarity across different genera of Magnoliaceae and Illiciaceae compared to the LSC and SSC regions. Phylogenetic analysis revealed high homology between the cp genome of I. verum and those of Illicium burmanicum, Illicium simonsii, and Illicium anisatum. These findings suggest that the cp genome of I. verum may serve as a valuable genomic resource for elucidating the phylogenetic positions and relationships within the Illiciaceae family. This information will be instrumental for future taxonomic research on Illicium species and for advancing genomic studies of these plants.

The mitogenomes of two species of sea pigs, Scotoplanes clarki and Protelpidia murrayi (Elasipodida: Holothuroidea: Echinodermata)

Mitochondrial genomes of Scotoplanes clarki and Protelpidia murrayi are presented, each with 13 protein coding genes, two rRNA genes, and 22 tRNA genes. That of Scotoplanes clarki has 15,909 base pairs and that of Protelpidia murrayi is 15,896 base pairs. There is a suspected tandem repeat region of undetermined length in the assemblies of both Scotoplanes clarki and Protelpidia murrayi. The gene order of both mitogenomes is identical to that of other Elasipodida. Phylogenetic analysis revealed that Protelpidia murrayi lies within the Scotoplanes clade, suggesting that Scotoplanes is paraphyletic. Sequencing of the type species, Scotoplanes globosa, is needed to confirm if Protelpidia murrayi should be renamed as Scotoplanes murrayi.

The first complete mitochondrial genome of Phellinus pomaceus var. prunastri (Pers.) Pat. 1926 (Hymenochaetales: Hymenochaetaceae) and phylogenetic analysis

Phellinus pomaceus var. prunastri (Pers.) Pat. 1926 is a famous medicinal fungus that has attracted considerable interest in biotechnology because of its diverse biologically active ingredients. Here, we provide the full mitochondrial genome sequence of P. pomaceus, which spans 122,850 bp and has a GC content of 26.04%. The genome comprises 15 essential protein-coding genes, 26 distinct ORFs, 24 intronic ORFs, 25 tRNAs, and 2 rRNA genes. Bayesian inference (BI) was employed for phylogenetic analysis, revealing the evolutionary relationships among 17 Basidiomycota fungi. The results strongly supported distinct clades and indicated that P. pomaceus is closely related to Fomitiporia mediterranea.

The complete mitochondrial genome of Proedromys bedfordi Thomas 1911 (Arvicolinae, Rodentia)

The Duke of Bedford's vole (Proedromys bedfordi Thomas 1911) is distributed only at the border areas of the Sichuan and Gansu Provinces, China. In this study, the first complete mitochondrial genome of P. bedfordi is generated and characterized. The assembled genome is 16,262 base pairs in length and the base compositions present clearly the A-T bias (60.84%). Its genetic constitution and arrangement are consistent with the taxon of the voles, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 main non-coding regions, D-loop region and OL region. This mitochondrial genome will be a significant supplement for the genus Proedromys and whole mitogenome phylogenetic analysis provided insights into further evolutionary research of the subfamily Arvicolinae.

Comparative Genomics Provides Insights into Adaptive Evolution and Demographics of Bats

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

Intracellular gene transfer (IGT) events from the mitochondrial genome to the plastid genome of the subtribe ferulinae drude (Apiaceae) and their implications

BACKGROUND

Intracellular gene transfer (IGT) is a phenomenon in genome evolution that occurs between the nuclear and organellar genomes of plants or between the genomes of different organelles. The majority of the plastid genomes (plastomes) in angiosperms have a conserved structure, but some species exhibit unexpected structural variations.

RESULTS

In this study, we focused on the Ferulinae, which includes Ferula, one of the largest genera in the Apiaceae family. We discovered IGTs in the rps12-trnV IGS region of the plastome's inverted repeat (IR). We found that partial mitochondrial genome (mitogenome) sequences, ranging in length from about 2.8 to 5.8 kb, were imported into the plastome. In addition to these, that are known from other Scandiceae subtribes, the Ferulinae plastomes contained two unique mitogenome sequences. We have named these sequences Ferula Mitochondrial Plastid sequences (FeMP). FeMP1 varies in length from 336 bp to 1,100 bp, while FeMP2 ranges from 50 bp to 740 bp in length, with the exception of F. conocaula and F. kingdon-wardii, which do not possess FeMP2. Notably, FeMP2 includes a complete rps7 gene of mitogenome origin. In the maximum likelihood (ML) tree constructed from 79 protein-coding genes, Ferulinae appears as a monophyletic group, while Ferula shows paraphyly. Dorema and Fergania are nested within the Ferula clade, sharing the unusual characteristics of the Ferula plastome. Based on these findings, a reclassification of Dorema and Fergania is warranted.

CONCLUSIONS

Our results shed light on the mechanism of plastome evolution in the Scandiceae with a focus on the unique plastome structure found in the Apiaceae. These findings enhance our understanding of the evolution of plant organellar genomes.

Mitogenomics Provide New Phylogenetic Insights of the Family Apataniidae (Trichoptera: Integripalpia)

The family Apataniidae consists of two subfamilies, Apataniinae and Moropsychinae. Currently, there are 204 valid species of Apataniidae, which are widely distributed throughout the northern hemisphere. The larvae typically inhabit cold-water environments, and they serve as biological indicators for monitoring the health of freshwater ecosystems. The phylogenetic relationships within Apataniidae are not fully understood. Moreover, the available molecular data of Apataniidae are still limited. Herein, we provided the mitochondrial genomes of eight apataniid species and compared them with the published mitochondrial genomes of Apataniidae. The nine newly obtained sequences ranged from 15,070 bp to 16,737 bp in length. The results of the nonsynonymous with synonymous substitution rates displayed that ATP8 had the highest evolutionary rate, while COXI exhibited the lowest. The ND4L may be an effective molecular marker for the classification of the Apataniidae. Based on the published mitogenomes, we constructed a phylogenetic tree for Limnephiloidea and conducted a preliminary analysis of its advanced phylogeny. The ML and BI analyses recover the monophyly of Apataniidae and Limnephilidae. Except for PCG, BI tree based on other matrices consistently showed the topology: (Apataniana + (Moropsyche + (Apatidelia + Apatania))). The taxonomic status of Apatania and Apatidelia were also preliminarily explored. The mitochondrial genome of Apataniidae provides critical genomic resources for understanding the phylogenetic relationships of Apataniidae.

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

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

Repeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations

Parastagonospora nodorum is necrotrophic fungal pathogen of wheat with significant genomic resources. Population-level pangenome data for 173 isolates, of which 156 were from Western Australia (WA) and 17 were international, were examined for overall genomic diversity and effector gene content. A heterothallic core population occurred across all regions of WA, with asexually-reproducing clonal clusters in dryer northern regions. High potential for SNP diversity in the form of repeat-induced point mutation (RIP)-like transitions, was observed across the genome, suggesting widespread 'RIP-leakage' from transposon-rich repetitive sequences into non-repetitive regions. The strong potential for RIP-like mutations was balanced by negative selection against non-synonymous SNPs, that was observed within protein-coding regions. Protein isoform profiles of known effector loci (SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5) indicated low-levels of non-synonymous and high-levels of silent RIP-like mutations. Effector predictions identified 186 candidate secreted predicted effector proteins (CSEPs), 69 of which had functional annotations and included confirmed effectors. Pangenome-based effector isoform profiles across WA were distinct from global isolates and were conserved relative to population structure, and may enable new approaches for monitoring crop disease pathotypes.

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

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

Comparative chloroplast genomes analysis of nine Primulina (Gesneriaceae) rare species, from karst region of southwest China

Guizhou Province is one of the most important karst regions of southwest China, with 22 Primulina species. These species are highly habitat-specialized and dependent on the soils of the karst region, and many inter-species classifications are unclear. Therefore, studying the chloroplast genomes and estimating the divergence times of there species can not only provide a better understanding of interspecific relationships but also help to know the species speciation and divergence in the karst environment. So, we sequenced and assembled the chloroplast genomes of nine Primulina species (including six endemic species of Guizhou) and conducted chloroplast genome comparison analysis and phylogenetic study. The chloroplast genome structures of the nine Primulina species were quadripartite with total lengths of 152,869-153,364 base pairs (bp) and GC content of 37.55-37.64%. There are 132 functional genes annotated, respectively. A total of 375 simple sequence repeats and 375 interspersed nuclear elements were identified. The 30 highly preferred codons identified were used at similar frequencies in different species, respectively. A phylogenetic tree constructed on the basis of the 38 chloroplast genomes showed that Primulina species form a monophyletic group. Eleven mutational hotspot regions that could serve as potential molecular markers were identified, of which two regions near the 3' and 5' ends of the ycf1 gene were of appropriate size and can serve as molecular markers for phylogenetic studies of Primulina. The results of molecular clock analyses indicate that the three major branches of Primulina begin to diverge in the Miocene, and the number of species proliferated in the Pliocene and Pleistocene. Most of the species of Primulina in Guizhou Province were formed in the Pleistocene and rapidly diverged within a short period of time. This research study enriches the genetic resource information of Primulina and deepens the understanding of the phylogenetic relationships of the genus.

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

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

The complete chloroplast genome of Syzygium zeylanicum (Myrtaceae, Myrtales) and its phylogenetic analysis

The complete chloroplast genome of Syzygium zeylanicum (L.) DC. 1828 has been sequenced and analyzed for the first time. The S. zeylanicum chloroplast genome is 159,445 bp in length, comprised of a large single-copy region (88,034 bp), a small single-copy region (18,455 bp), and a pair of inverted repeat regions (26,478 bp each). The genome encoded 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that S. zeylanicum is closely related to S. acuminatissimum. This research provides essential genomic data for S. zeylanicum, offering valuable resources for future comparative genomics, phylogenetics, and conservation biology studies.

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.

The complete mitogenome dataset of the heptageniid mayfly Afronurus levis (Ephemeroptera: Heptageniidae: Ecdyonurinae) from South Korea

The Heptageniidae family stands out as one of the most abundant and widespread among mayflies, distinguished by its unique mitochondrial characteristics in intergenic spacers and duplication of transfer RNA (tRNA) genes. In this dataset, we present the complete mitochondrial genome sequence of Afronurus levis (Navás, 1912), a member of the Heptageniidae family of mayflies. The total length of the A. levis mitogenome was determined to be 15,362 base pairs, encompassing 13 protein-coding genes (PCGs), 23 tRNA genes, and two ribosomal RNA genes. An additional trnM gene was detected in the A. levis genome, consistent with observations in other Heptageniid species. The base composition of the A. levis mitogenome was determined to be 31.7 % A, 32.7 % T, 14.1% G, and 21.5 % C. Phylogenetic analysis using PCGs confirmed that the newly sequenced A. levis mitogenome clusters within the genus Afronurus, showing closer proximity to that of A. drepanophyllus.

Reduced Representation and Whole-Genome Sequencing Approaches Highlight Beluga Whale Populations Associated to Eastern Canada Summer Aggregations

Effective conservation strategies inherently depend on preserving populations, which in turn requires accurate tools for their detection. Beluga whales (Delphinapterus leucas) inhabit the circumpolar Arctic and form discrete summer aggregations. Previous genetic studies using mitochondrial and microsatellite loci have delineated distinct populations associated to summer aggregations but the extent of dispersal and interbreeding among these populations remains largely unknown. Such information is essential for the conservation of populations in Canada as some are endangered and harvested for subsistence by Inuit communities. Here, we used reduced representation and whole-genome sequencing approaches to characterize population structure of beluga whales in eastern Canada and examine admixture between populations. A total of 905 beluga whales sampled between 1989 and 2021 were genotyped. Six main genomic clusters, with potential subclusters, were identified using multiple proxies for population structure. Most of the six main genomic clusters were consistent with previously identified populations, except in southeast Hudson Bay where two clusters were identified. Beluga summer aggregations may consequently be comprised of more than one distinct population. A low number of dispersers were identified between summer aggregations and limited interbreeding was detected between the six genomic clusters. Our work highlights the value of genomic approaches to improve our understanding of population structure and reproductive behavior in beluga whales, offering insights applicable to other cetacean species of conservation concern. An expansion of the geographical scope and increase in number of genotyped individuals will, however, be needed to improve the characterization of the finer scale structure and of the extent of admixture between populations.

Characterisation of the complete chloroplast genome of Solanum tuberosum cv. White Lady

Potato (Solanum tuberosum) is considered worldwide as one of the most important non-cereal food crops. As a result of its adaptability and worldwide production area, potato displays a vast phenotypical variability as well as genomic diversity. Chloroplast genomes have long been a core issue in plant molecular evolution and phylogenetic studies, and have an important role in revealing photosynthetic mechanisms, metabolic regulations and the adaptive evolution of plants. We sequenced the complete chloroplast genome of the Hungarian cultivar White Lady, which is 155 549 base pairs (bp) in length and is characterised by the typical quadripartite structure composed of a large- and small single-copy region (85 991 bp and 18 374 bp, respectively) interspersed by two identical inverted repeats (25 592 bp). The genome consists of 127 genes of which 82 are protein-coding, eight are ribosomal RNAs and 37 are transfer RNAs. The overall gene content and distribution of the genes on the White Lady chloroplast was the same as found in other potato chloroplasts. The alignment of S. tuberosum chloroplast genome sequences resulted in a highly resolved tree, with 10 out of the 13 nodes recovered having bootstrap values over 90%. By comparing the White Lady chloroplast genome with available S. tuberosum sequences we found that gene content and synteny are highly conserved. The new chloroplast sequence can support further studies of genetic diversity, resource conservation, evolution and applied agricultural research. The new sequence can support further potato genetic diversity and evolutionary studies, resource conservation, and also applied agricultural research.

Phylogenomics and adaptive evolution of hydrophytic umbellifers (tribe Oenantheae, Apioideae) revealed from chloroplast genomes

BACKGROUND

Tribe Oenantheae consists mainly of aquatic species within the Apioideae. The unique morphology and habitat distinguish this group from other Apioideae groups. However, the genomic information of these group species has not been widely developed, and the molecular mechanisms of adaptive evolution remain unclear.

RESULTS

We provide comparative analyses on 30 chloroplast genomes of this tribe representing five genera to explore the molecular variation response to plant adaptations. The Oenantheae chloroplast genomes presented typical quadripartite structures, with sizes ranging from 153,024 bp to 155,006 bp. Gene content and order were highly conserved with no significant expansion or contraction observed. Seven regions (rps16 intron-trnK, rpoB-trnC, trnE-trnT-psbD, petA-psbJ, ndhF-rpl32-trnL, ycf1a-rps15, and ycf1a gene) were identified as remarkable candidate DNA markers for future studies on species identification, biogeography, and phylogeny of tribe Oenantheae. Our study elucidated the relationships among the genera of tribe Oenantheae and subdivided the genera of Sium and Oenanthe. However, relationships among the Oenanthe I clade remain to be further clarified. Eight positively selected genes (accD, rbcL, rps8, ycf1a, ycf1b, ycf2, ndhF, and ndhK) were persuasively detected under site models tests, and these genes might have played roles in Oenantheae species adaptation to the aquatic environments.

CONCLUSIONS

Our results provide sufficient molecular markers for the subsequent molecular studies of the tribe Oenantheae, and promote the understanding of the adaptation of the Oenantheae species to aquatic environments.

New Mitochondrial Genomes of Ithonidae (Neuroptera) and Higher Phylogenetic Implications

Ithonidae (moth lacewings) are an enigmatic, small family of the insect order Neuroptera (lacewings). Its phylogenetic position within Neuroptera and internal subfamily relationships remain unresolved. In this study, the complete mitochondrial genome (mitogenome) of Ithone fulva Tillyard, 1916 representing the first mitogenome of Ithoninae, as well as the complete mitogenome of Rapisma gaoligongensis Liu, Li and Yang, 2018, were newly reported. Molecular phylogenetic trees recovered Ithonidae as the sister group to Chrysopidae + Hemerobiidae. Ithoninae was demonstrated to be the sister group to Polystoechotinae + Rapismatinae across all topologies. Divergence time estimation revealed that Ithonidae originated during the Mid-Triassic. Ithoninae diverged from Polystoechotinae and Rapismatinae in the Late Triassic, while Polystoechotinae diverged from Rapismatinae in the Middle Jurassic. Moreover, more comprehensive samplings, as well as whole genome data, are needed to reconstruct a comprehensive framework of the phylogeny of Ithonidae, as well as Neuropteida.

The first complete mitochondrial genome of Loimia arborea (Polychaeta: Terebellidae) and phylogenetic analysis

In order to understand the molecular insights within the Terebellida, the complete mitochondrial genome of Loimia arborea was sequenced. The mitochondrial genome is 16,023 bp, with 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding region (D-loop). Notably, two adjacent copies of methionine tRNA genes (trnMs) were detected. The phylogeny of Terebellida was constructed based on 13 PCGs from 13 species, two main clades were strongly supported, i.e., Cirratuliformia (clade A) and Terebelliformia (clade B). And the monophyly of the Terebellidae was restored.

A comprehensive study on the mitochondrial genome of Volva habei and exploring phylogenetic relationships in Littorinimorpha

In order to enrich our taxonomic and systematic comprehension of Ovulidae within the evolutionary framework of Littorinimorpha. we present a comprehensive analysis of the mitochondrial genome (mitogenome) sequence of Volva habei using next-generation sequencing technology (GenBank accession number OR492307). The mitogenome spans a total length of 16,519 bp, encompassing a complete set of 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs and two rRNAs, demonstrating a distinct AT bias. Notably, trnS2 lacks a dihydrouracil (DHU) arm, thus preventing the formation of a typical secondary structure. In contrast, the remaining tRNAs exhibit a characteristic cloverleaf-like secondary structure. Comparative analysis with ancestral gastropods reveals substantial differences in three gene clusters (or genes), incorporating fifteen tRNAs and eight PCGs. Of particular significance are the observed inversions and translocations, representing the predominant types of rearrangements in V. habei. Phylogenetic analysis strongly supports the monophyletic grouping of all Littorinimorpha species, with V. habei forming a distinct Ovulidae clade. It is noteworthy that V. habei forms a sister group with Cypraeidae, collectively belonging to the Cypraeoidea. In summary, this study not only advances our comprehension of the entire mitochondrial dataset for Calyptraeoidea but also provides novel insights into the phylogenetic relationships within Littorinimorpha.

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

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

Comparative analysis of chloroplast genome of Lonicera japonica cv. Damaohua

Lonicera japonica is a well-known medicinal plant, and the Damaohua cultivar is one of the oldest known honeysuckle cultivars in China. The 155,151 bp chloroplast genome of this cultivar was obtained through Illumina sequencing. The genome includes a pair of inverted repeats (IRa and IRb; 23,789 bp each), a large single-copy region (88,924 bp), and a small single-copy (SSC) region (18,649 bp). In total, 127 unique genes were identified: 80 protein-coding, 39 tRNA, and 8 rRNA genes. Only ycf3 contained two introns. Eighty-nine large repetitive sequences and 54 simple sequence repeats were detected. Fifty potential RNA editing sites were predicted. Adaptive evolution analysis revealed that infA, matK, petB, petD, rbcL, rpl16, rpl2, rps3, ycf1, and ycf2 were positively selected, possibly reflecting the specific environmental adaptations of this cultivar. Sequence alignment and analysis revealed several candidate fragments for Lonicera species identification, such as the intergenic regions rpoB-petN, rbcL-accD, and psaA-ycf3. The IR region boundary and phylogenetic analysis revealed that the L. japonica cv. Damaohua chloroplast genome was most closely related to the L. japonica genome, but there were five distinct differences between the two. There are four sites with high variability between L. japonica and L. japonica cv. Damaohua with nucleotide variability (Pi) greater than 0.002, including rps2-rpoC2, atpB-rbcL, ycf1, and ycf1-trnN GUU. The differences between L. japonica and L. japonica cv. Damaohua were further confirmed by the single nucleotide polymorphism sites between these two species. Therefore, this study revealed that the chloroplast genome can serve as a universal super barcode for plant identification, which can identify differences and help distinguish Lonicera japonica from related species. An understanding of Lonicera japonica cv. Damaohua chloroplast genomics and a comparative analysis of Lonicera species will provide a scientific basis for breeding, species identification, systematic evolution analysis, and chloroplast genetic engineering research on medicinal honeysuckle plants.

Rapid speciation in the holopelagic ctenophore Mnemiopsis following glacial recession

Understanding how populations diverge is one of the oldest and most compelling questions in evolutionary biology. An in depth understanding of how this process operates in planktonic marine animals, where barriers for gene flow are seemingly absent, is critical to understanding the past, present, and future of ocean life. Mnemiopsis plays an important ecological role in its native habitat along the Atlantic coast of the Americas and is highly destructive in its non-native habitats in European waters. Although historical literature described three species of Mnemiopsis, the lack of stable morphological characters has led to the collapse of this group into a single species, Mnemiopsis leidyi. We generate high-quality reference genomes and use a whole-genome sequencing approach to reveal that there are two species of Mnemiopsis along its native range and show that historical divergence between the two species coincides with historical glacial melting. We define a hybridization zone between species and highlight that environmental sensing genes likely contribute to the invasive success of Mnemiopsis. Overall, this study provides insights into the fundamental question of how holopelagic species arise without clear barriers to gene flow and sheds light on the genomic mechanisms important for invasion success in a highly invasive species.

Deciphering the complex organelle genomes of two Rhododendron species and insights into adaptive evolution patterns in high-altitude

BACKGROUND

The genomes within organelles are crucial for physiological functions such as respiration and photosynthesis and may also contribute to environmental adaptation. However, the limited availability of genetic resources, particularly mitochondrial genomes, poses significant challenges for in-depth investigations.

RESULTS

Here, we explored various assembly methodologies and successfully reconstructed the complex organelle genomes of two Rhododendron species: Rhododendron nivale subsp. boreale and Rhododendron vialii. The mitogenomes of these species exhibit various conformations, as evidenced by long-reads mapping. Notably, only the mitogenome of R. vialii can be depicted as a singular circular molecule. The plastomes of both species conform to the typical quadripartite structure but exhibit elongated inverted repeat (IR) regions. Compared to the high similarity between plastomes, the mitogenomes display more obvious differences in structure, repeat sequences, and codon usage. Based on the analysis of 58 organelle genomes from angiosperms inhabiting various altitudes, we inferred the genetic adaptations associated with high-altitude environments. Phylogenetic analysis revealed partial inconsistencies between plastome- and mitogenome-derived phylogenies. Additionally, evolutionary lineage was determined to exert a greater influence on codon usage than altitude. Importantly, genes such as atp4, atp9, mttB, and clpP exhibited signs of positive selection in several high-altitude species, suggesting a potential link to alpine adaptation.

CONCLUSIONS

We tested the effectiveness of different organelle assembly methods for dealing with complex genomes, while also providing and validating high-quality organelle genomes of two Rhododendron species. Additionally, we hypothesized potential strategies for high-altitude adaptation of organelles. These findings offer a reference for the assembly of complex organelle genomes, while also providing new insights and valuable resources for understanding their adaptive evolution patterns.

The complete mitochondrial genome of Periphyllus koelreuteriae (Takahashi, 1919) (Hemiptera: Aphididae: Chaitophorinae)

We sequenced the complete mitochondrial genome of the aphid Periphyllus koelreuteriae. It is 16,828 bp long and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosome RNA genes (rRNAs), a control region, and a repeat region. The control region contains a 273-bp repeat motif repeated 2.3 times. The species-specific repeat region between trnE and trnF comprises two 340-bp repeat units. The maximum-likelihood tree based on all 37 mitochondrial genes indicated a close relationship between P. koelreuteriae and Periphyllus diacerivorus. This study provides a valuable mitogenomic resource for future research on Chaitophorinae phylogeny and P. koelreuteriae diversification.

The complete genome sequence of the chloroplast of Bidens aurea

Bidens aurea (Asteraceae), a native of tropical America is now widespread in Asia and the Americas. We explored the B. aurea chloroplast genome and conducted a phylogenetic analysis. The chloroplast genome was circular, consisting of a large single copy (LSC) of 83,909 base pairs (bp), a small single copy (SSC) of 18,407 bp, and two inverted repeat regions (IR) of 24,729 bp each. Phylogenetic analysis showed that the 19 Bidens taxa were divided into five major clades, and B. aurea was most closely related to two species. Our findings offer a high-quality B. aurea chloroplast genome, aiding DNA barcode development and evolutionary history reconstruction.

New mitochondrial genomes of three whip spider species from the Amazon (Arachnida, Amblypygi) with phylogenetic relationships and comparative analysis

The complete mitochondrial genomes of the whip spiders Charinus carajas, C. ferreus, and Heterophrynus longicornis were sequenced, annotated, and compared with other mitogenomes of whip spiders and arachnids. The three new mitogenomes have the 37 genes usually observed in Metazoa: 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs), plus a non-coding control region (CR). Most PCGs presented an ATN start codon, except cox1 in both Charinus species, initiating with TTA. Most PCGs terminated with stop codons TAA or TAG, except nad5 of C. carajas and cox3 of H. longicornis, which presented an incomplete stop codon (T). The Ka/Ks ratios were less than one for all the PCGs, indicating these genes are under purifying selection. All the tRNAs, except for serine 1 (trnS1), had the typical cloverleaf-shaped secondary structure. All the phylogenetic analyses resolved Charinus carajas and C. ferreus as monophyletic groups. Nonetheless, we did not recover the monophyly of Heterophrynus longicornis. The phylogenies under partitioned models did not recover suprageneric taxonomic groups as clades, but the Bayesian inference under the CAT infinite mixture model recovered the family Phrynidae and the superfamily Phrynoidea as monophyletic groups.

Population Genomics of Adaptive Radiations: Exceptionally High Levels of Genetic Diversity and Recombination in an Endemic Spider From the Canary Islands

The spider genus Dysdera has undergone a remarkable diversification in the oceanic archipelago of the Canary Islands, with ~60 endemic species having originated during the 20 million years since the origin of the archipelago. This evolutionary radiation has been accompanied by substantial dietary shifts, often characterised by phenotypic modifications encompassing morphological, metabolic and behavioural changes. Hence, these endemic spiders represent an excellent model for understanding the evolutionary drivers and to pinpoint the genomic determinants underlying adaptive radiations. Recently, we achieved the first chromosome-level genome assembly of one of the endemic species, D. silvatica, providing a high-quality reference sequence for evolutionary genomics studies. Here, we conducted a low coverage-based resequencing study of a natural population of D. silvatica from La Gomera island. Taking advantage of the new high-quality genome, we characterised genome-wide levels of nucleotide polymorphism, divergence and linkage disequilibrium, and inferred the demographic history of this population. We also performed comprehensive genome-wide scans for recent positive selection. Our findings uncovered exceptionally high levels of nucleotide diversity and recombination in this geographically restricted endemic species, indicative of large historical effective population sizes. We also identified several candidate genomic regions that are potentially under positive selection, highlighting relevant biological processes, such as vision and nitrogen extraction as potential adaptation targets. These processes may ultimately drive species diversification in this genus. This pioneering study of spiders that are endemic to an oceanic archipelago lays the groundwork for broader population genomics analyses aimed at understanding the genetic mechanisms driving adaptive radiation in island ecosystems.

Phylogenetics and biogeography of the olive family (Oleaceae)

BACKGROUND AND AIMS

Progress in the systematic studies of the olive family (Oleaceae) during the last two decades provides the opportunity to update its backbone phylogeny and to investigate its historical biogeography. We also aimed to understand the factors underlying the disjunct distribution pattern between East Asia and both West Asia and Europe that is found more commonly in this family than in any other woody plant family.

METHODS

Using a sampling of 298 species out of ~750, the largest in a phylogenetic study of Oleaceae thus far, with a set of 36 plastid and nuclear markers, we reconstructed and dated a new phylogenetic tree based on maximum likelihood and Bayesian methods and checked for any reticulation events. We also assessed the relative support of four competing hypotheses [Qinghai-Tibet Plateau uplift (QTP-only hypothesis); climatic fluctuations (climate-only hypothesis); combined effects of QTP uplift and climate (QTP-climate hypothesis); and no effects (null hypothesis)] in explaining these disjunct distributions.

KEY RESULTS

We recovered all tribes and subtribes within Oleaceae as monophyletic, but uncertainty in the position of tribe Forsythieae remains. Based on this dataset, no reticulation event was detected. Our biogeographical analyses support the QTP-climate hypothesis as the likely main explanation for the East-West Eurasian disjunctions in Oleaceae. Our results also show an earlier origin of Oleaceae at ~86 Mya and the role of Tropical Asia as a main source of species dispersals.

CONCLUSION

Our new family-wide and extensive phylogenetic tree highlights both the stable relationships within Oleaceae, including the polyphyly of the genus Chionanthus, and the need for further systematic studies within the largest and most undersampled genera of the family (Chionanthus and Jasminum). Increased sampling will also help to fine-tune biogeographical analyses across spatial scales and geological times.

The Complete Mitochondrial Genome of Nephropsis grandis: Insights into the Phylogeny of Nephropidae Mitochondrial Genome

The systematic phylogeny of Pleocyemata species, particularly within the family Nephropidae, remains incomplete. In order to enhance the taxonomy and systematics of Nephropidae within the evolutionary context of Pleocyemata, we embarked upon a comprehensive study aiming to elucidate the phylogenetic position of Nephropsis grandis. Consequently, we determined the complete mitochondrial DNA sequence for N. grandis. The circular genome spans a length of 15,344 bp and exhibits a gene composition analogous to that observed in other metazoans, encompassing a comprehensive set of 37 genes. Additionally, the genome features an AT-rich region. The rRNAs exhibited the highest AT content among the 37 genes (70.41%), followed by tRNAs (67.42%) and protein-coding genes (PCGs) (62.76%). The absence of a dihydrouracil arm in trnS1 prevented the formation of the canonical cloverleaf secondary structure. Selective pressure analysis indicated that the PCGs underwent purifying selection. The Ka/Ks ratios for cox1, cox2, cox3, and cob were considerably lower compared to other PCGs, implying strong purifying selection acting upon these particular genes. The mitochondrial gene order in N. grandis was consistent with the reported order in ancestral Pleocyemata. Phylogenetic revealed that N. grandis forms a cluster with the genus Metanephrops, and this cluster further groups with Homarus and the genus Nephrops within the Nephropidae family. These findings provide robust support for N. grandis as an ancestral member of the Nephropidae family. This study highlights the significance of employing complete mitochondrial genomes in phylogenetic analysis and deepens our understanding of the evolution of the Nephropidae family.

The complete chloroplast genome of Erodium cicutarium (Linnaeus) l' Héritier ex Aiton 1789 (Geraniaceae): genome characterization and phylogenetic consideration

Erodium cicutarium is an annual herbaceous plant valued for its applications in traditional medicine. However, the chloroplast genome of E. cicutarium has yet to be reported. In this study, we assembled chloroplast genomes of Erodium cicutarium using Illumina sequencing reads. The chloroplast genome was 114,652 bp long, harbored 111 complete genes, and its overall GC content was 39.1%. In Maximum Likelihood (ML) and Bayesian inference (BI) trees, the 13 Erodium species divided into three main clades, with E. cicutarium and E. carvifolium forming a monophyletic group, suggesting a close relationship between the two species. The E. cicutarium cp genome presented in this study lays a good foundation for the Erodium.

The complete mitochondrial genome of the shining leaf chafer Mimela junii (Duftschmidt, 1805) (Coleoptera: Scarabaeidae)

The complete mitochondrial genome of the shining leaf chafer Mimela junii was sequenced and is herein described. The mitogenome consists of a circular molecule of 16,805 bp, with an overall AT content of 75.7%. It encodes for 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and contains a non-coding Control Region (CR) characterized by the presence of tandem repeats. The gene order corresponds to the ancestral Pancrustacea model and mitogenome characteristics are congruous with those of hexapods. In the phylogenetic analysis, M. junii is nested within a paraphyletic Anomala with high support, and is herein associated with Anomala corpulenta with medium/low support.

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.

The complete chloroplast genome sequence of Arytera littoralis (Sapindoideae, Sapindaceae)

Arytera littoralis Blume 1847 is an evergreen small tree belonging to the Sapindaceae family. It is distributed in South China to SE Asia and the Solomon Islands. However, the chloroplast genome of A. littoralis has yet to be reported. In this study, the complete chloroplast genome of Arytera littoralis was determined. The total genome size was 161,091 bp in length, consisting of two inverted repeats (IRs) (28,432 bp) separated by the large single-copy (LSC) (85,737 bp) and small single-copy (SSC) (18,490 bp) regions. The genome contained 133 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The GC content of the complete chloroplast genome was 37.8%. A maximum-likelihood (ML) phylogenetic tree of A. littoralis and 13 related species from the family Sapindaceae indicated that A. littoralis was close to a clade composed of Sapindus, Nephelium, Litchi, and Dimocarpus. This study will offer essential genetic resources of A. littoralis and provide insights into the phylogeny and evolution of Sapindaceae.

Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China

BACKGROUND

The sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the "Queen of the Tea Family", most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.

RESULTS

In this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836 bp (C. nitidissima) to 1,098,121 bp (C. tianeensis) with GC content of 45.71-45.78% and contained 48-58 genes, including 28-37 protein-coding genes, 17-20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.

CONCLUSIONS

In this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.

The complete chloroplast genome of Fuchsia standishii J. Harrison, 1840 (Onagraceae) from Yunnan, China

Fuchsia standishii J. Harrison, 1840, a perennial shrub, is renowned for its vividly colored and uniquely shaped blooms, which have an extended flowering season. Commonly cultivated as an ornamental potted plant, it is utilized in traditional Chinese medicine. In this study, we successfully sequenced and assembled the complete chloroplast genome of F. standishii using high-throughput Illumina sequencing technology. The assembled chloroplast genome displays a typical quadripartite structure, with a total length of 156,391 bp. It consists of a pair of inverted repeat regions (IRs), each measuring 25,069 bp, separated by a large single-copy region (LSC) of 87,754 bp and a small single-copy region (SSC) of 18,499 bp. The overall GC content of the genome is 37.60%. The genome includes a total of 129 genes, comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of 17 complete chloroplast genomes revealed that F. standishii forms a monophyletic group with the entire Circaea. This study provides a molecular foundation for future phylogenetic research on Fuchsia.

Complete chloroplast genome sequence of Artemisia littoricola (Asteraceae) from Dokdo Island Korea: genome structure, phylogenetic analysis, and biogeography study

The Asteraceae family, particularly the Artemisia genus, presents taxonomic challenges due to limited morphological characteristics and frequent natural hybridization. Molecular tools, such as chloroplast genome analysis, offer solutions for accurate species identification. In this study, we sequenced and annotated the chloroplast genome of Artemisia littoricola sourced from Dokdo Island, employing comparative analyses across six diverse Artemisia species. Our findings reveal conserved genome structures with variations in repeat sequences and junction boundaries. Notably, the chloroplast genome of A. littoricola spans 150,985 bp, consistent with other Artemisia species, and comprises 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Among these genes, 16 possess a single intron, while clpP and ycf3 exhibit two introns each. Furthermore, 18 genes display duplicated copies within the IR regions. Moreover, the genome possesses 42 Simple Sequence Repeats (SSRs), predominantly abundant in A/T content and located within intergenic spacer regions. The analysis of codon usage revealed that the codons for leucine were the most frequent, with a preference for ending with A/U. While the chloroplast genome exhibited conservation overall, non-coding regions showed lower conservation compared to coding regions, with the Inverted Repeat (IR) region displaying higher conservation than single-copy regions. Phylogenetic analyses position A. littoricola within subgenus Dracunculus, indicating a close relationship with A. scoparia and A. desertorum. Additionally, biogeographic reconstructions suggest ancestral origins in East Asia, emphasizing Mongolia, China (North East and North Central and South Central China), and Korea. This study underscores the importance of chloroplast genomics in understanding Artemisia diversity and evolution, offering valuable insights into taxonomy, evolutionary patterns, and biogeographic history. These findings not only enhance our understanding of Artemisia's intricate biology but also contribute to conservation efforts and facilitate the development of molecular markers for further research and applications in medicine and agriculture.

Comparison of Mitochondrial Genome Expression Differences among Four Skink Species Distributed at Different Latitudes under Low-Temperature Stress

Continual climate change strongly influences temperature conditions worldwide, making ectothermic animals as suitable species for studying the potential impact of climate change on global biodiversity. However, the study of how lizards distributed at different latitudes respond to climate change at the transcriptome level is still insufficient. According to the Climatic Variability Hypothesis (CVH), the range of climate fluctuations experienced by terrestrial animals throughout the year increases with latitude, so individuals at higher latitudes should exhibit greater thermal plasticity to cope with fluctuating environments. Mitochondria, as the energy center of vertebrate cells, may indicate species' plasticity through the sensitivity of gene expression. In this study, we focused on the changes in transcript levels of liver mitochondrial protein-coding genes (PCGs) in skinks from the genus Plestiodon (P. capito and P. elegans) and the genus Scincella (S. modesta and S. reevesii) under low-temperature conditions of 8 °C, compared to the control group at 25 °C. Species within the same genus of skinks exhibit different latitudinal distribution patterns. We found that the two Plestiodon species, P. elegans and P. capito, employ a metabolic depression strategy (decreased transcript levels) to cope with low temperatures. In contrast, the two Scincella species show markedly different patterns: S. modesta exhibits significant increases in the transcript levels of six genes (metabolic compensation), while in S. reevesii, only two mitochondrial genes are downregulated (metabolic depression) compared to the control group. We also found that P. capito and S. modesta, which live at mid-to-high latitudes, exhibit stronger adaptive responses and plasticity at the mitochondrial gene level compared to P. elegans and S. reevesii, which live at lower latitudes. We suggest that this enhanced adaptability corresponds to more significant changes in a greater number of genes (plasticity genes).

An acidophilic fungus promotes prey digestion in a carnivorous plant

Leaves of the carnivorous sundew plants (Drosera spp.) secrete mucilage that hosts microorganisms, but whether this microbiota contributes to prey digestion is unclear. We identified the acidophilic fungus Acrodontium crateriforme as the dominant species in the mucilage microbial communities, thriving in multiple sundew species across the global range. The fungus grows and sporulates on sundew glands as its preferred acidic environment, and its presence in traps increased the prey digestion process. A. crateriforme has a reduced genome similar to other symbiotic fungi. During A. crateriforme-Drosera spatulata coexistence and digestion of prey insects, transcriptomes revealed significant gene co-option in both partners. Holobiont expression patterns during prey digestion further revealed synergistic effects in several gene families including fungal aspartic and sedolisin peptidases, facilitating prey digestion in leaves, as well as nutrient assimilation and jasmonate signalling pathway expression. This study establishes that botanical carnivory is defined by adaptations involving microbial partners and interspecies interactions.

Repeated migration, interbreeding and bottlenecking shaped the phylogeography of the selfing grass Brachypodium stacei

Brachypodium stacei is the most ancestral lineage in the genus Brachypodium, a model system for grass functional genomics. B. stacei shows striking and sometimes contradictory biological and evolutionary features, including a high selfing rate yet extensive admixture, an ancient Miocene origin yet with recent evolutionary radiation, and adaptation to different dry climate conditions in its narrow distribution range. Therefore, it constitutes an ideal system to study these life history traits. We studied the phylogeography of 17 native circum-Mediterranean B. stacei populations (39 individuals) using genome-wide RADseq SNP data and complete plastome sequences. Nuclear SNP data revealed the existence of six distinct genetic clusters, low levels of intra-population genetic diversity and high selfing rates, albeit with signatures of admixture. Coalescence-based dating analysis detected a recent split between crown lineages in the Late Quaternary. Plastome sequences showed incongruent evolutionary relationships with those recovered by the nuclear data, suggesting interbreeding and chloroplast capture events between genetically distant populations. Demographic and population dispersal coalescent models identified an ancestral origin of B. stacei in the western-central Mediterranean islands, followed by an early colonization of the Canary Islands and two independent colonization events of the eastern Mediterranean region through long-distance dispersal and bottleneck events as the most likely evolutionary history. Climate niche data identified three arid niches of B. stacei in the southern Mediterranean region. Our findings indicate that the phylogeography of B. stacei populations was shaped by recent radiations, frequent extinctions, long-distance dispersal events, occasional interbreeding, and adaptation to local climates.

Characterization of the complete mitochondrial genome of the medical fungus Ganoderma resinaceum Boud., 1889 (Polyporales: Ganodermataceae)

The medical mushroom Ganoderma resinaceum Boud., 1889, is of great interest in pharmacy due to its diverse functional active ingredients. However, the mitochondrial genome of G. resinaceum remains unexplored. Here, we present the complete mitochondrial genome of G. resinaceum, which spans 67,458 bp and has a GC content of 25.65%. This genome encompasses 15 core protein-coding genes, 8 independent ORFs, 15 intronic ORFs, 27 tRNAs, and 2 rRNA genes. Through phylogenetic analysis using Bayesian inference (BI), we elucidated the evolutionary relationships among 34 Basidiomycota fungi, revealing distinct clades and indicating a close relationship between G. resinaceum and G. subamboinense.

The complete chloroplast genomes and phylogenetic analysis of Exbucklandia longipetala and Exbucklandia populnea (Hamamelidaceae)

Exbucklandia longipetala and Exbucklandia populnea are two evergreen trees of the genus Exbucklandia in the family Hamamelidaceae. In this study, the complete chloroplast genomes of E. longipetala and E. populnea were sequenced, assembled, and annotated. The total lengths of the chloroplast genomes were 160,723 bp and 160,744 bp, respectively, and both had a GC content of 38.1%. The complete chloroplast genomes of these two species had typical quadripartite structures: LSC region (88,972 bp and 88,989 bp), SSC region (18,907 bp and 18,911 bp) and a pair of inverted repeats both of 26,422 bp. Both species contained 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis indicated that E. longipetala and E. populnea are sister species to each other. Our results provide useful genetic resources for further studies on the origin and evolution of Hamamelidaceae.

Multiple origins of freshwater invasion and parental care reflecting ancient vicariances in the bivalve family Cyrenidae (Mollusca)

Habitat transitions in living organisms are key innovations often coupled with species diversification after their successful adaptation to new environment. The Cyrenidae is among the most well-known heterodont bivalve groups that have successfully invaded freshwater systems from brackish water environments and display diverse lineage-specific developmental modes. Phylogenetic and molecular clock-based divergence time analyses using 12 complete mitochondrial genome sequences suggest that Cyrenidae species independently colonized freshwater habitats during three distinct spatial and geological periods: one from the American continents approximately in the Early Jurassic and the two others from Australasian/East Asian continents in the Early/Middle Cretaceous and the Paleogene-Neogene boundary, respectively. This study provides significant insight into the temporal and spatial patterns of multiple freshwater invasions, aligning with ancient vicariance events inferred from different geological timelines of plate tectonics. Additionally, mitogenome phylogeny confirms the earlier hypothesis of the repeated parallel evolution of parental care system within this bivalve group.

The mitochondrial genome sequence of Manchurian Hare (Lepus mandshuricus)

The Manchurian hare (Lepus mandshuricus) is widely distributed in eastern Russia and northeastern China, but due to limited research, its taxonomic status remains somewhat ambiguous. The mitochondrial genome of the Manchurian hare was 16,705 bp in length, which was consisted of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and one control region. The overall nucleotide composition is 31.7% A, 29.4% T, 13.3% G, and 25.6% C, indicating a high AT content. Phylogenetic analysis reveals a closer relationship of the Manchurian hare with the Korean hare (Lepus coreanus) and the Iberian hare (Lepus granatensis), while its relationship with the Hainan rabbit (Lepus hainanus), European hare (Lepus europaeus) and the snowshoe hare (Lepus americanus) is more distant. The mitochondrial genome of the Manchurian hare is of vital importance for the phylogenetic analysis of lagomorphs and provides valuable data for deeper evolutionary inquiries.

Species limits and hybridization in Andean leaf-eared mice (Phyllotis)

Leaf-eared mice (genus Phyllotis) are among the most widespread and abundant small mammals in the Andean Altiplano, but species boundaries and distributional limits are often poorly delineated due to sparse survey data from remote mountains and high-elevation deserts. Here we report a combined analysis of mitochondrial DNA variation and whole-genome sequence (WGS) variation in Phyllotis mice to delimit species boundaries, to assess the timescale of diversification of the group, and to examine evidence for interspecific hybridization. Estimates of divergence dates suggest that most diversification of Phyllotis occurred during the past 3 million years. Consistent with the Pleistocene Aridification hypothesis, our results suggest that diversification of Phyllotis largely coincided with climatically induced environmental changes in the mid- to late Pleistocene. Contrary to the Montane Uplift hypothesis, most diversification in the group occurred well after the major phase of uplift of the Central Andean Plateau. Species delimitation analyses revealed surprising patterns of cryptic diversity within several nominal forms, suggesting the presence of much undescribed alpha diversity in the genus. Results of genomic analyses revealed evidence of ongoing hybridization between the sister species Phyllotis limatus and P. vaccarum and suggest that the contemporary zone of range overlap between the two species represents an active hybrid zone.

A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. 'WA 38'

Genome sequencing for agriculturally important Rosaceous crops has made rapid progress both in completeness and annotation quality. Whole genome sequence and annotation gives breeders, researchers, and growers information about cultivar specific traits such as fruit quality and disease resistance, and informs strategies to enhance postharvest storage. Here we present a haplotype-phased, chromosomal level genome of Malus domestica, 'WA 38', a new apple cultivar released to market in 2017 as Cosmic Crisp®. Using both short and long read sequencing data with a k-mer based approach, chromosomes originating from each parent were assembled and segregated. This is the first pome fruit genome fully phased into parental haplotypes in which chromosomes from each parent are identified and separated into their unique, respective haplomes. The two haplome assemblies, 'Honeycrisp' originated HapA and 'Enterprise' originated HapB, are about 650 Megabases each, and both have a BUSCO score of 98.7% complete. A total of 53,028 and 54,235 genes were annotated from HapA and HapB, respectively. Additionally, we provide genome-scale comparisons to 'Gala', 'Honeycrisp', and other relevant cultivars highlighting major differences in genome structure and gene family circumscription. This assembly and annotation was done in collaboration with the American Campus Tree Genomes project that includes 'WA 38' (Washington State University), 'd'Anjou' pear (Auburn University), and many more. To ensure transparency, reproducibility, and applicability for any genome project, our genome assembly and annotation workflow is recorded in detail and shared under a public GitLab repository. All software is containerized, offering a simple implementation of the workflow.

Chloroplast genomes of Simarouba Aubl., molecular evolution and comparative analyses within Sapindales

Simarouba, a neotropical genus in the family Simaroubaceae, currently lacks comprehensive genomic data in existing databases. This study aims to fill this gap by providing genomic resources for three Simarouba species, S. amara, S. versicolor, and S. glauca. It also aims to perform comparative molecular evolutionary analyses in relation to other species within the order Sapindales. The analysis of these three Simarouba species revealed the presence of the typical quadripartite structure expected in plastomes. However, some pseudogenization events were identified in the psbC, infA, rpl22, and ycf1 genes. In particular, the CDS of the psbC gene in S. amara was reduced from 1422 bp to 584 bp due to a premature stop codon. Nucleotide diversity data pointed to gene and intergenic regions as promising candidates for species and family discrimination within the group, specifically matK, ycf1, ndhF, rpl32, petA-psbJ, and trnS-trnG. Selection signal analyses showed strong evidence for positive selection on the rpl23 gene. Phylogenetic analyses indicated that S. versicolor and S. glauca have a closer phylogenetic relationship than S. amara. We provide chloroplast genomes of three Simaruba species and use them to elucidate plastome evolution, highlight the presence of pseudogenization, and identify potential DNA barcode regions.

Complete mitochondrial genome sequence of the white root rot pathogen Dematophora necatrix (Xylariaceae: Xylariales)

The mitochondrial genome of Dematophora necatrix is 121,350 base pairs in length with a G + C content of 30.19%. Phylogenetic analysis showed that D. necatrix grouped with other members of the Xylariaceae, with which its mitogenome also shares a broadly similar architecture and gene content. The D. necatrix mitogenome contains 14 protein-coding and 26 tRNA-encoding genes, as well as one copy each of the rnl, rns, rps3 and nat1 genes. However, as much as 80% of this genome is intronic or non-coding. This is likely due to expansions and rearrangements caused by the large number of group I introns and the homing endonucleases and reverse-transcriptases they encode. Our study thus provides a valuable foundation from which to explore the mitochondrion's role in the biology of D. necatrix, and also serves as a resource for investigating the pathogen's population biology and general ecology.