Phylogenetic Implications Research Articles

Insights into the structural features and phylogenetic implications of the complete mitochondrial genome of Fasin rainbow fish (Melanotaenia fasinensis).

The Fasin rainbow fish, scientifically named Melanotaenia fasinensis, is highly prized by aquarium enthusiasts for its vibrant colors and adaptability to artificial aquatic environments. This species is endemic to the karst landscape of the Bird's Head region in Papua, Indonesia, and belongs to the family Melanotaeniidae. Discovered relatively recently in 2010, this species was designated as endangered by the International Union for Conservation of Nature (IUCN) in 2021. However, there is currently insufficient data regarding its phylogenetic position. To address this gap, our study employed next-generation sequencing (NGS) to analyze the entire mitochondrial genome of M. fasinensis. The mitochondrial genome comprises 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with a total length of 16,731 base pairs. The base composition of the mitogenome revealed percentages of 27.76% adenine (A), 27.34% thymine (T), 16.15% guanine (G), and 28.75% cytosine (C) residues. Our phylogenetic analysis based on sequence data indicated that all species of the Melanotaeniidae family clustered together on the same branch. Furthermore, the intergeneric and interspecific taxonomic positions were explicit and clear. Phylogenetically, Melanotaeniidae were more closely related to the family Isonidae than to the family Atherinomorus. The phylogenetic position of M. fasinensis was relatively basal within the genus Melanotaenia. This study provides valuable molecular insights for further exploration of the phylogeography and evolutionary history of M. fasinensis and other members of the genus Melanotaenia.

Insights into phylogenetic relationships and gene rearrangements: complete mitogenomes of two sympatric species in the genus Rana (Anura, Ranidae).

Mitochondrial genomes (also known as mitogenomes) serve as valuable molecular markers and have found widespread applications in molecular biology and ecology. There is abundant sequence variation in vertebrate mitogenomes, and occasionally, they exhibit gene rearrangements. In this study, two Chinese endemic Rana species, Ranajiemuxiensis and Ranahanluica, were sequenced and analyzed to obtain their complete mitogenomes. The two species were sympatrically distributed in the Zhangjiajie National Forest Park, in Wulingyuan District, Zhangjiajie City, Hunan Province, China. The mitogenome of R.jiemuxiensis was 17,506 bp, while that of R.hanluica was 17,505 bp, each comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a non-coding control region (D-loop). The gene content, nucleotide composition, and evolutionary rates of each mitogenome were analyzed and compared with those of congeners. A phylogenetic analysis based on 22 mitogenomes in Rana revealed that the two sympatric species were in two different lineages, indicating that they were genetically separated to a certain extent. Three types of gene rearrangement patterns were identified when examining the gene orders of the 22 Rana mitogenomes. Most of the species shared a second and dominant gene rearrangement pattern that originated from the first ancient pattern. A "tandem duplication - multiple deletion" hypothesis was proposed to explain the evolution of these different gene rearrangement patterns. This study provided valuable data references and enhanced our understanding of the phylogenetic implications and gene rearrangements of Rana species.

Sequence comparison of the mitochondrial genomes of five caridean shrimps of the infraorder Caridea: phylogenetic implications and divergence time estimation

BackgroundThe Caridea, affiliated with Malacostraca, Decapoda, and Pleocyemata, constitute one of the most significant shrimp groups. They are widely distributed across diverse aquatic habitats worldwide, enriching their evolutionary history. In recent years, considerable attention has been focused on the classification and systematic evolution of Caridea, yet controversies still exist regarding the phylogenetic relationships among families.MethodsHere, the complete mitochondrial genome (mitogenome) sequences of five caridean species, namely Heterocarpus sibogae, Procletes levicarina, Macrobrachium sp., Latreutes anoplonyx, and Atya gabonensis, were determined using second-generation high-throughput sequencing technology. The basic structural characteristics, nucleotide composition, amino acid content, and codon usage bias of their mitogenomes were analyzed. Selection pressure values of protein-coding genes (PCGs) in species within the families Pandalidae, Palaemonidae, and Atyidae were also computed. Phylogenetic trees based on the nucleotide and amino acid sequences of 13 PCGs from 103 caridean species were constructed, and divergence times for various families within Caridea were estimated.ResultsThe mitogenome of these five caridean species vary in length from 15,782 to 16,420 base pairs, encoding a total of 37 or 38 genes, including 13 PCGs, 2 rRNA genes, and 22 or 23 tRNA genes. Specifically, L. anoplonyx encodes an additional tRNA gene, bringing its total gene count to 38. The base composition of the mitogenomes of these five species exhibited a higher proportion of adenine-thymine (AT) bases. Six start codons and four stop codons were identified across the five species. Analysis of amino acid content and codon usage revealed variations among the five species. Analysis of selective pressure in Pandalidae, Palaemonidae, and Atyidae showed that the Ka/Ks values of PCGs in all three families were less than 1, indicating that purifying selection is influencing on their evolution. Phylogenetic analysis revealed that each family within Caridea is monophyletic. The results of gene rearrangement and phylogenetic analysis demonstrated correlations between these two aspects. Divergence time estimation, supported by fossil records, indicated that the divergence of Caridea species occurred in the Triassic period of the Mesozoic era, with subsequent differentiation into two major lineages during the Jurassic period.ConclusionsThis study explored the fundamental characteristics and phylogenetic relationships of mitogenomes within the infraorder Caridea, providing valuable insights into their classification, interspecific evolutionary patterns, and the evolutionary status of various Caridea families. The findings provide essential references for identifying shrimp species and detecting significant gene rearrangements within the Caridea infraorder.

Characterization and phylogenetic implications of the mitochondrial genomes of the Phyllidiidae (Gastropoda, Nudibranchia) from the South China Sea

Characterization and phylogenetic implications of the mitochondrial genomes of the Phyllidiidae (Gastropoda, Nudibranchia) from the South China Sea

Ultrastructural Characteristics of the Mature Spermatozoon of Artyfechinostomum malayanum (Digenea: Echinostomatidae), an Intestinal Parasite of Rattus norvegicus (Rodentia: Muridae) in Vietnam.

The study of sperm characteristics has proven useful for elucidating interrelationships in several groups of Platyhelminthes, such as digeneans. Thus, in the present work, the ultrastructural organization of the mature spermatozoon of the digenean Artyfechinostomum malayanum (Echinostomatidae), a parasite of Rattus norvegicus (Rodentia: Muridae) from Dong Thap Province, Vietnam, was investigated for the first time using transmission electron microscopy. The male gamete of A. malayanum exhibits two axonemes of different lengths, showing the 9 + '1' pattern of the Trepaxonemata, a nucleus, two mitochondria, two lateral expansions, two bundles of parallel cortical microtubules, external ornamentation, spine-like bodies, and granules of glycogen. Thus, the mature spermatozoon follows a Type V sperm model proposed for digeneans. We also highlight some noteworthy characteristics in Echinostomatidae with possible phylogenetic implications, such as two lateral expansions in the anterior region of the spermatozoon and two mitochondria.

Complete mitochondrial genome assembly of Juglans regia unveiled its molecular characteristics, genome evolution, and phylogenetic implications

BackgroundThe Persian walnut (Juglans regia), an economically vital species within the Juglandaceae family, has seen its mitochondrial genome sequenced and assembled in the current study using advanced Illumina and Nanopore sequencing technology.ResultsThe 1,007,576 bp mitogenome of J. regia consisted of three circular chromosomes with a 44.52% GC content encoding 39 PCGs, 47 tRNA, and five rRNA genes. Extensive repetitive sequences, including 320 SSRs, 512 interspersed, and 83 tandem repeats, were identified, contributing to genomic complexity. The protein-coding sequences (PCGs) favored A/T-ending codons, and the codon usage bias was primarily shaped by selective pressure. Intracellular gene transfer occurred among the mitogenome, chloroplast, and nuclear genomes. Comparative genomic analysis unveiled abundant structure and sequence variation among J. regia and related species. The results of selective pressure analysis indicated that most PCGs underwent purifying selection, whereas the atp4 and ccmB genes had experienced positive selection between many species pairs. In addition, the phylogenetic examination, grounded in mitochondrial genome data, precisely delineated the evolutionary and taxonomic relationships of J. regia and its relatives. We identified a total of 539 RNA editing sites, among which 288 were corroborated by transcriptome sequencing data. Furthermore, expression profiling under temperature stress highlighted the complex regulation pattern of 28 differently expressed PCGs, wherein NADH dehydrogenase and ATP synthase genes might be critical in the mitochondria response to cold stress.ConclusionsOur results provided valuable molecular resources for understanding the genetic characteristics of J. regia and offered novel perspectives for population genetics and evolutionary studies in Juglans and related woody species.

The first report of complete mitogenomes of two endangered species of genus Propomacrus (Coleoptera: Scarabaeidae: Euchirinae) and phylogenetic implications.

To understand the mitochondrial genome structure of two endangered and long-armed scarab beetles, Propomacrus davidi and Propomacrus bimucronatus, their complete mitogenomes were sequenced for the first time in this study. The complete mitogenomes of P. davidi and P. bimucronatus were 18, 042 bp and 18, 104 bp in length, respectively. The gene orders of their mitogenomes were highly consistent with other Coleopteran species, and the typical ATN was used as the start codon in most protein coding genes. The incomplete stop codon T was used in cox1, cox2, and nad5, and TAN was used as a complete stop codon in most protein coding genes. All predicted tRNAs could form a typical cloverleaf secondary structure, except that trnS1 lacked the dihydrouridine arm. Based on the maximum likelihood and the Bayesian inference methods, phylogenetic trees of 50 species were reconstructed. The results showed that P. davidi, P. bimucronatus, Cheirotonus jansoni and Cheirotonus gestroi clustered in the same branch, and were the most closely related. The results supported that subfamily Euchirinae is a monophyletic group of Scarabaeidae, which was consistent with the morphological classification. These molecular data enriched the complete mitogenome database of Euchirinae, and improved our understanding of the phylogenetic relationship and evolutionary characteristics of these two endangered species.

Hypodermis or multiple epidermis: Leaf ontogenesis in nine species of subfamily Myrtoideae (Myrtaceae)

The ninth largest family of angiosperms is Myrtaceae, which comprises 127 genera and over 6000 species. The leaf anatomy of Myrtaceae has been widely studied and can be used in phylogenetic analyses and species delimitations in complexes within the family. A multiple epidermis and hypodermis have been described for the leaves of representatives of the family but have not been confirmed using ontogenetic studies, which could lead to incorrect interpretations about these tissues. Thus, we studied the leaf ontogenesis of the following 9 species in subfamily Myrtoideae: tribe Syzigieae - Syzigium cumini; tribe Myrteae - Myrceugenia alpigena and M. euosma (subtribe Luminae), Psidium sartorianum, P. guajava, Campomanesia adamantium and Pimenta pseudocaryophyllus (subtribe Pimentinae), Myrcianthes pungens and M. gigantea (subtribe Eugeniinae). Shoot apices and leaves up to the fourth node were transversally and longitudinally sectioned following techniques used for plant anatomy. Leaf development in all species is from apical, intercalary, dorsal, marginal and plate meristematic activity. Protodermal periclinal divisions only occur to give rise to secretory cavities. The results show that in all the species the subepidermal layer is a hypodermis, which originates from periclinal divisions of the ground meristem. The occurrence of this layer could have phylogenetic implications according to reports in the literature, reinforcing the relationships among the subtribes in current topologies of Myrteae. However, the occurrence of a hypodermis in representatives of other subtribes of Myrteae and Syzigieae need to be better studied and discussed in relation to the phylogeny of Myrtaceae.

The first complete mitochondrial genome of Grossulariaceae: Molecular features, structure recombination, and genetic evolution

BackgroundMitochondria play crucial roles in the growth, development, and adaptation of plants. Blackcurrant (Ribes nigrum L.) stands out as a significant berry species due to its rich nutritional profile, medicinal properties, and health benefits. Despite its importance, the mitochondrial genome of blackcurrant remains unassembled.ResultsThis study presents the first assembly of the mitochondrial genome of R. nigrum in the Grossulariaceae family. The genome spans 450,227 base pairs (bp) and encompasses 39 protein-coding genes (PCGs), 19 transfer RNAs (tRNAs), and three ribosomal RNAs (rRNAs). Protein-coding regions constitute 8.88% of the entire genome. Additionally, we identified 180 simple sequence repeats, 12 tandem repeats, and 432 pairs of dispersed repeats. Notably, the dispersed sequence R1 (cotig3, 1,129 bp) mediated genome recombination, resulting in the formation of two major conformations, namely master and double circles. Furthermore, we identified 731 C-to-U RNA editing sites within the PCGs. Among these, cox1-2, nad1-2, and nad4L-2 were associated with the creation of start codons, whereas atp6-718 and rps10-391 were linked to termination codons. We also detected fourteen plastome fragments within the mitogenome, constituting 1.11% of the total length. Phylogenetic analysis suggests that R. nigrum might have undergone multiple genomic reorganization and/or gene transfer events, resulting in the loss of two PCGs (rps2 and rps11) during its evolutionary history.ConclusionsThis investigation unveils the molecular characteristics of the R. nigrum mitogenome, shedding light on its evolutionary trajectory and phylogenetic implications. Furthermore, it serves as a valuable reference for evolutionary research and germplasm identification within the genus.

Morphological Structure Identification, Comparative Mitochondrial Genomics and Population Genetic Analysis toward Exploring Interspecific Variations and Phylogenetic Implications of Malus baccata 'ZA' and Other Species.

Malus baccata, a valuable germplasm resource in the genus Malus, is indigenous to China and widely distributed. However, little is known about the lineage composition and genetic basis of 'ZA', a mutant type of M. baccata. In this study, we compared the differences between 'ZA' and wild type from the perspective of morphology and ultrastructure and analyzed their chloroplast pigment content based on biochemical methods. Further, the complete mitogenome of M. baccata 'ZA' was assembled and obtained by next-generation sequencing. Subsequently, its molecular characteristics were analyzed using Geneious, MISA-web, and CodonW toolkits. Furthermore, by examining 106 Malus germplasms and 42 Rosaceae species, we deduced and elucidated the evolutionary position of M. baccata 'ZA', as well as interspecific variations among different individuals. In comparison, the total length of the 'ZA' mitogenome (GC content: 45.4%) is 374,023 bp, which is approximately 2.33 times larger than the size (160,202 bp) of the plastome (GC: 36.5%). The collinear analysis results revealed abundant repeats and genome rearrangements occurring between different Malus species. Additionally, we identified 14 plastid-driven fragment transfer events. A total of 54 genes have been annotated in the 'ZA' mitogenome, including 35 protein-coding genes, 16 tRNAs, and three rRNAs. By calculating nucleotide polymorphisms and selection pressure for 24 shared core mitochondrial CDSs from 42 Rosaceae species (including 'ZA'), we observed that the nad3 gene exhibited minimal variation, while nad4L appeared to be evolving rapidly. Population genetics analysis detected a total of 1578 high-quality variants (1424 SNPs, 60 insertions, and 94 deletions; variation rate: 1/237) among samples from 106 Malus individuals. Furthermore, by constructing phylogenetic trees based on both Malus and Rosaceae taxa datasets, it was preliminarily demonstrated that 'ZA' is closely related to M. baccata, M. sieversii, and other proximate species in terms of evolution. The sequencing data obtained in this study, along with our findings, contribute to expanding the mitogenomic resources available for Rosaceae research. They also hold reference significance for molecular identification studies as well as conservation and breeding efforts focused on excellent germplasms.

Craniomandibular osteology and the first record of the ocular skeleton in a South American rhynchosaur (Archosauromorpha, Hyperodapedontinae)

A new rhynchosaur specimen from the Upper Triassic (Candelária Sequence) of Southern Brazil is presented in this contribution. While these reptiles constitute some of the most sampled fossils from these beds, their taxonomic, phylogenetic, and palaeobiological status remain understudied. Delving into the cranial elements of the new specimen we performed a taxonomic and phylogenetic assessment, assigning it to “Hyperodapedon” sanjuanensis, a form that occurs in Brazil and Argentina. This assignment was based on distinctive craniomandibular features such as the absence of lingual teeth in the dentary, a unique feature among hyperodapedontine rhynchosaurs. Furthermore, our phylogenetic analysis supports this scenario. Our approach emphasizes the broader need for comprehensive anatomical descriptions of South American rhynchosaurs, particularly in Brazil, where some crucial taxa remain undescribed and/or unfigured. This study also reinforces the need for a revision of the clade Hyperodapedontinae and the Hyperodapedon genus. The orbital region of the new specimen reveals delicate scleral ossicles, presenting a unique window into the visual adaptations and habits of these reptiles. This is the first record of the ocular skeleton for a rhynchosaur of South America. Beyond the taxonomic and phylogenetic implications, this study elucidates the role of the ocular skeleton in regards to sensory adaptations in hyperodapedontine rhynchosaurs.

The First Three Mitochondrial Genomes for the Characterization of the Genus Egeirotrioza (Hemiptera: Triozidae) and Phylogenetic Implications.

(1) Background: Mitochondrial genomes are important markers for the study of phylogenetics and systematics. Triozidae includes some primary pests of Populus euphratica. The phylogenetic relationships of this group remain controversial due to the lack of molecular data. (2) Methods: Mitochondria of Egeirotrioza Boselli were sequenced and assembled. We analyzed the sequence length, nucleotide composition, and evolutionary rate of Triozidae, combined with the 13 published mitochondrial genomes. (3) Results: The evolutionary rate of protein-coding genes was as follows: ATP8 > ND6 > ND5 > ND2 > ND4 > ND4L > ND1 > ND3 > APT6 > CYTB > COX3 > COX2 > COX1. We reconstructed the phylogenetic relationships of Triozidae based on 16 triozid mitochondrial genomes (thirteen ingroups and three outgroups) using the maximum likelihood (ML) and Bayesian inference (BI) approaches. The phylogenetic analysis of the 16 Triozidae mitochondrial genomes showed that Egeirotrioza was closely related to Leptynoptera. (4) Conclusions: We have identified 13 PCGs, 22 tRNAs, 2 rRNAs, and 1 control region (CR) of all newly sequenced mitochondrial genomes, which were the mitochondrial gene type in animals. The results of this study provide valuable genomic information for the study of psyllid species.

Geolocation and immersion loggers reveal year‐round residency and facilitate nutrient deposition rate estimation of adult red‐footed boobies in the Chagos Archipelago, tropical Indian Ocean

Bio‐logging has revealed much about high‐latitude seabird migratory strategies, but migratory behaviour in tropical species may differ, with implications for understanding nutrient deposition. Here we use combined light‐level and saltwater immersion loggers to study the year‐round movement behaviour of adult red‐footed boobies Sula sula rubripes from the Chagos Archipelago, tropical Indian Ocean, to assess migratory movements and estimate nutrient deposition rates based on the number of days they spent ashore. Light levels suggest that red‐footed boobies are resident in the Chagos Archipelago year‐round, although there are large latitudinal errors this close to the equator. Immersion data also indicate residency with tracked birds returning to land every one or two days. Spending an average of 79.86 ± 2.80 days and 280.84 ± 2.64 nights per year on land allows us to estimate that the 21 670 pairs of red‐footed boobies deposit 37.34 ± 0.56 tonnes year−1 of guano‐derived nitrogen throughout the archipelago. Our findings have implications for tropical seabird conservation and phylogenetics, as well as for assessing the impact of seabird nutrients on coral reef ecosystems.

Morphology of the pterothoracic musculature in Paraneoptera and its phylogenetic implication (Insecta: Neoptera).

Although the monophyly of Paraneoptera (=hemipteroid orders or Acercaria, composed of Psocodea, Thysanoptera and Hemiptera) has been widely accepted morphologically, the results from molecular phylogenetic and phylogenomic analyses contradict this hypothesis. In particular, phylogenomic analyses provide strong bootstrap support for the sister group relationship between Psocodea and Holometabola, that is, paraphyly of Paraneoptera. Here, we examined the pterothoracic musculature of Paraneoptera, as well as a wide range of other neopterous insect orders, and analysed its phylogenetic implication. By using the synchrotron microcomputed tomography (µCT) and parsimony-based ancestral state reconstruction, several apomorphic conditions suggesting the monophyly of Paraneoptera, such as the absence of the II/IIItpm7, IIscm3, IIIspm2 and IIIscm3 muscles, were identified. In contrast, no characters supporting Psocodea + Holometabola were recovered from the thoracic muscles. These results provide additional support for the monophyly of Paraneoptera, together with the previously detected morphological apomorphies of the head, wing base, and abdomen.

Osteological redescription of the holotype of Plateosaurus trossingensis (Dinosauria: Sauropodomorpha) from the Upper Triassic of SW Germany and its phylogenetic implications

Plateosaurus von Meyer, 1837, from the Norian of central Europe, was one of the first named dinosaurs. With close to 200 referred specimens found all over central Europe, it is one of the best-known dinosaurs from Europe. Over the past 200 years it has become one of the most important sauropodomorph dinosaurs and is used in many comparative studies in almost all fields of dinosaur palaeontology. Here we present a full osteological redescription of the holotype of Plateosaurus trossingensis, the almost entirely complete, historic specimen SMNS 13200. We use it as a basis for a revised diagnosis of P. trossingensis that consists of autapomorphies in a unique combination of features. An updated phylogeny of basal sauropodomorph taxa, with P. trossingensis restricted to the holotype, recovers P. trossingensis within Plateosauridae together with Sellosaurus and Unaysaurus. The revised anatomy and cladistic scoring can be used in many future studies involving comparative anatomy, phylogenetics, biostratigraphy and early dinosaur evolution.

De novo assembly of the complete mitochondrial genome of pepino (Solanum muricatum) using PacBio HiFi sequencing: insights into structure, phylogenetic implications, and RNA editing

BackgroundSolanum muricatum is an emerging horticultural fruit crop with rich nutritional and antioxidant properties. Although the chromosome-scale genome of this species has been sequenced, its mitochondrial genome sequence has not been reported to date.ResultsPacBio HiFi sequencing was used to assemble the circular mitogenome of S. muricatum, which was 433,466 bp in length. In total, 38 protein-coding, 19 tRNA, and 3 rRNA genes were annotated. The reticulate mitochondrial conformations with multiple junctions were verified by polymerase chain reaction, and codon usage, sequence repeats, and gene migration from chloroplast to mitochondrial genome were determined. A collinearity analysis of eight Solanum mitogenomes revealed high structural variability. Overall, 585 RNA editing sites in protein coding genes were identified based on RNA-seq data. Among them, mttB was the most frequently edited (52 times), followed by ccmB (46 times). A phylogenetic analysis based on the S. muricatum mitogenome and those of 39 other taxa (including 25 Solanaceae species) revealed the evolutionary and taxonomic status of S. muricatum.ConclusionsWe provide the first report of the assembled and annotated S. muricatum mitogenome. This information will help to lay the groundwork for future research on the evolutionary biology of Solanaceae species. Furthermore, the results will assist the development of molecular breeding strategies for S. muricatum based on the most beneficial agronomic traits of this species.

Taxonomy of the Panorpa semifasciata group (Mecoptera: Panorpidae: Panorpinae), with descriptions of fourteen new species from China

Summary Previously, the Panorpa semifasciata group sensu Wang & Hua, 2021 comprised four known species that are endemic to Southwestern China. In this paper, I illustrate and describe 14 new species, increasing the species number of this group to 18. The new species are: P. ashima n. sp., P. duanyanqing n. sp., P. jialiangjiei n. sp., P. jiumozhi n. sp., P. kasyapa n. sp., P. kurong n. sp., P. liangdu n. sp., P. liyufeii n. sp., P. qumahei n. sp., P. wumengshana n. sp., P. wuyazi n. sp., P. yeerniang n. sp., P. yuelaosan n. sp., and P. yunzhonghe n. sp. The diagnostic characters for this group are herein revised to take the new species into account. The keys to species and a distributional map are also provided. Also discussed are the biology, distributional pattern, and phylogenetic implications of this group.

The complete mitochondrial genome of the sand bubbler crab Scopimera longidactyla Shen 1932 (Decapoda: Dotillidae) and its phylogenetic analysis

The sand bubbler crab, Scopimera longidactyla Shen, 1932 (Arthropoda: Malacostraca: Decapoda: Thoracotremata: Dotillidae), is commonly found along tropical and subtropical sandy shores of China, Korea, and Taiwan. Ecologically, it plays an important role in the productivity of sandy shores through their feeding and burrowing activities. In this study, the first complete mitochondrial genome (mitogenome) of S. longidactyla was analyzed using next-generation sequencer. Its mitogenome, circular in structure, spans 15,965 bp with a GC content of 29.97%, consisting of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one putative control region. Its mitogenome arrangement and composition are identical to its two congeners, S. globosa and S. intermedia. Phylogenetic analysis fully supports for the monophyly of the genus Scopimera and the sister relationship between S. longidactyla and S. globosa. The complete mitogenome of S. longidactyla and its phylogenetic implications will provide valuable insights for further studies in phylogenetic and evolutionary biology.

Seed morphology in the genus Matthiola R. Br. (Brassicaceae): Identification of species and systematic implications

AbstractSeed coat morphology of 34 species of Matthiola R.Br. has been studied using light and scanning electron microscopy to assess their investigative value for systematic studies. Macro‐ and micromorphological characters, including seed shape, color, size, wing, and radicle position relative to cotyledons, epidermal cell shape, anticlinal boundaries, and periclinal cell wall are presented. Seed shape, color, and radicle position relative to cotyledons have limited taxonomic significance, as their variation is unhelpful. There against, seed size, wing, and seed coat ornamentation present informative characteristics that can be used professionally in distinguishing the studied taxa. Six different types of seed anticlinal cell wall boundaries are recognized and five different outer periclinal cell wall shapes are described. The sculpture of the secondary cell wall varies from striate, micropapillate to microreticulate, and smooth to fine folds. The taxonomic and phylogenetic implications of seed coat micromorphology were compared with those of the existing gross morphological and molecular data. Seed character analysis offered useful data for evaluating the taxonomy of Matthiola both on subgeneric and sectional levels. Seed micromorphological characters provide evidence that M. odoratissima and M. ovatifolia should be preserved as separate species. In addition, M. ghorana is not conspecific with M. graminea. Furthermore, M. tricuspidata was unique in the seed characters. A key to the identification of the examined taxa based on seed characters is provided.

Structural Features and Phylogenetic Implications of Crinoid Echinoderms Based on Thirteen Novel Mitochondrial Genomes

Crinoids, as integral echinoderms, play a crucial ecological role in benthic communities, serving as significant indicators reflecting the health of marine ecosystems. However, the phylogenetic relationships within crinoids are unclear. More molecular data can help to facilitate biodiversity assessment and elucidate evolutionary relationships by the phylogenetic tree. In this study, 13 complete mitochondrial genomes of the Crinoidea class were sequenced, annotated, and compared with other same class species available on NCBI. The results reveal five different gene order patterns among these mitochondrial genomes, indicating that crinoids have undergone gene rearrangements during evolution. The complete mitochondrial genome length of crinoids ranges from 15,772 bp to 16,850 bp. High A + T content, ranging from 64.5% to 74.2%, was observed. Additionally, our analysis of protein-coding genes highlights a preference for A + T nucleotides, along with specific start and stop codon usage, offering insights into codon bias and its implications for protein synthesis and function. The phylogenetic topology shows that the stalkless crinoid and stalked crinoid are distinct, and the phylogenetic trees generated based on maximum likelihood and Bayesian inference are almost identical at the family and order topology levels. The phylogenetic relationships of each family were fully clarified in four orders. A total of eleven positive selection sites were detected within six genes: cytb, nad2, nad3, nad4, nad4L and nad5. This study reveals the phylogenetic relationships of crinoid species, the mitochondrial gene differences, and the selective pressure on the evolution of stalked crinoids. This study significantly enhanced the crinoid mitochondrial genome database and contributed to a better understanding of the phylogenetic relationships among crinoid echinoderms.