Nucleotide Data Sets Research Articles

Genome-scale approach to reconstructing the phylogenetic tree of psyllids (superfamily Psylloidea) with account of systematic bias

Psyllids (class Insecta: order Hemiptera: superfamily Psylloidea) are a taxonomically and phylogenetically challenging clade. Recent studies have largely advanced the phylogeny of this group, yet the family-level relationships among Aphalaridae, Carsidaridae, and others remain unresolved. Genome-scale phylogenetic analysis is known to provide a finer resolution for problems like that. However, such phylogenomics also introduces new problems: incorrect trees with high confidence yielded due to systematic error (bias). Here we addressed these issues using hundreds of single-copy orthologous (SCO) genes in psyllid transcriptomes and genomes. Our analyses revealed conflicts between the nucleotide-based and amino-acid-based phylogenetic trees. While the nucleotide-based phylogeny strongly supported the (Aphalaridae + Carsidaridae) + Others relationship, the amino-acid-based one recovered Aphalaridae + (Carsidaridae + Others) with 100% support. Further inspection revealed significant compositional heterogeneity in nucleotide sequences for 67% of SCO genes, but not in the corresponding translated amino acid sequences. We then used different strategies to combat this compositional bias, and found that using the RY-coding strategy (coding the standard nucleotides as purines and pyrimidines) the nucleotide-based phylogeny became consistent with the amino-acid-based one. We further applied RY-coding to a published concatenated nucleotide dataset and recovered the Aphalaridae monophyly (which is refuted by the original literature on non-recoded sequences) at the base of psyllid tree. Moreover, it was found that variations in evolutionary rate could lead to errors in nucleotide-based phylogeny. The fast-evolving Heteropsylla cubana (Psyllidae: Ciriacreminae) was incorrectly placed within the subfamily Psyllinae. This bias can be avoided by using data removal or RY-coding strategies. Together, our results strongly support the family relationship of Aphalaridae + (Carsidaridae + Others), and show that the amino-acid-based concatenation analysis is more robust than nucleotide-based one. Future phylogenomic analysis of psyllid nucleotide sequences should take into account methods such as the RY-coding scheme to address potential systematic biases arising from composition and rate heterogeneities.

Identification and genetic characterization of Angiostrongylus cantonensis isolated from the human eye.

Angiostrongylus cantonensis, or the rat lungworm, is the causative agent of human angiostrongyliasis associated with eosinophilic meningitis or meningoencephalitis. Additionally, this nematode can cause ocular angiostrongyliasis, though this is rare. The worm can cause permanent damage to the affected eye and sometimes even blindness. Genetic characterization of the worm from clinical samples is limited. In the present study, we investigated the genetics of A. cantonensis recovered from a patient's eye in Thailand. We sequenced two mitochondrial genes (cytochrome c oxidase subunit I, or COI, and cytochrome b, or cytb) and nuclear gene regions (66-kDa protein and internal transcribed spacer 2, or ITS2) from a fifth-stage larva of Angiostrongylus sample that was surgically removed from the human eye. All sequences of the selected nucleotide regions were highly similar (98-100%) to the sequences of A. cantonensis in the GenBank database. The maximum likelihood and neighbor-joining trees of the COI gene indicated that A. cantonensis was closely related to the AC4 haplotype, whereas the cytb and 66-kDa protein genes were closely clustered with the AC6 and Ac66-1 haplotypes, respectively. In addition, the phylogeny of the concatenated nucleotide datasets of the COI and cytb revealed that the worm was closely related to the Thai strain and strains from other countries. This study confirms the identification and genetic variation of the fifth-stage larvae of A. cantonensis recovered from a patient's eye in Thailand. Our findings are important for future research on the genetic variation of A. cantonensis that causes human angiostrongyliasis.

Compositional shifts associated with major evolutionary transitions in plants.

Heterogeneity in gene trees, morphological characters, and composition has been associated with several major plant clades. Here, we examine heterogeneity in composition across a large transcriptomic dataset of plants to better understand whether locations of shifts in composition are shared across gene regions and whether directions of shifts within clades are shared across gene regions. We estimate mixed models of composition for both nucleotide and amino acids across a recent large-scale transcriptomic dataset for plants. We find shifts in composition across both nucleotide and amino acid datasets, with more shifts detected in nucleotides. We find that Chlorophytes and lineages within experience the most shifts. However, many shifts occur at the origins of land, vascular, and seed plants. While genes in these clades do not typically share the same composition, they tend to shift in the same direction. We discuss potential causes of these patterns. Compositional heterogeneity has been highlighted as a potential problem for phylogenetic analysis, but the variation presented here highlights the need to further investigate these patterns for the signal of biological processes.

Phylogeny and classification of Endromidae (Lepidoptera: Bombycoidea) based on mitochondrial genomes

The small, relict-like moth family Endromidae is well-established within the superfamily Bombycoidea, but relationships within the family have remained vague for the last decade, primarily due to very limited taxon sampling. This resulted in the explicit removal of all internal suprageneric classification by Zwick et al. (2011) when they synonymized Mirinidae and the bombycid subfamilies Oberthueriinae and Prismostictinae with Endromidae. Nucleotide and amino acid data sets of the 13 mitochondrial, protein-coding genes from representatives of 13 of the 16 accepted endromid genera were used to estimate phylogenetic relationships based on maximum likelihood and Bayesian inference methods. The results strongly support Endromidae as a monophyletic group and enable the establishment and diagnosis of four subfamilies (Endrominae, Mirininaestat. rev., Oberthueriinaestat. rev. and Prismostictinaestat. rev.). Within subfamily Oberthueriinae, we establish three tribes: Oberthueriinistat. rev., Andracinitribe nov. and Mustiliinitribe nov. We provide morphological diagnoses and a genus-level checklist for the three tribes. Promustilia yajiangensis Wang, X. & Zolotuhin, 2015 is transferred to Mustilizans as M. yajiangensiscomb. nov. to establish reciprocal monophyly of the two genera, and Andraca gongshanensis is transferred to Pseudandraca as P. gongshanensiscomb. nov. We also synonymize Andraca (Chrypathemola)syn. nov. with Andraca (Andraca), as the latter is deeply nested within the former.

NRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets

MotivationCompositional heterogeneity—when the proportions of nucleotides and amino acids are not broadly similar across the dataset—is a cause of a great number of phylogenetic artefacts. Whilst a variety of methods can identify it post-hoc, few metrics exist to quantify compositional heterogeneity prior to the computationally intensive task of phylogenetic tree reconstruction. Here we assess the efficacy of one such existing, widely used, metric: Relative Composition Frequency Variability (RCFV), using both real and simulated data.ResultsOur results show that RCFV can be biased by sequence length, the number of taxa, and the number of possible character states within the dataset. However, we also find that missing data does not appear to have an appreciable effect on RCFV. We discuss the theory behind this, the consequences of this for the future of the usage of the RCFV value and propose a new metric, nRCFV, which accounts for these biases. Alongside this, we present a new software that calculates both RCFV and nRCFV, called nRCFV_Reader.Availability and implementationnRCFV has been implemented in RCFV_Reader, available at: https://github.com/JFFleming/RCFV_Reader. Both our simulation and real data are available at Datadryad: https://doi.org/10.5061/dryad.wpzgmsbpn.

The mitochondrial genome of the bioluminescent fish Malacosteusniger Ayres, 1848 (Stomiidae, Actinopterygii) is large and complex, and contains an inverted-repeat structure.

We determined the complete mitogenome sequence of the bioluminescent fish Malacosteusniger using long-read sequencing technologies. The 21,263 bp mitogenome features a complex structure with two copies of a 1198-bp inverted-repeat and a region of 2616-bp containing alternating copies of 16 and 26 bp repeat elements. Whole mitogenome phylogenies inferred from both nucleotide and amino-acid datasets place M.niger among Melanostomiinae. The need for additional complete mitogenome sequences from the subfamily Malacosteinae is discussed.

Description of the Three Complete Mitochondrial Genomes of Click Beetles (Coleoptera, Elateridae) with Phylogenetic Implications

The family Elateridae, known as click beetles, is a mega-diverse lineage of Coleoptera. Wireworms are the larval stage of click beetles, which are generalist herbivores and which are recognized as economically important pests of crops. To more effectively control and monitor wireworms, it is crucial to understand the genetics, taxonomy and phylogenetics of Elateridae. Here, we sequenced and characterized three complete mitochondrial genomes (mitogenomes) from the subfamily Elaterinae using a next-generation sequencing approach. In addition, we provided the annotated mitogenomes of the newly sequenced species, namely Parasilesis musculus (Candèze, 1873), Melanotus cribricollis Candèze, 1860 and Glyphonyx sp., and compared their arrangement with other closely related species. The secondary structures of tRNA genes and rRNA genes were predicted. Combined with the published mitogenomes of elaterid species, we reconstructed the phylogenetic framework for Elateridae under maximum likelihood and Bayesian inference methods using nucleotide and amino acid sequence datasets separately. The results from the Bayesian analysis based on the nucleotide dataset PCGRNA including all 37 mitochondrial genes were congruent with previous studies. Within the monophyletic Elateridae, two main clades were recovered. The first clade included Elaterinae and Melanotus. The second clade consisted of the remaining subfamilies. Physodactylinae and Cardiophorinae formed a sister group. Agrypninae was monophyletic. A subclade comprised Negastriinae and Dendrometrinae.

The Complete Mitochondrial Genome of the Hermit Crab Diogenes edwardsii (Anomura: Diogenidae) and Phylogenetic Relationships within Infraorder Anomura.

A complete mitochondrial genome (mitogenome) can provide important information for gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few mitogenomes of hermit crabs (superfamily Paguridae) in the infraorder Anomura have been reported. This study reports the first complete mitogenome of the hermit crab Diogenes edwardsii assembled using high-throughput sequencing. The mitogenome of Diogenes edwardsii is 19,858 bp in length and comprises 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. There are 28 and six genes observed on the heavy and light strands, respectively. The genome composition was highly A + T biased (72.16%), and exhibited a negative AT-skew (-0.110) and positive GC-skew (0.233). Phylogenetic analyses based on the nucleotide dataset of 16 Anomura species indicated that D. edwardsii was closest related to Clibanarius infraspinatus in the same family, Diogenidae. Positive selection analysis showed that two residues located in cox1 and cox2 were identified as positively selected sites with high BEB value (>95%), indicating that these two genes are under positive selection pressure. This is the first complete mitogenome of the genus Diogenes, and this finding helps us to represent a new genomic resource for hermit crab species and provide data for further evolutionary status of Diogenidae in Anomura.

Isolation, molecular characterization and first report of Dothiorella gregaria associated with fruit rot of walnuts of Jammu and Kashmir, India.

Walnuts are known for their high levels of antioxidants, which are linked to various health benefits. However, challenges related to distribution and storage, as well as the risk of fungal infections, can affect the quality of walnut kernels. Fungal pathogens from the Botryosphaeriaceae family, including Dothiorella species and Diplodia species, can damage fruit and reduce its antioxidant content. To comprehend the cause of fruit rot in walnuts, Dothiorella gregaria isolates were studied using polyphasic methods, including multiple gene sequences and morphological identification, as well as analysis of polyphenol content and pathogenicity. The walnuts kernels purchased from market places of Jammu and Kashmir (J&K), India were observed to be affected by Dothiorella gregaria species causing the quality detoriation and decrease in polyphenol content thus undeniably with decreased antioxidant properties. D. gregaria Infected walnut kernels were having some brown and black spots and some were having white mycelial growth and however, most samples were asymptomatic. Pathogenicity testing revealed that the pathogen was able to develop all the symptoms under experimental conditions and the reisolated pathogen was morphologically similar to D. gregaria. The samples infected with this pathogen showed considerable decrease in polyphenol content, 10.9±2.66 mgGAE/g (mean±standard deviation) thus decreased antioxidant quality as compared to the samples which showed zero incidence of this pathogen, 52.50±4.27 mgGAE/g (mean±standard deviation). Furthermore, the pathogen was studied using polyphasic approach involving morphological, molecular and phylogenetic analysis. Combined nucleotide dataset of nuclear ribosomal ITS and tef1-α revealed that Dothiorella gregaria (NY6) formed a clade with Dothiorlla iberica (MAEC33), Dothiorella sarmentorium (MAEC28) and Dothiorella iberica (CAA905) strains with 83% bootstrap support. Besides, we observed six nucleotide changes, four were insertions or deletions and two were substitutions in the 502-bp region of the ITS rRNA gene when we compared our isolate to the most equivalent sequences submitted to NCBI GenBank. This is the first report of Dothiorella gregaria affecting walnuts purchased from various markets in J&K, India, causing fruit rot in walnuts after harvest. Given that local farmers store and export walnuts, it could pose an emerging threat to their livelihood. Thus, creating post-harvesting interventions for D. gregaria and knowing more about the fruit rot in walnuts can be benefited from morphological and molecular identification using several gene loci, genetic variability in the ITS rRNA gene, and total phenol analysis.

Transcriptomic data recover a new superfamily-level phylogeny of Cucujiformia (Coleoptera, Polyphaga)

Cucujiformia, the largest taxon in the order Coleoptera, exhibits extraordinary morphological, ecological, and behavioral diversity. This infraorder is currently divided into seven superfamilies, but considerably incongruent relationships among superfamilies have been reported by recent phylogenomic studies. Here, we combined the 21 newly sequenced transcriptomes representing six superfamilies with nine previously published cucujiform genomes/transcriptomes to elucidate the phylogeny and evolution of Cucujiformia. The monophyly of each of five superfamilies were consistently supported by all phylogenetic analyses based on the twelve datasets (matrix occupancy, amino acid and nucleotide data) and the two analytical methods (maximum likelihood method and Bayesian inference). Both the amino acid datasets and the RY recoded nucleotide datasets recovered the monophyly of Cucujoidea. Topology test results statistically supported the following robust superfamily-level phylogeny in Cucujiformia: (Coccinelloidea, (Cleroidea, (Tenebrionoidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))). Our divergence time analyses recovered a Permian origin of Cucujiformia and a Jurassic–Cretaceous origin of most superfamilies. The diversification of phytophagous beetles that occurred in the Cretaceous can be attributed to its co-evolution with angiosperms, supporting the hypothesis of a Cretaceous Terrestrial Revolution.

Intraspecific variation in the mitochondrial genomes of the black carpet beetle, Attagenus unicolor japonicus Reitter (1877) (Coleoptera: Dermestidae)

Dermestid beetles are economically important pests of various stored products but their genetic studies remain insufficient on contrary to their diversity and importance. In this study, the complete mitochondrial genome (mitogenome) of the black carpet beetle, Attagenus unicolor japonicus Reitter 1877, was reported and compared with the previously sequenced one. The two A. unicolor japonicus mitogenomes had an identical set of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes as well as a large non-coding control region. The new mitogenome was longer than the previous one due to its longer control region. A total of 126 variable sites were detected between the new and previous mitogenomes and most of them were found in PCGs. Synonymous mutations in PCGs frequently occurred on the third codon positions and did not change most translated amino acids. The phylogenetic results based on both the nucleotide dataset and amino acid dataset corresponded with previous molecular studies at both generic and subfamilial levels and helped to determine the correct identity of two misidentified or unidentified dermestid species from GenBank and previous studies.

Mitochondrial phylogenomics reveals deep relationships of scarab beetles (Coleoptera, Scarabaeidae).

In this study, we newly sequenced the complete mitochondrial genomes (mitogenomes) of two phytophagous scarab beetles, and investigated the deep level relationships within Scarabaeidae combined with other published beetle mitogenome sequences. The complete mitogenomes of Dicronocephalus adamsi Pascoe (Cetoniinae) and Amphimallon sp. (Melolonthinae) are 15,563 bp and 17,433 bp in size, respectively. Both mitogenomes have the typical set of 37 genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) and an A+T-rich region, with the same gene arrangement found in the majority of beetles. The secondary structures for ribosomal RNA genes (rrnL and rrnS) were inferred by comparative analysis method. Results from phylogenetic analyses provide support for major lineages and current classification of Scarabaeidae. Amino acid data recovered Scarabaeidae as monophyletic. The Scarabaeidae was split into two clades. One clade contained the subfamilies Scarabaeinae and Aphodiinae. The other major clade contained the subfamilies Dynastinae, Rutelinae, Cetoniinae, Melolonthinae and Sericini. The monophyly of Scarabaeinae, Aphodiinae, Dynastinae, Cetoniinae and Sericini were strongly supported. The Scarabaeinae was the sister group of Aphodiinae. The Cetoniinae was sister to the Dynastinae + Rutelinae clade. The Melolonthinae was a non-monophyletic group. The removal of fast-evolving sites from nucleotide dataset using a pattern sorting method (OV-sorting) supported the family Scarabaeidae as a monophyletic group. At the tribe level, the Onthophagini was non-monophyletic with respect to Oniticellini. Ateuchini was sister to a large clade comprising the tribes Onthophagini, Oniticellini and Onitini. Eurysternini was a sister group of the Phanaeini + Ateuchini clade.

Characterization of the Complete Mitochondrial Genome of the Spotted Catfish Arius maculatus (Thunberg, 1792) and Its Phylogenetic Implications.

The spotted catfish, Arius maculatus (Siluriformes), is an important economical aquaculture species inhabiting the Indian Ocean, as well as the western Pacific Ocean. The bioinformatics data in previous studies about the phylogenetic reconstruction of Siluriformes were insufficient and incomplete. In the present study, we presented a newly sequenced A. maculatus mitochondrial genome (mtDNA). The A. maculatus mtDNA was 16,710 bp in length and contained two ribosomal RNA (rRNA) genes, thirteen protein-coding genes (PCGs), twenty-two transfer RNA (tRNA) genes, and one D-loop region. The composition and order of these above genes were similar to those found in most other vertebrates. The relative synonymous codon usage (RSCU) of the 13 PCGs in A. maculatus mtDNA was consistent with that of PCGs in other published Siluriformes mtDNA. Furthermore, the average non-synonymous/synonymous mutation ratio (Ka/Ks) analysis, based on the 13 PCGs of the four Ariidae species, showed a strong purifying selection. Additionally, phylogenetic analysis, according to 13 concatenated PCG nucleotide and amino acid datasets, showed that A. maculatus and Netuma thalassina (Netuma), Occidentarius platypogon (Occidentarius), and Bagre panamensis (Bagre) were clustered as sister clade. The complete mtDNA of A. maculatus provides a helpful dataset for research on the population structure and genetic diversity of Ariidae species.

Molecular phylogeny of selected dorid nudibranchs based on complete mitochondrial genome

Dorid nudibranchs are a large group of mollusks with approximately 2,000 recorded species. Although agreement exists on the monophyletic nature of the dorid nudibranch group, the interfamily relationships of the suborder are subject to debate. Despite efforts to elucidate this issue using short molecular markers, the conclusiveness of the findings has been hindered by branching polytomy. Mitogenomes are known to be effective markers for use in phylogenetic investigations. In this study, eight mitogenomes of dorid nudibranchs were decoded and analyzed. Gene content and structure showed little change among species, reflecting the conserved mitogenomes of dorid nudibranchs. For most genes, the direction was typical for nudibranchs; nevertheless, tRNACys had an inverse direction in Cadlinidae species. Phylogenetic trees based on nucleotide and amino acid datasets revealed a relatively consistent pattern of interfamily relationships with little difference for positions of Phyllidiidae and Cadlinidae. Species of Cadlinidae were clustered together and did not form a clade with Chromododidae. Additionally, Goniodorididae was sister to Aegiridae, whereas Discodoridae was sister to Dorididae. This finding was supported by tree topology test based on mitogenome data. The results of the present study indicate that complete mitogenomes are promising markers for investigating interfamily relationships among dorid nudibranchs.

Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes

Giant clams are conspicuous bivalves that inhabit in coral reefs. Among the giant clams, eight species of subfamily Tridacninae are the most common in the Asia-Pacific. However, very little is known about their evolutionary history. Here, we determined the complete mitochondria genome of Hippopus porcellanus, which was 29,434 bp in size and contained 13 protein-coding genes, 2 rRNAs and 23 tRNAs. The A+T composition of protein-coding regions was 57.99%, and the AT composition of the 3rd codon position was 59.33%, of which in agreement with the invertebrate bias favoring codons ending in A or T. Analysis of phylogenetic relationships according to the concatenated nucleotide data set containing 18S rRNA gene and 13 protein-coding genes, the phylogenetic relationship was analyzed by Maximum likelihood and Bayesian inference methods. The results showed that T. maxima was placed with the clade comprising T. noae, T. squamosa, and T. crocea, in which T. squamosa was highly similar to T. crocea and is consistent with the results of the previous studies using15 mitochondrial markers and nuclear 18S rRNA. Moreover, the inferred divergence time of Tridacnidae species is generally consistent with the fossil record of Tridacnidae. The divergence time of H. porcellanus and H. hippopus was about 10.64 Mya, this result is in agreement with the speculation that H. porcellanus also originated in Miocene. The availability of molecular phylogeny and divergence time estimation provides information genetic relationship of Tridacninae, which could be helpful to the ecological research and conservation of giant clams.

Systematics and evolution of predatory flower flies (Diptera: Syrphidae) based on exon‐capture sequencing

AbstractFlower flies (Diptera: Syrphidae) are one of the most species‐rich dipteran families and provide important ecosystem services such as pollination, biological control of pests, recycling of organic matter and redistributions of essential nutrients. Flower fly adults generally feed on pollen and nectar, but their larval feeding habits are strikingly diverse. In the present study, high‐throughput sequencing was used to capture and enrich phylogenetically and evolutionary informative exonic regions. With the help of thebaitfishersoftware, we developed a new bait kit (SYRPHIDAE1.0) to target 1945 CDS regions belonging to 1312 orthologous genes. This new bait kit was successfully used to exon capture the targeted loci in 121 flower fly species across the different subfamilies of Syrphidae. We analysed different amino acid and nucleotide data sets (1302 loci and 154 loci) with maximum likelihood and multispecies coalescent models. Our analyses yielded highly supported similar topologies, although the degree of the SRH (global stationarity, reversibility and homogeneity) conditions varied greatly between amino acid and nucleotide data sets. The sisterhood of subfamilies Pipizinae and Syrphinae is supported in all our analyses, confirming a common origin of taxa feeding on soft‐bodied arthropods. Based on our results, we define Syrphinistat.rev.to include the generaToxomerusandParagus. Our divergence estimate analyses withbeastinferred the origin of the Syrphidae in the Lower Cretaceous (125.5–98.5 Ma) and the diversification of predatory flower flies around the K–Pg boundary (70.61–54.4 Ma), coinciding with the rise and diversification of their prey.

Detection and genetic variation analysis of apple chlorotic leaf spot virus and apple stem grooving virus in wild apple (Malus sieversii) from Xinjiang, China

AbstractHere, we produced nucleotide and amino acid sequences of the movement protein (MP) and the coat protein (CP) genes of apple chlorotic leaf spot virus (ACLSV) and apple stem grooving virus (ASGV) from wild apple of Xinjiang, the main progenitor of the domesticated apple. Genetic variation and phylogenetics were assessed using these and previously reported sequences. Phylogenetic analysis of ACLSV nucleotide and amino acid data sets assigned some ACLSV variants to known groups and others to novel clades. In an MP‐based phylogenetic tree, ASGV sequences downloaded from GenBank and those of wild apple isolates were assigned to separate groups. A recombinant sequence was identified in a ACLSV variant (MS‐GL‐1‐c‐3) of wild apple, and both parents of the recombinant had been isolated from the same plant (GL). Two potential recombination events of ASGV (MS‐GL‐2‐g‐3 and MS‐NF‐1‐g‐3) were identified in this study. These findings may constitute a valuable basis for future studies on variability of virus genetics and pathogenicity.

The complete mitochondrial genome of Meloeproscarabaeus (Coleoptera, Meloidae): genome descriptions and phylogenetic inferences.

Oil beetles are meloids, which are characterised for their cleptoparasitic habits in bee nests and oily fluid of cantharidin that causes blistering and swelling of the skin. The complete mitochondrial genome of Meloeproscarabaeus is determined using the next-generation sequencing technology and its genomic characteristics are described. The 15,653-bp long genome is a circular molecule consisting of 13 protein-coding genes (PCG), 22 transport RNA, two ribosomal RNA, and a control region. The A + T bias of the mitochondrial genome is manifested in the complete sequence and the codon usage of protein-coding genes. The genetic distance within and between genera is calculated to confirm the taxonomic status of M.proscarabaeus. The phylogenetic relationships among 15 available meloid taxa are inferred by the maximum likelihood (ML) method based on 13 mitochondrial PCGs. The ML trees resulting from nucleotide and amino acid datasets recover both the monophyly of Meloe and Epicauta and the polyphyly comprising Hycleus and Mylabris. This study provides the first description of a mitochondrial genome belonging to the genus Meloe. The mitochondrial genome sequence and its characteristics are expected to be conducive to future studies on taxonomy, systematics, and molecular phylogenetics of the family Meloidae.

Chloroplast phylogenomics of unicellular and colonial Volvocales provides perspectives on the evolution of morphological characters

AbstractVolvocales forms a species‐rich clade with wide morphological variety and is regarded as an ideal model for tracing the evolutionary transitions in multicellularity. The phylogenetic relationships among the colonial volvocine algae and its relatives are important for investigating the origin of multicellularity in the clade Reinhardtinia. Therefore, a robust phylogenetic framework of the unicellular and colonial volvocine algae with broad taxon and gene sampling is essential for illuminating the evolution of multicellularity. Recent chloroplast phylogenomic studies have uncovered five major orders in the Chlorophyceae, but the family‐level relationships within Sphaeropleales and Volvocales remain elusive due to the uncertain positions of some incertae sedis taxa. In this study, we contributed six newly sequenced chloroplast genomes in the Volvocales and analyzed a dataset with 91 chlorophycean taxa and 58 protein‐coding genes. Conflicting phylogenetic signals were detected among chloroplast genes that resulted in discordant tree topologies among different analyses. We compared the phylogenetic trees inferred from original nucleotide, RY‐coding, codon‐degenerate, and amino acid datasets, and improved the robustness of phylogenetic inference in the Chlorophyceae by reducing base compositional bias. Our analyses indicate that the unicellular Chlamydomonas and Vitreochlamys are close to or nested within the colonial taxa, and all the incertae sedis taxa are nested within the monophyletic Sphaeropleales s.l. We propose that the colonial taxa in the Reinhardtinia are paraphyletic and multicellularity evolved once in the volvocine green algae and might be lost in Chlamydomonas and Vitreochlamys.

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics.

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.