Gene Arrangement Research Articles

High-Grade B-Cell Lymphoma with Effusion as the Initial presentation

Abstract Introduction/Objective Malignant effusion is usually caused by metastatic carcinoma. Lymphoma is often not included in the differential diagnoses. Here, we describe two cases of young females with no significant past medical history, presenting with fluid overload. Methods/Case Report The first case is a 41-year-old female with abdominal ascites and pleural effusion. Microscopic examination of the ascitic fluid showed intermediate to large lymphoid cells with irregular nuclear contours and fine chromatin. Flow cytometry showed CD10-positive lambda restricted B-cells. She had retropectoral mass biopsy showing sheets of intermediate to large-sized lymphoma cells with abundant apoptotic bodies and necrosis. The lymphoma cells are positive for CD20, CD10, BCL-2, BCL-6, and C-MYC (~50%,) while negative for TdT and cyclin D1. Proliferative index by Ki-67 stain is ~80%). Fluorescence in situ hybridization (FISH) analysis demonstrated rearrangements of BCL2/18q (80%) and MYC/8q (82%). The patient had a diagnosis of high-grade B-cell lymphoma with MYC and BCL-2 gene rearrangements. The second case is a 43-year-old woman with abdominal pain. She was diagnosed with acute cholecystitis and underwent cholecystectomy. Peritoneal fluid showed numerous neoplastic cells with irregular nuclei, prominent nucleoli, and cytoplasmic vacuoles. Flow cytometry demonstrated CD10-positive B-cells with lambda restriction. The cells were positive for CD10, CD20, BCL-2, BCL-6, and PAX5, and negative for CD34, cyclin D1, HHV-8, and TDT. EBER ISH was negative. The proliferation index by Ki67 stain was >90%. FISH studies showed MYC, BCL2 and BCL6 gene arrangements. Cytogenetic analysis revealed a complex karyotype. A diagnosis of HGBL with triple-hit rearrangements was rendered. Despite receiving aggressive chemotherapy, the patient expired 8.5 months after the diagnosis. Results (if a Case Study enter NA) NA. Conclusion HGBL is an aggressive and often stage IV disease. It should be considered in the differential diagnoses of malignant effusions. Flow cytometry and FISH analysis of the body fluid specimen are essential to reach an accurate diagnosis in a timely manner.

Mitogenome of a monotypic genus, Oliotius Kottelat, 2013 (Cypriniformes: Cyprinidae): Genomic characterization and phylogenetic position

We examined the evolutionary status of the genus Oliotius Kottelat, 2013, clarified the mitogenome structure of Smiliogastrinae, and analyzed its phylogenetic information to provide a reference for the taxonomy, evolutionary genetics, and germplasm identification of Smiliogastrinae. Using next-generation sequencing, the complete mitogenome sequence of the monotypic species Oliotius oligolepis was obtained, annotated, and characterized. The mitogenomic sequences of Smiliogastrinae fish were compared and analyzed, and a phylogenetic tree was constructed. The mitogenome of O. oligolepis was 16,636 base pairs long and contained 22 tRNAs, 13 protein-coding genes, 2 rRNAs, and 1 D-loop. The Smiliogastrinae species exhibited gene arrangement consistency, with slight differences in their genome lengths and compositions. Among the 13 protein-coding genes, ND3 showed the highest polymorphism rate and largest genetic distance. Our phylogenetic analysis showed that the target species O. oligolepis is closely related to Barbodes binotatus. The genus Oliotius is monotypic, and the genus Barbodes is not supported as a monophyletic group. This molecular information provides a foundation for further research on the phylogeny of the genera Oliotius and Barbodes and provides insight into the phylogenetic features of fishes belonging to Smiliogastrinae.

Complete Mitogenomes of Ticks Ixodes acutitarsus and Ixodes ovatus Parasitizing Giant Panda: Deep Insights into the Comparative Mitogenomic and Phylogenetic Relationship of Ixodidae Species.

Ticks rank second in the world as vectors of disease. Tick infestation is one of the factors threatening the health and survival of giant pandas. Here, we describe the mitogenomes of Ixodes acutitarsus and Ixodes ovatus parasitizing giant pandas, and perform comparative and phylogenetic genomic analyses on the newly sequenced and other available mitogenomes of hard ticks. All six newly determined mitogenomes contain a typical gene component and share an ancient Arthropoda gene arrangement pattern. Our study suggests that I. ovatus is a species complex with high genetic divergence, indicating that different clades of I. ovatus represent distinct species. Comparative mitogenomic analyses show that the average A + T content of Ixodidae mitogenomes is 78.08%, their GC-skews are strongly negative, while AT-skews fluctuate around 0. A large number of microsatellites are detected in Ixodidae mitogenomes, and the main microsatellite motifs are mononucleotide A and trinucleotide AAT. We summarize five gene arrangement types, and identify the trnY-COX1-trnS1-COX2-trnK-ATP8-ATP6-COX3-trnG fragment is the most conserved region, whereas the region near the control region is the rearrangement hotspot in Ixodidae mitogenomes. The phylogenetic trees based on 15 genes provide a very convincing relationship (Ixodes + (Robertsicus + ((Bothriocroton + Haemaphysalis) + (Amblyomma + (Dermacentor + (Rhipicentor + (Hyalomma + Rhipicephalus))))))) with very strong supports. Remarkably, Archaeocroton sphenodonti is embedded in the Haemaphysalis clade with strong supports, resulting in paraphyly of the Haemaphysalis genus, so in-depth morphological and molecular studies are essential to determine the taxonomic status of A. sphenodonti and its closely related species. Our results provide new insights into the molecular phylogeny and evolution of hard ticks, as well as basic data for population genetics assessment and efficient surveillance and control for the giant panda-infesting ticks.

Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum

Examination of the changes in order and arrangement of homologous genes is key for understanding the mechanisms of genome evolution in eukaryotes. Previous comparisons between eukaryotic genomes have revealed considerable conservation across species that diverged hundreds of millions of years ago (e.g., vertebrates,1,2,3 bilaterian animals,4,5 and filamentous fungi6). However, understanding how genome organization evolves within and between eukaryotic major lineages remains underexplored. We analyzed high-quality genomes of 120 representative budding yeast species (subphylum Saccharomycotina) spanning ∼400 million years of eukaryotic evolution to examine how their genome organization evolved and to compare it with the evolution of animal and plant genome organization.7 We found that the decay of both macrosynteny (the conservation of homologous chromosomes) and microsynteny (the conservation of local gene content and order) was strongly associated with evolutionary divergence across budding yeast major clades. However, although macrosynteny decayed very fast, within ∼100 million years, the microsynteny of many genes-especially genes in metabolic clusters (e.g., in the GAL gene cluster8)-was much more deeply conserved both within major clades and across the subphylum. We further found that when genomes with similar evolutionary divergence times were compared, budding yeasts had lower macrosynteny conservation than animals and filamentous fungi but higher conservation than angiosperms. In contrast, budding yeasts had levels of microsynteny conservation on par with mammals, whereas angiosperms exhibited very low conservation. Our results provide new insight into the tempo and mode of the evolution of gene and genome organization across an entire eukaryotic subphylum.

The complete mitochondrial genome of Numenius minutus (Charadriiformes: Scolopacidae): comparative and phylogenetic analysis

In this study, we used the next-generation sequencing method to obtain mitochondrial DNA (mtDNA) of Numenius minutus Gould 1841 in Scolopacidae, after which we analyzed the structure and phylogeny of the Charadriiformes. The complete mtDNA was 17,047 bp in length, and contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and one control region (CR). The gene structure and arrangement of the mitochondrial genome of 64 Charadriiformes species were basically the same as most birds. The reconstructed phylogenetic tree demonstrated that Numenius species were sister groups and monophyletic in Scolopacidae.

The complete mitochondrial genome of the zebra seabream Diplodus cervinus (Perciformes, Sparidae) from the Mediterranean Sea

The complete nucleotide sequence of the mitochondrial (mt) genome of the demersal zebra seabream Diplodus cervinus (Lowe, 1838) was determined for the first time. The double stranded circular molecule is 16,559 base pairs (bp) in length and encodes for the typical 37 metazoan mitochondrial genes, and 2 non-coding regions (D-loop and L-origin). The gene arrangement of the D. cervinus mt genome follows the usual one for fishes. The nucleotide sequences of the mt protein coding and ribosomal genes of D. cervinus mt genome were aligned with orthologous sequences from representatives of the Sparidae family and phylogenetic relationships were inferred. Maximum likelihood analyses placed D. cervinus as a sister species of Diplodus sargus (Linnaeus, 1758).

Identification of the exuviae of larva from Teinopalpus aureus Mell, 1923 using the complete mitochondrial genome

Teinopalpus aureus Mell (Lepidoptera: Papilionidae) is distributed throughout China, Vietnam and Laos, and is listed as a Class I species in China. To identify whether the exuviae of larva is belonging to Teinopalpus aureus Mell, 1923 or not, and to compare the gene structure and genetic differences among the known populations, ten mitogenomes of T. aureus from the exuviae of larva collected in the Michelia maudiae were sequenced. This method of sequencing the mitogenomes of exuviae of larva can give us the chance to monitor the conservation of rare butterflies. Ten mitogenomes of T. aureus showed typical gene arrangements and contained 13 protein-coding genes (PCGs), two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). The two haplotypes with one base different in T. aureus were found. We also conducted phylogenetic analyses including all different populations of T. aureus to assess the phylogenetic relationship of T. aureus. The lengths of the 12S rRNA and 16S rRNA genes from both haplotypes were 776 base pairs (bp) and 1,334 bp, respectively. The genetic distance of the ten samples was calculated as 0-0.000065 on the basis of the whole mitogenomes. T. aureus found in Taishun, Zhejiang province, China had a close phylogenetic relationship with the clade of T. aureus found in Pingshan, Jiangxi province, China, which was supported by neighbour-joining analysis.

The complete mitochondrial genome of the Arctic fairy shrimp Branchinectapaludosa (Müller, 1788) (Anostraca, Branchinectidae) from Sirius Passet, North Greenland.

Here we report the complete mitochondrial genome of the Arctic fairy shrimp, Branchinectapaludosa (Müller, 1788) (Anostraca, Branchinectidae), which was collected in the High Arctic of North Greenland. A complete 16,059 bp mitochondrion of B.paludosa was sequenced and assembled with the Illumina next generation sequencing platform. The B.paludosa mitogenome contains 13 PCGs, 22 tRNAs and 2 rRNA genes that are commonly observed in most metazoans and shows the conserved gene arrangement pattern of Anostraca. Our results of the phylogenomic analysis are consistent with the previous phylogenetic relationship, based on nuclear 18S ribosomal DNA. The B.paludosa mitogenome will be useful for understanding the geographical distribution and phylogenetic relationship of anostracans.

The complete mitochondrial genome of the woodwasp Euxiphydria potanini (Hymenoptera, Xiphydrioidea) and phylogenetic implications for symphytans

The long-necked woodwasp superfamily Xiphydrioidea belongs to the suborder Symphyta (Hymenoptera). Here we newly characterize the complete mitochondrial genome of the South Korean Euxiphydria potanini (Xiphydriidae) using next-generation sequencing: 16,500 bp long with 84.27% A + T content and 37 typical mitochondrial genes including those encoding 13 PCGs, 2 rRNAs, 22 tRNAs, and one A + T rich region. We compare the patterns of symphytan mitochondrial gene arrangement with those of an ancestral insect form and found some synapomorphic rearrangements in phylogenetic context. We use a variety of nucleotide and amino acid sequence alignments (thirteen mtPCGs and/or eight nDNAs) alongside step-by-step exclusions of long-branched taxa to elucidate the phylogenetic position of Xiphydrioidea and phylogenetic relationships among the seven symphytan superfamilies, except for Anaxyeloidea of which no mtgenome was available. The monophyly of symphytan superfamilies (with weak support for Pamphilioidea), sister-group relationship of Xiphydrioidea and Cephoidea, and Symphyta being paraphyletic to Apocrita, etc. are consistently supported by maximum likelihood and Bayesian inference trees. We also discuss the problematic phylogenetic positions of Orussoidea and Siricoidea and propose a hypothetical scenario of morphological character transition during hymenopteran evolution based on morphological key characteristics, such as the cenchrus and the wasp-waist.

New mitogenomes in deep-water endemic Cocculinida and Neomphalida shed light on lineage-specific gene orders in major gastropod clades

Gastropoda is the most speciose class in Mollusca, the second largest animal phylum. The internal relationships of major gastropod groups remain largely unsettled, partly due to the insufficient data from key deep-water endemic lineages such as the subclass Neomphaliones. Neomphaliones currently includes two orders: Cocculinida, best known from sunken wood habitats, and Neomphalida, best known from hydrothermal vents and often referred to as the “hot vent clade.” Phylogenetic controversy has also been observed in this subclass across different studies, requesting additional investigations. Here, we assembled nine new mitogenomes from two Cocculinida and seven Neomphalida species and analyzed them with published gastropod mitogenomes, with a particular focus on Neomphaliones. The phylogenetic reconstruction of Gastropoda based on 13 mitochondrial protein-coding genes resulted in a topology largely congruent with previous reconstructions based on morphological characters. Furthermore, we recovered characteristic mitochondrial gene order arrangements of Cocculinida and Neomphalida compared to the hypothetical ancestral gastropod gene order, at a level similar to other subclass-level clades. Divergence time estimation showed that Cocculinida and Neomphalida diverged approximately 322.68 million years ago. In addition to characteristic gene order arrangements for the clade, Cocculinida mitogenomes also exhibit some minor rearrangements even among congeners. Within Neomphalida, our tree adds support to monophyletic Peltospiridae and Neomphalidae, with unique gene arrangement recovered for each family. Our results offer new insights into the rearrangement of mitogenomes in Gastropoda, providing another clue to the evolutionary history of gastropods.

Complete mitochondrial genomes of Boigakraepelini and Hebiuscraspedogaster (Reptilia, Squamata, Colubridae) and their phylogenetic implications.

The complete sequence of the mitochondrial genome is a powerful tool for studying phylogenetic relationships and molecular evolution in various species. In this work, the mitogenomes of Boigakraepelini and Hebiuscraspedogaster were sequenced and characterized for the first time. The lengths of the B.kraepelini and H.craspedogaster mitogenomes were 17,124 bp and 17,120 bp, respectively, and both included 13 protein-coding genes, 22 tRNAs, two rRNAs and two control regions. The arrangements of these mitochondrial genes were the same in B.kraepelini and H.craspedogaster. In addition, both genome compositions showed A+T bias (59.03%, 60.93%) and had positive AT skews (0.179, 0.117) and negative GC skews (-0.397, -0.348). The phylogenetic results illustrated a close relationship between B.kraepelini and the genus Lycodon. Moreover, H.craspedogaster was clustered with other Hebius snakes and closely related to other Natricinae species. These results will provide references for further research on the phylogeny of Colubridae.

Evolution of Gene Arrangements in the Mitogenomes of Ensifera and Characterization of the Complete Mitogenome of Schizodactylus jimo.

Gene arrangement (relative location of genes) is another evolutionary marker of the mitogenome that can provide extensive information on the evolutionary mechanism. To explore the evolution of gene arrangements in the mitogenome of diversified Ensifera, we sequenced the mitogenome of the unique dune cricket species found in China and used it for phylogenetic analysis, in combination with 84 known Ensiferan mitogenomes. The mitogenome of Schizodactylus jimo is a 16,428-bp circular molecule that contains 37 genes. We identified eight types of gene arrangement in the 85 ensiferan mitogenomes. The gene location changes (i.e., gene translocation and duplication) were in three gene blocks: I-Q-M-ND2, rrnl-rns-V, and ND3-A-R-N-S-E-F. From the phylogenetic tree, we found that Schizodactylus jimo and most other species share a typical and ancient gene arrangement type (Type I), while Grylloidea has two types (Types II and III), and the other five types are rare and scattered in the phylogenetic tree. We deduced that the tandem replication–random loss model is the evolutionary mechanism of gene arrangements in Ensifera. Selection pressure analysis revealed that purifying selection dominated the evolution of the ensiferan mitochondrial genome. This study suggests that most gene rearrangements in the ensiferan mitogenome are rare accidental events.

Mitogenomic Comparison of the Mole Crickets Gryllotalpidae with the Phylogenetic Implications (Orthoptera: Ensifera).

Simple SummaryWe sequenced the complete mitochondrial genomes (mitogenomes) of Gryllotalpa henana Cai & Niu, 1998 and the Chinese G. orientalis Burmeister, 1838 for the first time, and reconstructed the mitogenomic phylogeny of the infraorder Gryllidea. The results show that the two new mitogenomes are double-stranded circular molecules with a typical gene complement, gene arrangement and base composition, the same as those of other gryllotalpids and ancestral insects. Tandem repeats of the control region were discovered in Gryllotalpidae for the first time. Considering both the high nucleotide divergence and the elevated ratio of Ka/Ks, the genes nad2 and nad6 may be evaluated as potential markers for future phylogeny and species delimitation in Gryllotalpidae. The results of phylogenetic analyses provide supports for the mitogenomic and transcriptomic trees, but partially contradict those of the multilocus phylogenies.Owing to limited molecular data, the phylogenetic position of the family Gryllotalpidae is still controversial in the infraorder Gryllidea. Mitochondrial genome (mitogenome) plays a crucial role in reconstructing phylogenetic relationships and revealing the molecular evolution of insects. However, only four mitogenomes have been reported in Gryllotalpidae to date. Herein, we obtained the first mitogenomes of Gryllotalpa henana Cai & Niu, 1998 and the Chinese G. orientalis Burmeister, 1838, made a detailed comparison of all mitogenomes available in Gryllotalpidae and reconstructed the phylogeny of Gryllidea based on mitogenomes using Bayesian inference (BI) and maximum likelihood (ML) methods. The results show that the complete mitogenome sequences of G. henana (15,504 bp) and G. orientalis (15,497 bp) are conserved, both exhibiting the double-stranded circular structure, typical gene content and the ancestral insect gene arrangement. The complete mitogenome of G. henana exhibits the lowest average AT content ever detected in Gryllotalpidae, and even Gryllidea. The gene nad2 of both species has atypical initiation codon GTG. All tRNAs exhibit typical clover-leaf structure, except for trnS1 lacking the dihydrouridine (DHU) arm. A potential stem–loop structure, containing a (T)n(TC)2(T)n sequence, is detected in the control region of all gryllotalpids investigated and is likely related to the replication initiation of the minority strand. The phylogenetic analyses recover the six families of Gryllidea as Gryllotalpidae + (Myrmecophilidae + (Mogoplistidae + (Trigonidiidae + (Phalangopsidae + Gryllidae)))), similar to the trees based on transcriptomic and mitogenomic data. However, the trees are slightly different from the multilocus phylogenies, which show the sister-group relationship of Gryllotalpidae and Myrmecophilidae. The contradictions between mitogenomic and multilocus trees are briefly discussed.

Draft genome and multi-tissuetranscriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana.

Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.

Complete Mitogenome of Cruznema Tripartitum Confirms Highly Conserved Gene Arrangement within Family Rhabditidae.

Mitochondrial genomes have widely been used as molecular markers in understanding the patterns and processes of nematode evolution. The species in genus Cruznema are free-living bacterivores as well as parasites of crickets and mollusks. The complete mitochondrial genome of C. tripartitum was determined through high-throughput sequencing as the first sequenced representative of the genus Cruznema. The genome is comprised of 14,067 bp nucleotides, and includes 12 protein-coding, two rRNA, and 22 tRNA genes. Phylogenetic analyses based on amino acid data support C. tripartitum as a sister to the clade containing Caenorhabditis elegans and Oscheius chongmingensis. The analysis of gene arrangement suggested that C. tripartitum shares the same gene order with O. chongmingensis, Litoditis marina, Diplocapter coronatus, genus Caenorhabditis, and Pristionchus pacificus. Thus, the mitochondrial gene arrangement is highly conserved in the family Rhabditidae as well as some species in Diplogasteridae.

Genome-wide identification, evolutionary analysis, and antimicrobial activity prediction of CC chemokines in allotetraploid common carp, Cyprinus carpio

Chemokines are a group of secreted small molecules which are essential for cell migration in physiological and pathological conditions by binding to specific chemokine receptors. They are structurally classified into five groups, namely CXC, CC, CX3C, XC and CX. CC chemokine group is the largest one among them. In this study, we identified and characterized 61 CC chemokines from allotetraploid common carp (Cyprinus carpio). The sequence analyses showed that the majority of CC chemokines had an N-terminal signal peptide, and an SCY domain, and all CC chemokines were located in the extracellular region. Phylogenetic, evolutionary and syntenic analyses confirmed that CC chemokines were annotated as 11 different types (CCL19, CCL20, CCL25, CCL27, CCL32, CCL33, CCL34, CCL35, CCL36, CCL39, and CCL44), which exhibited unique gene arrangement pattern and chromosomal location respectively. Furthermore, genome synteny analyses between common carp and four representative teleost species indicated expansion of common carp CC chemokines resulted from the whole genome duplication (WGD) event. Additionally, the continuous evolution of gene CCL25s in teleost afforded a novel viewpoint to explain the WGD event in teleost. Then, we predicted the three-dimensional structures and probable function regions of common carp CC chemokines. All the CC chemokines core structures were constituted of an N-loop, a three-stranded β-sheet, and a C-terminal helix. Finally, 43 CC chemokines were predicted to have probable general antimicrobial activity. Their tertiary structures, cationic and amphiphilic physicochemical property supported the viewpoint. To verify the prediction, six recombinant CCL19s proteins were prepared and the antibacterial activity against Escherichia coli and Aeromonas hydrophila were verified. The results supported our prediction that rCCL19a.1s (rCCL19a.1_a, rCCL19a.1_b) and rCCL19bs (rCCL19b_a, rCCL19b_b), especially rCCL19bs, exhibited extremely significant inhibition to the growth of both E. coli and A. hydrophila. On the contrary, two rCCL19a.2s had no significant inhibitory effect. These studies suggested that CC chemokines were essential in immune system evolution and not monofunctional during pathogen infection.

The Complete Mitochondrial Genome of Spirobolus bungii (Diplopoda, Spirobolidae): The First Sequence for the Genus Spirobolus.

Millipedes (Diplopoda) comprise one of the most important groups of large soil arthropods in terrestrial ecosystems; however, their phylogenetic relationships are poorly understood. Herein, the mitochondrial genome (mitogenome) of Spirobolus bungii was sequenced and annotated, which was 14,879 bp in size and included 37 typical mitochondrial genes (13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs)). Most of the 13 PCGs had ATN (AT/A/T/G) as the start codon except for COX1, which used CGA, and most PCGs ended with the T end codon. By comparing the gene arrangements of the mitogenomes among Diplopoda species, rearrangement occurred between and within orders. In contrast to Narceus annularus, the mitogenome genes of S. bungii had consistent orders but were transcribed in completely opposite directions, which was a novel finding in Spirobolidae. Moreover, the phylogenetic relationships within Diplopoda, which were based on the sequences of 13 PCGs, showed that S. bungii was clustered with N. annularus, followed by Abacion magmun. This indicated that there might be a close relationship between Callipodida and Spirobolida. These results could contribute to further studies on the genetics and evolutionary processes of S. bungii and other Diplopoda species.

Study on the Chinese Subfamily Anabropsinae (Orthoptera: Anostostomatidae) VI: One new species of Anabropsis (Pteranabropsis) from Yunnan Province.

This paper is sixth study the Chinese Anabropsinae and reports one new species from Yunnan Province, China, viz. A. (Pteranabropsis) maguanensis sp. nov. (Chinese name: ). Meanwhile, the complete mitochondrical genome of the new species was determined and annotated. The 15, 962 bp circle genome consisted of 13 protein-coding, 22 transfer RNA, 2 ribosomal RNA genes, and an A+T-rich region. It has the typical invertebrate mitochondrial gene arrangement. All protein-coding genes (PCGs) were initiated by typical ATN codon. The nucleotide compositions were significant bias towards AT. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except trnS1 in which the base pairs of the dihydrouridine (DHU) arm was lacking. Overall, six domains and 49 helices were predicted for rrnL, and three structural domains and 27 helices were predicted for rrnS.

Comparative Mitogenomic Analyses of Hydropsychidae Revealing the Novel Rearrangement of Protein-Coding Gene and tRNA (Trichoptera: Annulipalpia).

Simple SummaryThe evolution of insect mitochondrial gene rearrangement is a hot topic, and such rearrangements are common in certain insect orders. Gene rearrangement characteristics can also provide effective information for phylogenetic reconstruction. As one of the most diverse families within Annulipalpia, Hydropsychidae Curtis, 1835 is distributed on all continents except Antarctica. Here, we generated 19 novel mitogenomes of hydropsychid species, and found two new mitochondrial gene rearrangements. Coupled with published mitogenomes of Hydropsychidae, we analyzed the main features of the mitogenomes among subfamilies and the possible evolution processes. The rearrangement of protein-coding genes is reported in the Hydropsychidae for the first time, and it can be explained by the tandem duplication/random loss model. Phylogenetic analyses show that the four monophyletic subfamilies (Arctopscychinae, Diplectroninae, Hydropsychinae, Macronematinae) were strongly supported by mitogenomes.Gene rearrangement of the mitochondrial genome of insects, especially the rearrangement of protein-coding genes, has long been a hot topic for entomologists. Although mitochondrial gene rearrangement is common within Annulipalpia, protein-coding gene rearrangement is relatively rare. As the largest family in Annulipalpia, the available mitogenomes from Hydropsychidae Curtis, 1835 are scarce, and thus restrict our interpretation of the mitogenome characteristic. In this study, we obtained 19 novel mitogenomes of Hydropsychidae, of which the mitogenomes of the genus Arctopsyche are published for the first time. Coupled with published hydropsychid mitogenome, we analyzed the nucleotide composition evolutionary rates and gene rearrangements of the mitogenomes among subfamilies. As a result, we found two novel gene rearrangement patterns within Hydropsychidae, including rearrangement of protein-coding genes. Meanwhile, our results consider that the protein-coding gene arrangement of Potamyia can be interpreted by the tandem duplication/random loss (TDRL) model. In addition, the phylogenetic relationships within Hydropsychidae constructed by two strategies (Bayesian inference and maximum likelihood) strongly support the monophyly of Arctopscychinae, Diplectroninae, Hydropsychinae, and Macronematinae. Our study provides new insights into the mechanisms and patterns of mitogenome rearrangements in Hydropsychidae.

Complete mitochondrial genome of freshwater pearl mussel Lamellidens marginalis (Lamarck, 1819) and its phylogenetic relation within unionidae family.

Freshwater mussels play a key role in ecology and are often considered as ecological indicators. Conversely, these molluscs are one of the most threatened groups due to several anthropogenic factors. Knowledge of phylogenetic diversity would assist in formulating effective management and conservation measures. Lamellidens marginalis is one of the most widely used freshwater mussel for pearl production in India. The genomic resources for investigating its evolutionary relationship within the Unionidae family are lacking. In this study, the f-type mitochondrial genome of L. marginalis was sequenced using the Illumina sequencing platform. The length of the mitochondrial genome was 15,732bp consisting of 23 tRNAs, 2 rRNAs and 13 protein coding genes. The arrangement of genes was UF1 type and gene overlap was observed between trnG and nad1. Comparative analysis with other Unionidae species showed a high divergence rate in nad6 followed by nad2 atp8 and nad5. The phylogenetic tree supported monophyly of the Unioninae subfamily and L. marginalis (Parreysiinae) formed a sister branch to this subfamily. The divergence time of the Parreysiinae from its most recent common ancestor (MRCA) was placed in the Mesozoic era. This information will be useful for the understanding the evolutionary pattern of the species of Parreysiinae subfamily.