Multigene phylogenetic analyses including diverse radiolarian species support the “Retaria” hypothesis — The sister relationship of Radiolaria and Foraminifera

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

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Mitochondrial DNA dataset suggest that the genus Sphaerirostris Golvan, 1956 is a synonym of the genus Centrorhynchus Lühe, 1911

Parasitology ◽

10.1017/s0031182020000906 ◽

2020 ◽

Vol 147 (10) ◽

pp. 1149-1157 ◽

Cited By ~ 1

Author(s):

Nehaz Muhammad ◽

Suleman ◽

Munawar Saleem Ahmad ◽

Liang Li ◽

Qing Zhao ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Systematic Position ◽

Likelihood Methods ◽

Sister Relationship ◽

Protein Coding ◽

Maximum Likelihood Methods ◽

Relationship Of ◽

First Time ◽

Mt Genome ◽

Rna Genes

AbstractOur present genetic data of Acanthocephala, especially the mitochondrial (mt) genomes, remains very limited. In the present study, the nearly complete mt genome sequences of Sphaerirostris lanceoides (Petrochenko, 1949) was sequenced and determined for the first time based on specimens collected from the Indian pond heron Ardeola grayii (Sykes) (Ciconiiformes: Ardeidae) in Pakistan. The mt genome of S. lanceoides is 13 478 bp in size and contains 36 genes, including 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Moreover, in order to clarify the phylogenetic relationship of the genera Centrorhynchus and Sphaerirostris, and to test the systematic position of S. lanceoides in the Centrorhynchidae, the phylogenetic analyses were performed using Bayesian inference and maximum likelihood methods, based on concatenated nucleotide sequences of 12 PCGs, rRNAs and tRNAs. The phylogenetic results further confirmed the monophyly of the order Polymorphida and the paraphyly of the order Echinorhynchida in the class Palaeacanthocephala. Our results also challenged the validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) and showed a sister relationship between S. lanceoides and S. picae (Rudolphi, 1819).

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Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

Plants ◽

10.3390/plants9091116 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1116 ◽

Cited By ~ 1

Author(s):

Xue-Li Zhao ◽

Zhang-Ming Zhu

Keyword(s):

Phylogenetic Analyses ◽

Evolutionary Process ◽

Rrna Genes ◽

Trna Genes ◽

Sister Relationship ◽

Protein Coding ◽

Variable Regions ◽

Chloroplast Genomes ◽

Distinct Genus ◽

Relationship Of

Taxonomic and phylogenetic relationships of Christia, Urariopsis, Uraria and related genera within the tribe Desmodieae (Fabaceae: Papilionoideae) have long been controversial. Here, we report the complete chloroplast (cp) genomes of Christia vespertilionis and Urariopsis brevissima and perform comparative and phylogenetic analyses with Uraria lagopodioides and other relatives in the Desmodieae. The cp genomes of C. vespertilionis and U. brevissima are 149,656 and 149,930 bp long, with 128 unique genes (83 protein-coding genes, 37 tRNA genes and 8 rRNA genes), respectively. Comparative analyses revealed 95-129 simple sequence repeats (SSRs) and eleven highly variable regions (trnK-rbcL, rbcL-atpB, ndhJ-trnF, trnL-trnT, psbD-rpoB, accD-cemA, petA-psbL, psbE-petL, rps11-rps19, ndhF-ccsA, and rps15-ycf1) among six Desmodieae species. Phylogenetic analyses clearly resolved two subtribes (Desmodiinae and Lespedezinae) of Desmodieae as monophyletic, and the newly reported C. vespertilionis and U. brevissima clustered in subtribe Desmodiinae. A sister relationship of C. vespertilionis to U. lagopodioides was supported. Evidence was presented to support the treatment of Urariopsis as a distinct genus rather than in synonymy with Uraria. The results provide valuable information for further studies on species delimitation, phylogenetics, population genetics, and the evolutionary process of speciation in the Desmodieae.

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The mitochondrial genomes of two walnut pests, Gastrolina depressa depressa and G. depressa thoracica (Coleoptera: Chrysomelidae), and phylogenetic analyses

PeerJ ◽

10.7717/peerj.4919 ◽

2018 ◽

Vol 6 ◽

pp. e4919 ◽

Cited By ~ 6

Author(s):

Qiqi Wang ◽

Guanghui Tang

Keyword(s):

Sanger Sequencing ◽

Insect Pests ◽

Phylogenetic Analyses ◽

Mitochondrial Genomes ◽

Sequencing Technology ◽

Sister Relationship ◽

Protein Coding ◽

Protein Coding Genes ◽

Genomic Analyses ◽

Relationship Of

In this study, the mitochondrial genomes (mitogenomes) of two walnut leaf insect pests, Gastrolina depressa depressa and G. depressa thoracica, were sequenced by Sanger sequencing technology. The mitogenome of G. depressa thoracica was complete at 16,109 bp in length, while the mitogenome of G. depressa depressa (14,277 bp) was partial. The genomic analyses indicated that both mitogenomes have the typical gene content and arrangement. The formerly identified elements, ‘TAGTA’ between trnSer(UCN) and nad2, and ‘ATGATAA’ between atp8 and atp6, were more conserved than that between nad4L and nad4, which was ‘ATGTTAA’ in Coleoptera excluding Polyphaga. Phylogenetic analyses of the 13 protein-coding genes from 36 coleopteran species well supported a close affinity between the subfamily Chrysomelinae including G. depressa thoracica and G. depressa depressa and Galerucinae, as well as a sister relationship of ((Eumolpinae + Cryptocephalinae) + Cassidinae) within Chrysomelidae.

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Pollen morphology of Ellisiophyllum and Sibthorpia (Plantaginaceae, tribe Sibthorpieae) and phylogenetics of the tribe

Plant Systematics and Evolution ◽

10.1007/s00606-021-01786-9 ◽

2021 ◽

Vol 307 (6) ◽

Author(s):

Dirk C. Albach ◽

Zoya M. Tsymbalyuk ◽

Sergei L. Mosyakin

Keyword(s):

Pollen Morphology ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Pollen Grains ◽

Pollen Type ◽

Sister Relationship ◽

Exine Sculpture ◽

Molecular Phylogenetic ◽

Type 3 ◽

Relationship Of

AbstractPollen morphology of six species belonging to genera Ellisiophyllum and Sibthorpia (Plantaginaceae tribe Sibthorpieae) was studied using light and scanning electron microscopy. The data were analyzed in the light of the first phylogenetic analysis including all but one species of the tribe using DNA sequence data from nuclear ribosomal (ITS) and plastid trnL-F region. Pollen grains in representatives of this tribe are 3-colpate, occasionally 3-porate, suboblate to prolate; mainly medium-sized, rarely small. One major pollen type (3-colpate) is recognized in the tribe. Within this pollen type, six subtypes are distinguished based on their exine sculpture, pollen grain size, length of the apertures, and exine thickness. The obtained results confirm that pollen characters are useful for species identification. Palynomorphological data are consistent with the results of the molecular phylogenetic analyses. All studies support a sister relationship of the widespread European Sibthorpia europaea with the widespread South American Sibthorpia repens and a sister relationship of two insular species, the Balearic Sibthorpia africana and the Madeiran Sibthorpia peregrina. Pollen grains in the tribe Sibthorpieae have both reticulate exine sculpture characteristic for representatives of the Russelieae–Cheloneae–Antirrhineae clades of Plantaginaceae, and also nanoechinate sculpture, which is typical for the Veroniceae and Plantagineae clades of that family. Also, in Sibthorpia repens, we observe a possible transition from the colpate type to the porate type typical for taxa of Plantago and Littorella.

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The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

Scientific Reports ◽

10.1038/s41598-019-57065-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Vikas Kumar ◽

Kaomud Tyagi ◽

Rajasree Chakraborty ◽

Priya Prasad ◽

Shantanu Kundu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Start Codon ◽

Gene Arrangement ◽

Sister Relationship ◽

Protein Coding ◽

Relationship Of ◽

Rna Genes ◽

Boundary Mapping ◽

Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

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The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽

10.1093/genetics/146.3.995 ◽

1997 ◽

Vol 146 (3) ◽

pp. 995-1010 ◽

Cited By ~ 1

Author(s):

Rafael Zardoya ◽

Axel Meyer

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Large Data ◽

Molecular Data ◽

Phylogenetic Position ◽

Data Set ◽

Living Fossil ◽

Latimeria Chalumnae ◽

Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

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Phylogenetic analysis of the caspase family in bivalves: implications for programmed cell death, immune response and development

BMC Genomics ◽

10.1186/s12864-021-07380-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Susanne Vogeler ◽

Stefano Carboni ◽

Xiaoxu Li ◽

Alyssa Joyce

Keyword(s):

Immune Response ◽

Caspase 3 ◽

Developmental Stages ◽

Phylogenetic Analyses ◽

Apoptotic Pathway ◽

Caspase Family ◽

Executioner Caspases ◽

And Function ◽

Relationship Of ◽

Inflammatory Caspases

Abstract Background Apoptosis is an important process for an organism’s innate immune system to respond to pathogens, while also allowing for cell differentiation and other essential life functions. Caspases are one of the key protease enzymes involved in the apoptotic process, however there is currently a very limited understanding of bivalve caspase diversity and function. Results In this work, we investigated the presence of caspase homologues using a combination of bioinformatics and phylogenetic analyses. We blasted the Crassostrea gigas genome for caspase homologues and identified 35 potential homologues in the addition to the already cloned 23 bivalve caspases. As such, we present information about the phylogenetic relationship of all identified bivalve caspases in relation to their homology to well-established vertebrate and invertebrate caspases. Our results reveal unexpected novelty and complexity in the bivalve caspase family. Notably, we were unable to identify direct homologues to the initiator caspase-9, a key-caspase in the vertebrate apoptotic pathway, inflammatory caspases (caspase-1, − 4 or − 5) or executioner caspases-3, − 6, − 7. We also explored the fact that bivalves appear to possess several unique homologues to the initiator caspase groups − 2 and − 8. Large expansions of caspase-3 like homologues (caspase-3A-C), caspase-3/7 group and caspase-3/7-like homologues were also identified, suggesting unusual roles of caspases with direct implications for our understanding of immune response in relation to common bivalve diseases. Furthermore, we assessed the gene expression of two initiator (Cg2A, Cg8B) and four executioner caspases (Cg3A, Cg3B, Cg3C, Cg3/7) in C. gigas late-larval development and during metamorphosis, indicating that caspase expression varies across the different developmental stages. Conclusion Our analysis provides the first overview of caspases across different bivalve species with essential new insights into caspase diversity, knowledge that can be used for further investigations into immune response to pathogens or regulation of developmental processes.

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A description of the second species of the genus Bleptus Eaton, 1885 (Ephemeroptera: Heptageniidae) from Japan, and phylogenetic relationships of two Bleptus mayflies inferred from mitochondrial and nuclear gene sequences

Zootaxa ◽

10.11646/zootaxa.4974.2.5 ◽

2021 ◽

Vol 4974 (2) ◽

pp. 333-360

Author(s):

KOJI TOJO ◽

KEN MIYAIRI ◽

YUTO KATO ◽

AYANA SAKANO ◽

TOMOYA SUZUKI

Keyword(s):

Phylogenetic Analyses ◽

Ribosomal Subunit ◽

Nuclear Gene ◽

Taxonomic Status ◽

16S Rrna Genes ◽

Rrna Genes ◽

Gene Sequences ◽

Molecular Phylogenetic ◽

Black Band ◽

Relationship Of

A new mayfly species, Bleptus michinokuensis sp. nov. (Ephemeroptera: Heptageniidae) is described on the basis of specimens of male and female adults and mature nymphs collected at a seepage zone of a small freshwater branch of the ‘Tachiya-zawa-gawa’ River located amongst the northern foothills of Mt. Gassan (Shonai-machi Town, Yamagata Prefecture, Japan). This new Bleptus species is characterized by its clear fore and hind wings. That is, they neither exhibit the distinct black band on the fore wings, nor the characteristic darkened margins along the edges of both the fore and hind wings. Rather it has a blackish colored terminal half of its fore legs (i.e., tibial, tarsal and pretarsal segments). These features differ clearly when comparing them to the other known species, Bleptus fasciatus Eaton. The information and data describing the habitat and distribution range of this new species are also noted. We also examined and discussed the genetic relationship of two Bleptus mayflies to settle the taxonomic status, inferred from the partially sequenced cytochrome c oxidase subunit I (COI) and large mitochondrial ribosomal subunit (16S rRNA) genes, and also the nuclear internal transcribed spacer 2 (ITS2) gene sequences. Consequently, phenetic and molecular phylogenetic analyses agreed well in terms of clustering.

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Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

Systematic Botany ◽

10.1600/036364421x16312067913318 ◽

2021 ◽

Author(s):

Sara Fuentes-Soriano ◽

Elizabeth A. Kellogg

Keyword(s):

Sequence Data ◽

Plastid Dna ◽

Sister Relationship ◽

Data Set ◽

Woody Perennial ◽

History Of ◽

Nuclear Its ◽

Phylogenetic Framework ◽

Phylogenetic Hypotheses ◽

Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

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