scholarly journals Identification and Phylogenetic Analysis of Entomopathogenic Fungal Isolates Using Molecular Approach

Elkawnie ◽  
2020 ◽  
Vol 6 (2) ◽  
pp. 359
Author(s):  
Syaukani Syaukani ◽  
Zulia Ananda ◽  
Suhartono Suhartono ◽  
Sirtina Sirtina ◽  
Oviana Lisa ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Aspergillus Fumigatus ◽  
Entomopathogenic Fungi ◽  
Phylogenetic Trees ◽  
Pcr Amplification ◽  
Penicillium Oxalicum ◽  
Its Rdna ◽  
Molecular Approach ◽  
Relationship Of ◽  
The Relationship

Abstract: Entomopathogenic fungi are essential to consider as one of the biological agents to control termite populations. This research aimed to molecularly identify entomopathogenic fungi isolates in termites based on the ITS rDNA region and to determine the relationship of fungi isolates. Identification was performed by DNA extraction, PCR amplification, electrophoresis, purification, and sequencing. Phylogenetic trees were generated using MEGA X.  Molecular identification showed that the ISO1 sample was Penicillium oxalicum, the ISO2 sample was Trichoderma ghanense the ISO3 sample was Aspergillus niger, the ISO4 sample was Aspergillus fumigatus and the ISO5 sample was Aspergillus pseudonomius. The phylogenetic tree showed that the ISO1, ISO2, ISO3, ISO4, and ISO5 samples had the closest relationship with Penicillium oxalicum strain FR6-CGR12, Trichoderma ghanense isolate TM2, Aspergillus niger isolate 77, Aspergillus fumigatus, and Aspergillus pseudonomius strain DTO 267D6, respectively.Abstrak: Kelimpahan jenis fungi entomopatogen adalah hal yang terpenting untuk dipertimbangkan sebagai agen hayati bagi populasi rayap.Penelitian ini bertujuan untuk mengidentifikasi secara molekular isolat fungi entomopatogen pada rayap, berdasarkan daerah ITS rDNA dan mengetahui hubungan kekerabatan dari isolat fungi tersebut. Identifikasi dilakukan dengan cara ekstraksi DNA, amplifikasi menggunakan PCR, elektroforesis, purifikasi dan sekuensing. Selanjutnya kontruksi pohon filogenetik menggunakan aplikasi MEGA X. Berdasarkan uji molekular menunjukkan bahwa sampel ISO1 merupakan Penicillium oxalicum.ISO2 merupakan Trichoderma ghanense.ISO3 merupakan Aspergillus niger. ISO4 merupakan Aspergillus fumigatus.ISO5 merupakan Aspergillus pseudonomius.Konstruksi pohon filogenetik menunjukkan bahwa, sampel ISO1 berkerabat dekat dengan Penicillium oxalicum strain FR6-CGR12. Sampel ISO2 berkerabat dekat dengan Trichoderma ghanense isolat TM2. Sampel ISO3 berkerabat dekat dengan Aspergillus nigerisolat 77. Sampel ISO4 berkerabat dekat dengan Aspergillus fumigatus.Sampel ISO5 berkerabat dekat dengan Aspergillus pseudonomius strain DTO 267D6.

scholarly journals Comparative genomics of Parolsenella catena and Libanicoccus massiliensis: Reclassification of Libanicoccus massiliensis as Parolsenella massiliensis comb. nov.

2019 ◽  
Vol 69 (4) ◽  
pp. 1123-1129 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Nao Ikeyama ◽  
Takumi Murakami ◽  
Hiroshi Mori ◽  
Masahiro Yuki ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Single Copy ◽  
Content Type ◽  
Monophyletic Cluster ◽  
Link Type ◽  
Relationship Of ◽  
High Degree ◽  
The Relationship

Previous analyses based on 16S rRNA and hsp60 genes indicated that Parolsenella catena and Libanicoccus massiliensis were closely related to each other and formed a monophyletic cluster independent of the related Olsenella species. To clarify the relationship of these two species, we determined the genome sequence of P. catena JCM 31932T and compared it with that already sequenced for L. massiliensis Marseille-P3237T. Phylogenetic trees based on the concatenated 37 single-copy ribosomal proteins or RpoB robustly supported the relationship observed in the previous studies. Digital DNA–DNA hybridization and average nucleotide identity (ANI) values between P. catena JCM 31932T and L. massiliensis Marseille-P3237T were 32.6 and 87.8 %, respectively, indicating that P. catena JCM 31932T and L. massiliensis Marseille-P3237T are independent species. Alignment fraction and ANI values between the two genomes were 0.75 and 88.84 %, respectively, thus indicating that the two species should be classified into the same genus. The number of putative orthologous genes shared between the two genomes was 1321, which was significantly larger than those (482–928) reported between L. massiliensis Marseille-P3237T and other closely related species. In addition, the genome of P. catena JCM 31932T had a high degree of synteny conservation with that of L. massiliensis Marseille-P3237T. On the basis of these findings, we propose that L. massiliensis should be reclassified as Parolsenella massiliensis comb. nov.; the type strain is Marseille-P3237T (=JCM 33000T=CCUG 71182T).

scholarly journals Changing ideas about eukaryotic origins

2015 ◽  
Vol 370 (1678) ◽  
pp. 20140318 ◽  
Author(s):  
Tom A. Williams ◽  
T. Martin Embley
Keyword(s):  
Phylogenetic Trees ◽  
Recent Progress ◽  
New Technologies ◽  
Genomic Data ◽  
Eukaryotic Cells ◽  
Theme Issue ◽  
Statistical Approaches ◽  
Relationship Of ◽  
The Relationship ◽  
Improved Methods

The origin of eukaryotic cells is one of the most fascinating challenges in biology, and has inspired decades of controversy and debate. Recent work has led to major upheavals in our understanding of eukaryotic origins and has catalysed new debates about the roles of endosymbiosis and gene flow across the tree of life. Improved methods of phylogenetic analysis support scenarios in which the host cell for the mitochondrial endosymbiont was a member of the Archaea, and new technologies for sampling the genomes of environmental prokaryotes have allowed investigators to home in on closer relatives of founding symbiotic partners. The inference and interpretation of phylogenetic trees from genomic data remains at the centre of many of these debates, and there is increasing recognition that trees built using inadequate methods can prove misleading, whether describing the relationship of eukaryotes to other cells or the root of the universal tree. New statistical approaches show promise for addressing these questions but they come with their own computational challenges. The papers in this theme issue discuss recent progress on the origin of eukaryotic cells and genomes, highlight some of the ongoing debates, and suggest possible routes to future progress.

scholarly journals First molecular approach to the octopus fauna from the southern Caribbean

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7300 ◽  
Author(s):  
Elena A. Ritschard ◽  
Jürgen Guerrero-Kommritz ◽  
Juan A. Sanchez
Keyword(s):  
Single Species ◽  
Caribbean Region ◽  
Molecular Evidence ◽  
Type I ◽  
Molecular Approach ◽  
Southern Caribbean ◽  
The Family ◽  
San Andres ◽  
Relationship Of ◽  
The Relationship

The octopus fauna from the southern Caribbean is an understudied field. However, recent taxonomic work in the Colombian Caribbean has led to the discovery of several new species in the family Octopodidae. To provide molecular evidence for recent descriptions in the area (i.e., Octopus taganga, O. tayrona and Macrotritopus beatrixi) and contribute to the systematics of the family, we reconstructed the first molecular phylogenies of the family including Colombian Caribbean octopus species. Using cytochrome c oxidase subunit I and rhodopsin sequences from specimens collected in three sites (Santa Marta, Old Providence and San Andrés Islands) we inferred maximum-likelihood trees and delimited species with PTP. Our mitochondrial analysis supported the monophyly of species found in the area (i.e., O. taganga, O. hummelincki and O. briareus). The genetic distinction of the species O. tayrona and O. insularis was not resolved, as these were found in one clade together with Caribbean O. vulgaris and O. aff. tayrona species (O. spB) and delimited as a single species. Additionally, our results suggest a distant relationship of the Type I O. vulgaris group (Caribbean region) from the other forms of the species complex (Old World and Brazil). Lastly, the third newly described species M. beatrixi emerged as an independent lineage and was delimited as a single species. However, its relationship to other species of its genus remains unknown due to the lack of sequences in databases. Altogether, our molecular approach to the octopus fauna from the southern Caribbean adds on information to the relationship of Octopodidae species world-wide by providing sequences from recently described species from an understudied region. Further studies employing higher taxon sampling and more molecular information are needed to fill taxonomic gaps in the area and account for single-locus resolution on the systematics of this group.

Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters

Phytotaxa ◽  
2021 ◽  
Vol 482 (2) ◽  
pp. 121-142
Author(s):  
WEI GOU ◽  
XIAN-LIN GUO ◽  
SONG-DONG ZHOU ◽  
XING-JIN HE
Keyword(s):  
Phylogenetic Trees ◽  
Morphological Characteristics ◽  
Deep Understanding ◽  
Plastid Dna ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Nrdna Its ◽  
Relationship Of ◽  
The Relationship ◽  
Ribosomal Dna Sequence

Meeboldia H.Wolff, Sinodielsia H.Wolff and their relatives (Apiaceae: Apioideae) are similar in morphology, of which taxonomic treatments were controversial. In this study, the nuclear ribosomal DNA sequence (ITS) and two plastid DNA markers (rps16 and rpl16) were applied to reconstruct phylogenetic trees. The results demonstrated that Meeboldia and Sinodielsia formed a monophyletic group in phylogenetic trees and their highly similar morphological characteristics in taproot, basal leaves, calyx teeth, ribs, and vittae of fruits also confirmed their close relationships. Consequently, the following results were obtained: (1) Sinodielsia should be merged into Meeboldia; (2) Sinodielsia delavayi was confirmed conspecific with Meeboldia yunnanensis and renamed as Meeboldia delavayi (Franch.) W.Gou & X.J.He; (3) Sinodielsia thibetica was away from other Sinodielsia species; (4) Sinodielsia microloba was a member of Meeboldia and renamed as Meeboldia microloba (Kljuykov) W.Gou & X.J.He; (5) The name of Sinodielsia clade was suggested to be replaced by Hymenidium clade. We applied multiple approaches to explore the relationship of morphologically similar taxa, which will facilitate a deep understanding of taxonomy and species diversity of Apiaceae.

Phylogenetic position of the genera Caryandoides, Paratoacris, Fer and Longchuanacris (Orthoptera:Acrididae) revealed by complete mitogenome sequences

2021 ◽  
Vol 35 (7) ◽  
pp. 725
Author(s):  
Xiang Zeng ◽  
Haiyang Xu ◽  
Jingxiao Gu ◽  
Benyong Mao ◽  
Zhilin Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bayesian Inference ◽  
Phylogenetic Trees ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Depth Study ◽  
Complete Mitogenome ◽  
Relationship Of ◽  
The Relationship ◽  
Generation Sequencing

Many taxa in the Acrididae have controversial phylogenetic positions. A typical example of such controversies is the phylogenetic positions of the genera Caryandoides, Paratoacris, Fer and Longchuanacris, as well as some other related taxa, which were placed in Oxyinae by some authors, but were considered members of the subfamily Catantopinae by others. In this study, the complete mitogenomes of nine species were sequenced using next-generation sequencing, the characteristics of the newly sequenced mitogenomes are presented briefly, and the phylogeny of the Oxyinae and Catantopinae are reconstructed using a selected dataset of mitogenome sequences under maximum likelihood and Bayesian inference frameworks. The results show that the four controversial genera were consistently assigned to the subfamily Oxyinae rather than Catantopinae in all phylogenetic trees deduced from different datasets under different frameworks, and this finding is entirely consistent with their morphological characters. Therefore, it is more appropriate to place them in Oxyinae rather than Catantopinae. In addition, the results from our analysis also confirm the membership of the genus Apalacris in Coptacrinae rather than Catantopinae, and indicate the uncertainty in the phylogenetic position of the genus Traulia, and a more in-depth study is necessary to resolve the relationship of Traulia with other catantopine groups or Coptacrinae.

scholarly journals Exploring the relationship of Homalosilpha and Mimosilpha (Blattodea, Blattidae, Blattinae) from a morphological and molecular perspective, including a description of four new species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10618
Author(s):  
Shuran Liao ◽  
Yishu Wang ◽  
Duting Jin ◽  
Rong Chen ◽  
Zongqing Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Close Relationship ◽  
Relationship Of ◽  
The Relationship ◽  
Six Genes

This study utilized six genes (12S, 16S, 18S, 28S, COII and H3) from a total of 40 samples to construct maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees in order to infer the relationships between the morphologically similar genera Homalosilpha Stål, 1874 and Mimosilpha Bey-Bienko, 1957. The phylogenetic analysis showed the two genera have a close relationship and were recovered as sister groups based on ML and BI analyses. Four new species are described among these samples, i.e., Homalosilpha obtusangula sp. nov., Homalosilpha recta sp. nov., Homalosilpha alba sp. nov. and Homalosilpha clavellata sp. nov. based on morphological and COI data. A key to the worldwide Homalosilpha is provided.

The relationship of the scleractinian corals to the rugose corals

Paleobiology ◽  
1980 ◽  
Vol 6 (02) ◽  
pp. 146-160 ◽  
Author(s):  
William A. Oliver
Keyword(s):  
Critical Points ◽  
Scleractinian Corals ◽  
Convincing Evidence ◽  
Early Triassic ◽  
Rugose Corals ◽  
History Of ◽  
The Subject ◽  
Relationship Of ◽  
The Relationship ◽  
Biologic Factors

The Mesozoic-Cenozoic coral Order Scleractinia has been suggested to have originated or evolved (1) by direct descent from the Paleozoic Order Rugosa or (2) by the development of a skeleton in members of one of the anemone groups that probably have existed throughout Phanerozoic time. In spite of much work on the subject, advocates of the direct descent hypothesis have failed to find convincing evidence of this relationship. Critical points are:(1) Rugosan septal insertion is serial; Scleractinian insertion is cyclic; no intermediate stages have been demonstrated. Apparent intermediates are Scleractinia having bilateral cyclic insertion or teratological Rugosa.(2) There is convincing evidence that the skeletons of many Rugosa were calcitic and none are known to be or to have been aragonitic. In contrast, the skeletons of all living Scleractinia are aragonitic and there is evidence that fossil Scleractinia were aragonitic also. The mineralogic difference is almost certainly due to intrinsic biologic factors.(3) No early Triassic corals of either group are known. This fact is not compelling (by itself) but is important in connection with points 1 and 2, because, given direct descent, both changes took place during this only stage in the history of the two groups in which there are no known corals.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

Studies on Leukemogenic and Sarcomagenic Viruses

1970 ◽  
Vol 28 ◽  
pp. 156-157
Author(s):  
Leon Dmochowski
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Morphological Properties ◽  
Mode Of Development ◽  
Relationship Of ◽  
The Relationship

Electron microscopy has proved to be an invaluable discipline in studies on the relationship of viruses to the origin of leukemia, sarcoma, and other types of tumors in animals and man. The successful cell-free transmission of leukemia and sarcoma in mice, rats, hamsters, and cats, interpreted as due to a virus or viruses, was proved to be due to a virus on the basis of electron microscope studies. These studies demonstrated that all the types of neoplasia in animals of the species examined are produced by a virus of certain characteristic morphological properties similar, if not identical, in the mode of development in all types of neoplasia in animals, as shown in Fig. 1.

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