Molecular identification of seven species of the genus Stigmaeopsis (Acari: Tetranychidae) and preliminary attempts to establish their phylogenetic relationship

The genus Stigmaeopsis (family Tetranychidae) has 11 species including the serious bamboo pest, S. nanjingensis. All Stigmaeopsis species are difficult to identify by their morphology, and the diagnostic character (the length of dorsal setae) can be used only to identify fresh specimens. To identify these species at the molecular level, we sequenced the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA and two nuclear ribosomal RNA genes (18S and 28S) of 20 strains of seven species of Stigmaeopsis [S. celarius, S. longus, S. miscanthi (both low- and high-aggression phenotypes), S. nanjingensis, S. tenuinidus, S. saharai and S. takahashii]. In maximum likelihood (ML) phylogenetic trees of both COI and combined 18S-28S genes, all but one Stigmaeopsis species could be identified as a monophyletic clade with high bootstrap values. The present results strongly suggested that the exceptional species, S. miscanthi, consists of three biologically different entities based on two phylogenetic trees. Though the phylogenetic trees did not comprehensively solve the phylogeny of Stigmaeopsis, a phylogenetic tree based on the combined nuclear genes showed a sibling relationship between two sub-social Stigmaeopsis species, S. miscanthi and S. longus. In addition, diagnostic PCR detected Wolbachia or Cardinium, which frequently affect mitochondrial haplotypes, in S. longus and S. nanjingensis. In the COI tree, S. longus was separated into two groups which were more consistent with their bacterial infection status than with their geographical distribution.

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Transoceanic voyages of drywood termites (Isoptera: Kalotermitidae) inferred from extant and extinct species

10.1101/2021.09.24.461667 ◽

2021 ◽

Author(s):

Aleš Buček ◽

Menglin Wang ◽

Jan Šobotník ◽

David Sillam-Dussès ◽

Nobuaki Mizumoto ◽

...

Keyword(s):

Ribosomal Rna ◽

Phylogenetic Trees ◽

Taxonomic Revision ◽

Terrestrial Ecosystems ◽

Distribution Patterns ◽

Global Distribution ◽

The Family ◽

Phylogenetic Framework ◽

Rna Genes ◽

Drywood Termites

Termites are major decomposers of organic matter in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae, the second-largest termite family, are widely distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes and nuclear ribosomal RNA genes of ~120 species, about 27% of kalotermitid diversity, including representatives of 22 of the 23 kalotermitid genera. We found that extant kalotermitids shared a common ancestor 81 Mya (72-91 Mya 95% HPD), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the ~40 disjunctions among biogeographic realms were dated at less than 50 Mya, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying that the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for a critical taxonomic revision of the family and for future comparative analyses of Kalotermitidae.

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Molecular Identification and Phylogenetic Relationships of Threadfin Breams (Family: Nemipteridae) Using mtDNA Marker

Notulae Scientia Biologicae ◽

10.15835/nsb427602 ◽

2012 ◽

Vol 4 (2) ◽

pp. 13-18 ◽

Cited By ~ 2

Author(s):

Vaithilingam RAVITCHANDIRANE ◽

Vaithianathan GEETHA ◽

Vijayan RAMYA ◽

Bilavendiran JANIFER ◽

Muthusamy THANGARAJ ◽

...

Keyword(s):

Fish Species ◽

Phylogenetic Trees ◽

Evolutionary Relationship ◽

Coi Gene ◽

Gene Sequences ◽

Mtdna Coi ◽

High Bootstrap ◽

Commercially Important ◽

Two Parameter ◽

Mtdna Marker

Cytochrome c oxidase-1 gene sequences of mitochondrial genome were analyzed for species identification and phylogenetic relationship among the commercially important Nemipterus species. Sequence analysis of COI gene clearly indicated that all the nine fish species fell into distinct clads, which are genetically distant from each other and exhibited identical phylogenetic reservation. All the COI gene sequences provide sufficient phylogenetic information and evolutionary relationship to distinguish the nine Nemipterus species unambiguously. As per the neighbour-joining (NJ) and maximum likelihood (ML) trees, all the nine species are genetically distant from each other and exhibited identical phylogenetic reservation. Based on the NJ and ML phylogenetic trees N. mesoprion, N. zysron, N. hexodon, N. nematophorus, N. virgatus and N. bipunctatus were closely related with high bootstrap value (97). The overall mean Kimura two parameter (K2P) distances between the nine species was 0.109. The intra species K2P distance was high in N. japonicus (0.069) followed by N. peronii (0.050) and N. mesoprion (0.002). This study proves the use of mtDNA COI gene sequence based approach is an alternative tool for identifying fish species at a faster pace.

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K-mer similarity, networks of microbial genomes and taxonomic rank

10.1101/125237 ◽

2017 ◽

Author(s):

Guillaume Bernard ◽

Paul Greenfield ◽

Mark A. Ragan ◽

Cheong Xin Chan

Keyword(s):

Ribosomal Rna ◽

Phylogenetic Trees ◽

Ribosomal Rna Genes ◽

Taxonomic Rank ◽

Variable Regions ◽

Microbial Life ◽

New Perspective ◽

Genomic Regions ◽

The Impact ◽

Rna Genes

AbstractAlignment-free (AF) methods have recently been adopted to infer phylogenetic trees. However, the evolutionary relationships among microbes, impacted by common phenomena such as lateral genetic transfer and rearrangement, cannot be adequately captured in a strictly tree-like structure. Bacterial and archaeal genomes consist of highly conserved regions, e.g. ribosomal RNA genes (commonly used as phylogenetic markers), more-variable regions and extrachromosomal elements, i.e. plasmids (that contain genes critical under a selective condition e.g. antibiotic resistance). The impact of these elements on genome-scale inference of microbial phylogeny remains little known. Here, using an AF approach, we inferred phylogenomic networks of microbial life based on 2785 completely sequenced bacterial and archaeal genomes, and systematically assessed the impact of ribosomal RNA genes and plasmid sequences in this network. Our results indicate that k-mer similarity can correlate with taxonomic rank of microbes. Using a relational database approach, we linked the implicatedk-mers to annotated genomic regions (thus functions), and defined core functions in specific phyletic groups and genera. We found that, in most phyla, highly conserved functions are often related to Amino acid metabolism and transport, and Energy production and conversion. Our findings indicate that AF phylogenomics can be used to infer reticulate relationships in a scalable manner and provide new perspective into microbial biology and evolution.

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Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs

Non-Coding RNA ◽

10.3390/ncrna7020030 ◽

2021 ◽

Vol 7 (2) ◽

pp. 30

Author(s):

Laeya Baldini ◽

Bruno Charpentier ◽

Stéphane Labialle

Keyword(s):

Ribosomal Rna ◽

Molecular Mechanisms ◽

Molecular Level ◽

Accurate Description ◽

Small Nucleolar Rnas ◽

Age Of Maturity ◽

Non Coding Rnas ◽

And Function ◽

Nucleolar Rnas

Box C/D small nucleolar RNAs (C/D snoRNAs) represent an ancient family of small non-coding RNAs that are classically viewed as housekeeping guides for the 2′-O-methylation of ribosomal RNA in Archaea and Eukaryotes. However, an extensive set of studies now argues that they are involved in mechanisms that go well beyond this function. Here, we present these pieces of evidence in light of the current comprehension of the molecular mechanisms that control C/D snoRNA expression and function. From this inventory emerges that an accurate description of these activities at a molecular level is required to let the snoRNA field enter in a second age of maturity.

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Structure and variation in ribosomal RNA genes of pea

Plant Molecular Biology ◽

10.1007/bf00016429 ◽

1987 ◽

Vol 8 (1) ◽

pp. 3-12 ◽

Cited By ~ 87

Author(s):

R. A. Jorgensen ◽

R. E. Cuellar ◽

W. F. Thompson ◽

T. A. Kavanagh

Keyword(s):

Ribosomal Rna ◽

Ribosomal Rna Genes ◽

Rna Genes

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Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)

Genes ◽

10.3390/genes12081185 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1185

Author(s):

Wenqian Wang ◽

Huan Zhang ◽

Jérôme Constant ◽

Charles R. Bartlett ◽

Daozheng Qin

Keyword(s):

Control Region ◽

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Start Codon ◽

Rrna Genes ◽

Rich Region ◽

Protein Coding ◽

Phylogenetic Implications ◽

Rna Genes ◽

Unpaired Base

The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.

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First Insight into Groundwater Copepods of the Polish Lowland

Water ◽

10.3390/w13152086 ◽

2021 ◽

Vol 13 (15) ◽

pp. 2086

Author(s):

Maciej Karpowicz ◽

Sabina Smolska ◽

Magdalena Świsłocka ◽

Joanna Moroz

Keyword(s):

Mitochondrial Dna ◽

Ribosomal Rna ◽

Dna Markers ◽

Coi Gene ◽

Molecular Characteristics ◽

Morphological Description ◽

Single Plate ◽

North Eastern ◽

Insight Into

Our results are the first insight into groundwater copepods of the Polish Lowland. The sampling was conducted in 28 wells in north-eastern Poland, and Copepoda were present in 16 wells. We have identified six Copepoda species and one Cladocera. We have classified four species as stygophiles—Eucyclops serrulatus, Diacyclops bisetosus, Diacyclops crassicaudis, and Cyclops furcifer. These species were frequently found in studied wells of different regions of north-eastern Poland, often in high numbers, and females with egg sacs were observed. We present a detailed morphological description of these species, together with molecular characteristics based on mitochondrial DNA markers (COI gene) for E. serrulatus, D. bisetosus, and D. crassicaudis, and 12S ribosomal RNA for C. furcifer. We also present the development of abnormal structures in one specimen of D. crassicaudis, where the upper part of furcal rami was fused to form a single plate.

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