scholarly journals Molecular phylogeny of Culex subgenus Melanoconion (Diptera: Culicidae) based on nuclear and mitochondrial protein-coding genes

2018 ◽  
Vol 5 (5) ◽  
pp. 171900 ◽  
Author(s):  
Carolina Torres-Gutierrez ◽  
Tatiane M. P. de Oliveira ◽  
Kevin J. Emerson ◽  
Eduardo Sterlino Bergo ◽  
Maria Anice Mureb Sallum
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Phylogenetic Signal ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Single Copy ◽  
Neotropical Region ◽  
Nuclear Genes ◽  
Morphological Identification ◽  
Protein Coding

The subgenus Melanoconion of the mosquito genus Culex is taxonomically diverse and is widely distributed in the Neotropical Region, with 10 species occurring in the Nearctic Region. Species of this subgenus pose a taxonomical challenge because morphological identification is based largely on anatomical characters of the male genitalia. We addressed the monophyly of the Spissipes and Melanoconion Sections of the subgenus Melanoconion and some of the informal groups in each section. Our sample taxa included 97 specimens representing 43 species, from which we analysed fragments of two single-copy nuclear genes ( CAD , HB ) and one mitochondrial gene ( COI ). Phylogenetic relationships within the subgenus are presented based on results of maximum-likelihood and Bayesian analyses using a multi-locus matrix of DNA sequences. We show a molecular phylogeny of Melanoconion in which both sections were recovered as monophyletic groups. The monophyly of the Atratus and Pilosus groups was confirmed. Within each section, other monophyletic groups were recovered highlighting the potential need for future nomenclature rearrangement. The phylogenetic signal contained in nuclear genes, when analysed together, was more informative than each gene analysed separately, corroborating monophyly of Melanoconion relative to Culex ( Culex ) species included in the analyses, the Melanoconion and Spissipes Sections and some species groups. Our results provide new information for the classification of the subgenus and additional data that can be used to improve species identification when a more representative taxon sampling is available.

scholarly journals Mitogenome Analysis of Four Lamiinae Species (Coleoptera: Cerambycidae) and Gene Expression Responses by Monochamus alternatus When Infected with the Parasitic Nematode, Bursaphelenchus mucronatus

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 453
Author(s):  
Zi-Yi Zhang ◽  
Jia-Yin Guan ◽  
Yu-Rou Cao ◽  
Xin-Yi Dai ◽  
Kenneth B. Storey ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Pine Wilt Disease ◽  
Bursaphelenchus Xylophilus ◽  
Monochamus Alternatus ◽  
Genome Database ◽  
Protein Coding ◽  
Nd5 Gene

We determined the mitochondrial gene sequence of Monochamus alternatus and three other mitogenomes of Lamiinae (Insect: Coleoptera: Cerambycidae) belonging to three genera (Aulaconotus, Apriona and Paraglenea) to enrich the mitochondrial genome database of Lamiinae and further explore the phylogenetic relationships within the subfamily. Phylogenetic trees of the Lamiinae were built using the Bayesian inference (BI) and maximum likelihood (ML) methods and the monophyly of Monochamus, Anoplophora, and Batocera genera was supported. Anoplophora chinensis, An. glabripennis and Aristobia reticulator were closely related, suggesting they may also be potential vectors for the transmission of the pine wood pathogenic nematode (Bursaphelenchus xylophilus) in addition to M. alternatus, a well-known vector of pine wilt disease. There is a special symbiotic relationship between M. alternatus and Bursaphelenchus xylophilus. As the native sympatric sibling species of B. xylophilus, B. mucronatus also has a specific relationship that is often overlooked. The analysis of mitochondrial gene expression aimed to explore the effect of B. mucronatus on the energy metabolism of the respiratory chain of M. alternatus adults. Using RT-qPCR, we determined and analyzed the expression of eight mitochondrial protein-coding genes (COI, COII, COIII, ND1, ND4, ND5, ATP6, and Cty b) between M. alternatus infected by B. mucronatus and M. alternatus without the nematode. Expression of all the eight mitochondrial genes were up-regulated, particularly the ND4 and ND5 gene, which were up-regulated by 4–5-fold (p < 0.01). Since longicorn beetles have immune responses to nematodes, we believe that their relationship should not be viewed as symbiotic, but classed as parasitic.

Transcriptional and posttranscriptional regulation of maize mitochondrial gene expression

1991 ◽  
Vol 11 (1) ◽  
pp. 533-543
Author(s):  
R M Mulligan ◽  
P Leon ◽  
V Walbot
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Posttranscriptional Regulation ◽  
Rank Order ◽  
Mitochondrial Gene ◽  
Initiation Site ◽  
Gene Copy ◽  
Promoter Strength ◽  
Protein Coding

Lysed maize mitochondria synthesize RNA in the presence of radioactive nucleoside triphosphates, and this assay was utilized to compare the rates of transcription of seven genes. The rates of incorporation varied over a 14-fold range, with the following rank order: 18S rRNA greater than 26S rRNA greater than atp1 greater than atp6 greater than atp9 greater than cob greater than cox3. The products of run-on transcription hybridized specifically to known transcribed regions and selectively to the antisense DNA strand; thus, the isolated run-on transcription system appears to be an accurate representation of endogenous transcription. Although there were small differences in gene copy abundance, these differences cannot account for the differences in apparent transcription rates; we conclude that promoter strength is the main determinant. Among the protein coding genes, incorporation was greatest for atp1. The most active transcription initiation site of this gene was characterized by hybridization with in vitro-capped RNA and by primer extension analyses. The DNA sequences at this and other transcription initiation sites that we have previously mapped were analyzed with respect to the apparent promoter strengths. We propose that two short sequence elements just upstream of initiation sites form at least a portion of the sequence requirements for a maize mitochondrial promoter. In addition to modulation at the level of transcription, steady-state abundance of protein-coding mRNAs varied over a 20-fold range and did not correlate with transcriptional activity. These observations suggest that posttranscriptional processes are important in the modulation of mRNA abundance.

Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

2021 ◽  
Vol 46 (1) ◽  
pp. 162-174
Author(s):  
Ming-Hui Yan ◽  
Chun-Yang Li ◽  
Peter W. Fritsch ◽  
Jie Cai ◽  
Heng-Chang Wang
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

scholarly journals Preliminary assessment of adaptive evolution of mitochondrial protein coding genes in darters (Percidae: Etheostomatinae)

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 464 ◽  
Author(s):  
Leos G. Kral ◽  
Sara Watson
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Gene Evolution ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Preliminary Assessment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Show Evidence ◽  
Selection Of

Background: Mitochondrial DNA of vertebrates contains genes for 13 proteins involved in oxidative phosphorylation. Some of these genes have been shown to undergo adaptive evolution in a variety of species. This study examines all mitochondrial protein coding genes in 11 darter species to determine if any of these genes show evidence of positive selection. Methods: The mitogenome from four darter was sequenced and annotated. Mitogenome sequences for another seven species were obtained from GenBank. Alignments of each of the protein coding genes were subject to codon-based identification of positive selection by Selecton, MEME and FEL. Results: Evidence of positive selection was obtained for six of the genes by at least one of the methods. CYTB was identified as having evolved under positive selection by all three methods at the same codon location. Conclusions: Given the evidence for positive selection of mitochondrial protein coding genes in darters, a more extensive analysis of mitochondrial gene evolution in all the extant darter species is warranted.

scholarly journals Phylogeny of water birds inferred from mitochondrial DNA sequences of nine protein coding genes

2014 ◽  
Author(s):  
Tsendsesmee Lkhagvajav Treutlein ◽  
Javier Gonzalez ◽  
Michael Wink
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Mitochondrial Protein ◽  
Sister Relationship ◽  
Protein Coding ◽  
Water Bird ◽  
Protein Coding Genes ◽  
Reconstruction Methods ◽  
Mtdna Sequence ◽  
Water Birds

Background: The phylogeny of birds which are adapted to aquatic environments is controversial because of convergent evolution. Methods: To understand water bird evolution in more detail, we sequenced the majority of mitochondrial protein coding genes (6699 nucleotides in length) of 14 water birds, and reconstructed their phylogeny in the context of other taxa across the whole class of birds for which complete mitochondrial DNA (mtDNA) sequences were available. Results: The water bird clade, as defined by Hackett et al. (2008) based on nuclear DNA (ncDNA) sequences, was also found in our study by Bayesian Inference (BI) and Maximum Likelihood (ML) analyses. In both reconstruction methods, genera belonging to the same family generally clustered together with moderate to high statistical support. Above the family level, we identified three monophyletic groups: one clade consisting of Procellariidae, Hydrobatidae and Diomedeidae, and a second clade consisting of Sulidae, Anhingidae and Phalacrocoracidae, and a third clade consisting of Ardeidae and Threskiornithidae. Discussion: Based on our mtDNA sequence data, we recovered a robust direct sister relationship between Ardeidae and Threskiornithidae for the first time for mtDNA. Our comprehensive phylogenetic reconstructions contribute to the knowledge of higher level relationships within the water birds and provide evolutionary hypotheses for further studies.

scholarly journals Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10017
Author(s):  
Raden Pramesa Narakusumo ◽  
Alexander Riedel ◽  
Joan Pons
Keyword(s):  
Amino Acid ◽  
Phylogenetic Signal ◽  
Mitochondrial Protein ◽  
Amino Acid Sequences ◽  
Mitochondrial Genomes ◽  
Length Variation ◽  
Codon Site ◽  
Protein Coding ◽  
Large Variability ◽  
Molecular Features

Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.

Towards a dated molecular phylogeny of the Tanypodinae (Chironomidae, Diptera)

2017 ◽  
Vol 31 (3) ◽  
pp. 302 ◽  
Author(s):  
M. N. Krosch ◽  
P. S. Cranston ◽  
L. M. Bryant ◽  
F. Strutt ◽  
S. R. McCluen
Keyword(s):  
Molecular Phylogeny ◽  
Mixed Model ◽  
Mitochondrial Protein ◽  
Divergence Time ◽  
Molecular Data ◽  
Ribosomal Gene ◽  
Protein Coding ◽  
Weak Support ◽  
Gene Coi ◽  
Inference Methods

A dated molecular phylogeny is proposed for the Tanypodinae, a diverse subfamily of Chironomidae (Diptera). We used molecular data from fragments of one ribosomal gene (28S), one nuclear protein-coding gene (CAD), and one mitochondrial protein-coding gene (COI), analysed using mixed model Bayesian and maximum likelihood inference methods. All proposed tribes were sampled, namely, Anatopyniini, Clinotanypodini, Coelopyniini, Fittkauimyiini, Macropelopiini, Natarsiini, Pentaneurini, Procladiini and Tanypodini. A multilocus dataset of 1938 characters was compiled from 123 individuals including outgroups. Monophyly was supported for all tribes although some relationships were not robust. Relationships between tribes and some genus groups are highly congruent with a morphology-based estimate. Relationships within tribe Pentaneurini mostly find weak support, yet previously hypothesised groupings and monophyly or lack thereof in well-sampled genera are revealed. The tempo of diversification of the family was deduced by divergence time analysis (BEAST). Origination of a subfamily stem group in the late Jurassic to early Cretaceous was inferred, with all tribes and many genera of Pentaneurini originating and diversifying in the Cretaceous. Some nodes are biogeographically informative. Gene sections supported the backbone, but more extensive sampling is needed to estimate shallower phylogenies and to better understand the tempo and diversification of Tanypodinae.

A molecular phylogeny of rainbow skinks (Scincidae: Carlia): taxonomic and biogeographic implications

2002 ◽  
Vol 50 (1) ◽  
pp. 39 ◽  
Author(s):  
Devi M. Stuart-Fox ◽  
Andrew F. Hugall ◽  
Craig Moritz
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Molecular Evidence ◽  
Previous Suggestion ◽  
Protein Coding ◽  
Single Clade ◽  
Form Part ◽  
Rapid Diversification ◽  
Interspecific Distance

The phylogenetic relationships amongst 29 species of Carlia and Lygisaurus were estimated using a 726-base-pair segment of the protein-coding mitochondrial ND4 gene. Results do not support the recent resurrection of the genus Lygisaurus. Although most Lygisaurus species formed a single clade, this clade is nested within Carlia and includes Carlia parrhasius. Due to this new molecular evidence, and the paucity of diagnostic morphological characters separating the genera, Lygisaurus de Vis 1884 is re-synonymised with Carlia Gray 1845. Our analysis is also inconsistent with a previous suggestion that Lygisaurus timlowi should be removed to Menetia, a genus that is distantly related relative to outgroups used here. Intraspecific variation in Carlia is, in several instances, greater than interspecific distance. The most strikingly divergent lineages are found within C. rubrigularis, which appears to be paraphyletic, with southern populations more closely related to C. rhomboidalis than to northern populations of C. rubrigularis. The two C. rubrigularis–C. rhomboidalis lineages form part of a major polytomy at an intermediate level of divergence. Lack of resolution at this level, however, does not appear to be due to saturation or loss of phylogenetic signal. Rather, the polytomy probably reflects a period of relatively rapid diversification that occurred sometime during the Miocene.

An assessment of the value of nuclear and mitochondrial genes in elucidating the origin and evolution of Isotoma klovstadi Carpenter (Insecta, Collembola)

1999 ◽  
Vol 11 (2) ◽  
pp. 160-174 ◽  
Author(s):  
Francesco Frati ◽  
Antonio Carapelli
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Codon Position ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Elongation Factor ◽  
Minimum Evolution ◽  
Protein Coding ◽  
Antarctic Species ◽  
Origin And Evolution

In order to infer the origin and the evolution of Antarctic Collembola, a correct phylogenetic analysis depicting relationships among Antarctic and non-Antarctic species is required. A preliminary assessment of the value of DNA sequences in reconstructing phylogenetic relationships among the Antarctic Isotoma klovstadi and other non-Antarctic species was carried out by sequencing one mitochondrial gene (Cytochrome c oxidase, subunit II) and two nuclear genes (a fragment of the 28S rDNA and the Elongation Factor-1α). Estimates of base composition heterogeneity revealed that in the two protein-coding genes (COII and EF-1α) 3rd codon position sites are compositionally very heterogeneous and the analysis of these two genes was therefore performed only on 1st and 2nd codon position sites. Phylogenetic analyses using Maximum Likelihood, Maximum Parsimony and Minimum Evolution revealed that the COII and the EF-1α genes are more suitable than the D3 fragment for the reconstruction of phylogenetic relationships within the Family Isotomidae to which Isotoma and several other genera of Antarctic Collembola belong.

Not endemic after all: Imparipecten Freeman, 1961 (Diptera: Chironomidae) described from the Neotropical Region

Zootaxa ◽  
2018 ◽  
Vol 4532 (3) ◽  
pp. 396 ◽  
Author(s):  
LÍVIA MARIA FUSARI ◽  
GALILEU P.S. DANTAS ◽  
NEUSA HAMADA ◽  
VANDERLY ANDRADE-SOUZA ◽  
KÁTIA M. LIMA ◽  
...  
Keyword(s):  
Nuclear Protein ◽  
Mitochondrial Protein ◽  
Neotropical Region ◽  
Genetic Distances ◽  
Ribosomal Gene ◽  
Monotypic Genus ◽  
Bayesian Phylogenetics ◽  
Protein Coding ◽  
Gene Coi ◽  
First Time

Imparipecten, a previously monotypic genus, was considered endemic to Australia. Here, we report Imparipecten from the Neotropical region for the first time and describe Imparipecten sychnacanthus sp. n. from Brazil. The association between larvae and adults was established by sequencing a fragment of one ribosomal gene (28S), two fragments of a nuclear protein-coding gene (CAD1 and CAD4), and one mitochondrial protein-coding gene (COI). We also show the close molecular proximity with Imparipecten pictipes through analyses of genetic distances and Bayesian phylogenetics. 

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