scholarly journals Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1403 ◽  
Author(s):  
Ehsan Kayal ◽  
Bastian Bentlage ◽  
Paulyn Cartwright ◽  
Angel A. Yanagihara ◽  
Dhugal J. Lindsay ◽  
...  
Keyword(s):  
Long Range ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Morphological Diversity ◽  
Sister Group ◽  
Rna Seq ◽  
Dna And Rna ◽  
Long Range Pcr ◽  
Group Relationships

Hydrozoans display the most morphological diversity within the phylum Cnidaria. While recent molecular studies have provided some insights into their evolutionary history, sister group relationships remain mostly unresolved, particularly at mid-taxonomic levels. Specifically, within Hydroidolina, the most speciose hydrozoan subclass, the relationships and sometimes integrity of orders are highly unsettled. Here we obtained the near complete mitochondrial sequence of twenty-six hydroidolinan hydrozoan species from a range of sources (DNA and RNA-seq data, long-range PCR). Our analyses confirm previous inference of the evolution of mtDNA in Hydrozoa while introducing a novel genome organization. Using RNA-seq data, we propose a mechanism for the expression of mitochondrial mRNA in Hydroidolina that can be extrapolated to the other medusozoan taxa. Phylogenetic analyses using the full set of mitochondrial gene sequences provide some insights into the order-level relationships within Hydroidolina, including siphonophores as the first diverging clade, a well-supported clade comprised of Leptothecata-Filifera III–IV, and a second clade comprised of Aplanulata-Capitatas.s.-Filifera I–II. Finally, we describe our relatively inexpensive and accessible multiplexing strategy to sequence long-range PCR amplicons that can be adapted to most high-throughput sequencing platforms.

scholarly journals Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7853 ◽  
Author(s):  
Yuchen Yan ◽  
Gengyun Niu ◽  
Yaoyao Zhang ◽  
Qianying Ren ◽  
Shiyu Du ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
New Genus ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Sister Group ◽  
Morphological Characters ◽  
Trna Genes ◽  
Sequencing Data ◽  
Link Type

Labriocimbex sinicus Yan & Wei gen. et sp. nov. of Cimbicidae is described. The new genus is similar to Praia Andre and Trichiosoma Leach. A key to extant Holarctic genera of Cimbicinae is provided. To identify the phylogenetic placement of Cimbicidae, the mitochondrial genome of L. sinicus was annotated and characterized using high-throughput sequencing data. The complete mitochondrial genome of L. sinicus was obtained with a length of 15,405 bp (GenBank: MH136623; SRA: SRR8270383) and a typical set of 37 genes (22 tRNAs, 13 PCGs, and two rRNAs). The results demonstrated that all PCGs were initiated by ATN codon, and ended with TAA or T stop codons. The study reveals that all tRNA genes have a typical clover-leaf secondary structure, except for trnS1. Remarkably, the secondary structures of the rrnS and rrnL of L. sinicus were much different from those of Corynis lateralis. Phylogenetic analyses verified the monophyly and positions of the three Cimbicidae species within the superfamily Tenthredinoidea and demonstrated a relationship as (Tenthredinidae + Cimbicidae) + (Argidae + Pergidae) with strong nodal supports. Furthermore, we found that the generic relationships of Cimbicidae revealed by the phylogenetic analyses based on COI genes agree quite closely with the systematic arrangement of the genera based on the morphological characters. Phylogenetic tree based on two methods shows that L. sinicus is the sister group of Praia with high support values. We suggest that Labriocimbex belongs to the tribe Trichiosomini of Cimbicinae based on adult morphology and molecular data. Besides, we suggest to promote the subgenus Asitrichiosoma to be a valid genus.

The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)

Zootaxa ◽  
2010 ◽  
Vol 2406 (1) ◽  
pp. 1 ◽  
Author(s):  
PEDRO IVO SIMÕES ◽  
ALBERTINA P. LIMA ◽  
IZENI PIRES FARIAS
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Sister Group ◽  
Sensu Stricto ◽  
Left Bank ◽  
Genetic Introgression ◽  
Nucleotide Substitutions ◽  
Advertisement Calls ◽  
Allobates Femoralis

We describe a new species of litter frog from western Brazilian Amazon previously referred to as Allobates femoralis (Boulenger 1883). The new species is allopatric to A. femoralis and its known occurrence is restricted to terra-firme forests on the left bank of the upper Madeira River and southeastern State of Acre. This species is distinguished from A. femoralis and from other species in the A. femoralis group by presenting two-note advertisement calls and conspicuous reddish-orange color on ventral surfaces of hind limbs and posterior abdomen. Phylogenetic analyses based on a fragment of the 16S rRNA mitochondrial gene suggest the new species is the sister group to a clade referred to as A. femoralis occurring in southern State of Acre, from which it is distinguished by six unambiguous nucleotide substitutions, in addition to exclusive advertisement calls and color patterns. The new species is more distantly related to A. femoralis sensu stricto occurring near the A. femoralis type locality in the Peruvian Amazon. Summarizing evidence from molecular phylogenetic analysis, genetic distances and available data on advertisement calls, we identify one possible case of genetic introgression between lineages in this group and highlight the potential for the description of more species within the A. femoralis complex.

A Multiplex PCR for Detection of Genetic Aberrations in Non-Hodkin’s Lymphoma.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4554-4554
Author(s):  
Charlotte Guldborg Nyvold ◽  
Knud Bendix ◽  
Stephen J. Hamilton-Dutoit ◽  
Dorte Melsvik ◽  
Hanne Tønder ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Long Range ◽  
Cell Lines ◽  
Clinical Setting ◽  
Residual Disease ◽  
Simultaneous Detection ◽  
Control Gene ◽  
Genetic Aberrations ◽  
Dna And Rna ◽  
Long Range Pcr

Abstract Aim: To develop a multiplex PCR method applicable in a clinical setting for the simultaneous detection of the chromosomal lesions t(11;14)(q13q32), t(14;18)(q32;q21), t(2;5)(p23;q35), t(11;18)(q21;q21), t(3q27;var), and t(8;14)(q24;q32) frequently found in non-Hodgkin lymphoma (NHL). Methods: DNA and RNA were prepared from 50μm lymph node (LN) sections by homogenization on a FastPrep instrument (Qbiogene, Cedex, France) followed by automated nucleic acid purification on a MagNa-Pure LC robot (Roche Diagnostics, Basel, Switzerland). The multiplex PCR was condensed in four PCR tubes. The first covered the MTC and mTCp94 region of BCL1/IGH fusion DNA, the MBR and MCR breakpoint regions of BCL2/IGH fusion DNA together with the control gene TCF20. The second included the API2/MLT and ALK/NPM breakpoints on cDNA along with β-ACTIN as a control gene. The third contained primers amplifying eight different fusions partners of BCL6 (IGH (14q32), IGL (22q11), HSP89α (14q32), HSP90β (6p12), PIM1 (6p21), TFR (3q26), TTF (4p13), and H4 (6p21)) on cDNA together with β-ACTIN as the control gene. The fourth tube harbored a long range PCR with primers detecting the CMYC/IGH breakpoints on genomic DNA (Cμ, Cγ, Cα, and joining region of the IGH (Basso et al., 1999, Am J Pathology)) together with ABL as a control gene. Patient samples and cell lines: One-hundred-and-twelve LN biopsies frozen in Tissue-Tek OCT Compound (Sakura, Vaerloese, Denmark) were randomly selected from consecutive patients referred with suspected hematological malignancy. The following cell lines were used as positive controls: B-CLL line JVM-2 (t(11;14)+), NHL lines DOHH-2 (t(14;18)+, t(8;14)+) and WSU-NHL (t(14;18)+), Burkitt’s lymphoma lines BL-41, BL-70 (t(8;14)+), and MD901 (t(3;22)+), T-NHL line Karpas 299 (t(2;5)+), and ALL line MD903 (t(3;14)+). Results: In pilot experiments employing cell lines and fresh LN material, this optimized multiplex PCR reaction proved to be simple and fast with a short turnover time, considering the large number of genetic aberrations detected. In a retrospective LN material encompassing 112 blinded samples, BCL1/IGH fusion DNA with breakpoint in the MTC region was detected once while BCL2/IGH was found in 20 samples (19 in MBR and one in MCR). BCL6/IGH fusion cDNA was found in three samples while the TTF gene was utilized twice as translocation partner to BCL6. Finally, CMYC/IGH fusion DNA was detected three times (1 IGHCα, 2 IGHCγ). All PCR products apart from CMYC/IGH were sequenced and verified the specific chromosomal lesions. Nineteen were excluded due to weak control bands in the first three PCR tubes, while 38 were excluded in the long range PCR detecting CMYC/IGH. Conclusion: We conclude that the NHL multiplex PCR described is an easy and timesaving method for identifying heterogeneous molecular disease markers in NHL. The standardized DNA- and RNA preparation together with the condensation into four PCR tubes, moreover, makes it convenient to the clinical setting. Application of this assay and identification of positive cases has the added advantage that quantitative real-time PCR monitoring residual disease can be applied.

scholarly journals A new species of Phrynops from Southern Brazil (Testudines, Chelidae), with comments on the phylogeny of the genus

2015 ◽  
Author(s):  
Natália Rizzo Friol ◽  
Flávio de Barros Molina ◽  
Hussam El Dine Zaher
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Sister Group ◽  
Molecular Data ◽  
Valid Species ◽  
Southern Brazil ◽  
Group Relationships ◽  
A New Species ◽  
Combined Data

Background. Phrynops present four valid species, including P. geoffroanus that might represents a complex of cryptic species. Here, we provide a preliminary analysis of the taxonomy and phylogenetic affinities within Phrynops, with special reference to the taxonomic status of populations of P. geoffroanus and P. tuberosus, and the recognition of a new species from Southern Brazil. Methods. We studied populations from ten Brazilian river basins. A linear morphometric analysis was performed in order to define taxonomically distinct populations. Also, a phylogenetic analysis using morphology and molecular data (sequenced for the genes R35, RAG2, c-mos, cytb, ND4, and 12S) were carried out. Three distinct sets of phylogenetic analyses were performed: parsimony to morphological and combined data, and maximum likelihood to molecular data. Results. The combined analysis shows that Phrynops represents a well supported clade. The set of skeletal data supports Mesoclemmys as the sister group of Phrynops, whereas the molecular and combined data sets show Phrynops as the sister group of a clade composed by all the remaining genera of Chelidae, except Hydromedusa. Our morphological analyses suggest that P. hilarii is the sister group of P. geoffroanus, but in both molecular and combined analyses, P. hilarii appears nested within the clade formed by the populations of P. geoffroanus. Futhermore, P. tuberosus and P. geoffroanus are not distinguishable by the set of osteological and morphometric data. On the other hand, both morphometric and osteological data show that the population of P. geoffroanus from the Paraná river basin is a distinct species. Discussion. The sister group relationships of Phrynops could not be clearly defined due to the different topologies achieved. Phrynops hilarii is included within of P. geoffroanus in both molecular and combined data, but this position has little statistical support and therefore does not express a clear position of P. hilarii within the genus Phrynops. Besides, we were not able to distinguish P. geoffroanus and P. tuberosus. However, a sampling of specific locations are still needed to objectively define the taxonomic status of P. tuberosus. Finally, the population of P. geoffroanus from the Paraná basin is clearly distinct from the remaining populations of this species. Qualitative osteological characters and morphometric results seem to demonstrate that this population is a new species of Phrynops.

HLA-DRB1, -DRB3, -DRB4 and -DRB5 genotyping at a super-high resolution level by long range PCR and high-throughput sequencing

2013 ◽  
Vol 83 (1) ◽  
pp. 10-16 ◽  
Author(s):  
Y. Ozaki ◽  
S. Suzuki ◽  
A. Shigenari ◽  
Y. Okudaira ◽  
E. Kikkawa ◽  
...  
Keyword(s):  
High Resolution ◽  
Long Range ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Resolution Level ◽  
Long Range Pcr

scholarly journals Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari

2019 ◽  
Vol 37 (3) ◽  
pp. 683-694 ◽  
Author(s):  
Paula Arribas ◽  
Carmelo Andújar ◽  
María Lourdes Moraza ◽  
Benjamin Linard ◽  
Brent C Emerson ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Mixed Forest ◽  
Morphological Diversity ◽  
Terrestrial Ecosystems ◽  
Great Promise ◽  
Ancestral State ◽  
Early Diversification ◽  
Critical Nodes ◽  
Minimum Age

Abstract High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian–Ordovician (likely within 455–552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.

scholarly journals Characterization of the rat developmental liver transcriptome

2013 ◽  
Vol 45 (8) ◽  
pp. 301-311 ◽  
Author(s):  
Richard H. Chapple ◽  
Polyana C. Tizioto ◽  
Kevin D. Wells ◽  
Scott A. Givan ◽  
JaeWoo Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput Sequencing ◽  
Mitochondrial Gene ◽  
Probe Design ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Biologically Relevant ◽  
Gradual Process ◽  
Intergenic Regions ◽  
Sequencing Platforms

Gene regulation and transcriptome studies have been enabled by the development of RNA-Seq applications for high-throughput sequencing platforms. Next generation sequencing is remarkably efficient and avoids many issues inherent in hybridization-based microarray methodologies including the exon-specific dependence of probe design. Biologically relevant transcripts including messenger and regulatory RNAs may now be quantified and annotated regardless of whether they have previously been observed. We used RNA-Seq to investigate global patterns of gene expression in early developing rat liver. Liver samples from timed-pregnant Lewis rats were collected at six fetal and neonatal stages [embryonic day (E)14, E16, E18, E20, postnatal day (P)1, P7], transcripts were sequenced using an Illumina HiSeq 2000, and data analysis was performed with the Tuxedo software suite. Genes and isoforms differing in abundance were queried for enrichment within functionally related gene groups using the Functional Annotation Tool of the DAVID Bioinformatics Database. While hematopoietic gene expression is initiated by E14, hepatocyte maturation is a gradual process involving clusters of genes responsible for response to nutrients and enzymes responsible for glycolysis and fatty acid catabolism. Following birth, a large cluster of differentially abundant genes was enriched for mitochondrial gene expression and cholesterol synthesis indicating that by 1 wk of age, the liver is engaged in lipid sensing and bile production. Clustering results for differentially abundant genes and isoforms were similar with the greatest difference for the E14/E16 comparison. Finally, a bioinformatic approach was used to annotate 1,307 novel liver transcripts assembled from sequences that aligned to intergenic regions of the rat genome.

scholarly journals Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12104
Author(s):  
Bastian Bentlage ◽  
Allen G. Collins
Keyword(s):  
Maximum Likelihood ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Life Cycles ◽  
Tree Topologies ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Inference Methods

Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydroidolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.

scholarly journals Different gene rearrangements of the genus Dardanus (Anomura: Diogenidae) and insights into the phylogeny of Paguroidea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ying Zhang ◽  
Lei Meng ◽  
Liming Wei ◽  
Xinting Lu ◽  
Bingjian Liu ◽  
...  
Keyword(s):  
Gene Order ◽  
Gene Rearrangement ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Purifying Selection ◽  
Sister Group ◽  
Genetic Distances ◽  
Hermit Crabs

AbstractComplete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and molecular evolution. In this study, the complete mitogenomes of two hermit crabs, Dardanus arrosor and Dardanus aspersus, were sequenced for the first time and compared with other published mitogenomes of Paguroidea. Each of the two mitogenomes contains an entire set of 37 genes and a putative control region, but they display different gene arrangements. The different arrangements of the two mitogenomes might be the result of transposition, reversal, and tandem duplication/random loss events from the ancestral pancrustacean pattern. Genome sequence similarity analysis reveals the gene rearrangement in 15 Paguroidea mitogenomes. After synteny analysis between the 15 Paguroidea mitogenomes, an obvious rearranged region is found in D. aspersus mitogenome. Across the 13 protein-coding genes (PCGs) tested, COI has the least and ND6 has the largest genetic distances among the 15 hermit crabs, indicating varied evolution rates of PCGs. In addition, the dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. The phylogenetic analyses based on both gene order and sequence data present the monophyly of three families (Paguridae, Coenobitidae, and Pylochelidae) and the paraphyly of the family Diogenidae. Meanwhile, the phylogenetic tree based on the nucleotide sequences of 13 PCGs shows that two Dardanus species formed a sister group with five Coenobitidae species. These findings help to better understand the gene rearrangement and phylogeny of Paguroidea, as well as provide new insights into the usefulness of mitochondrial gene order as a phylogenetic marker.

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