scholarly journals Discovery of novel representatives of bilaterian neuropeptide families and reconstruction of neuropeptide precursor evolution in ophiuroid echinoderms

2017 ◽  
Author(s):  
Meet Zandawala ◽  
Ismail Moghul ◽  
Luis Alfonso Yañez Guerra ◽  
Jérôme Delroisse ◽  
Nikara Abylkassimova ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Copy ◽  
Intercellular Signaling ◽  
Eclosion Hormone ◽  
Transcriptome Sequence Data ◽  
Neuronal Regulation ◽  
Amphiura Filiformis ◽  
Precursor Proteins ◽  
Multiple Copies ◽  
First Time

AbstractNeuropeptides are a diverse class of intercellular signaling molecules that mediate neuronal regulation of many physiological and behavioural processes. Recent advances in genome/transcriptome sequencing are enabling identification of neuropeptide precursor proteins in species from a growing variety of animal taxa, providing new insights into the evolution of neuropeptide signaling. Here detailed analysis of transcriptome sequence data from three brittle star species, Ophionotus victoriae, Amphiura filiformis and Ophiopsila aranea, has enabled the first comprehensive identification of neuropeptide precursors in the class Ophiuroidea of the phylum Echinodermata. Representatives of over thirty bilaterian neuropeptide precursor families were identified, some of which occur as paralogs. Furthermore, homologs of endothelin/CCHamide, eclosion hormone, neuropeptide-F/Y and nucleobinin/nesfatin were discovered here in a deuterostome/echinoderm for the first time. The majority of ophiuroid neuropeptide precursors contain a single copy of a neuropeptide, but several precursors comprise multiple copies of identical or non-identical, but structurally-related, neuropeptides. Here we performed an unprecedented investigation of the evolution of neuropeptide copy-number over a period of ~270 million years by analysing sequence data from over fifty ophiuroid species, with reference to a robust phylogeny. Our analysis indicates that the composition of neuropeptide “cocktails” is functionally important, but with plasticity over long evolutionary time scales.

scholarly journals Discovery of novel representatives of bilaterian neuropeptide families and reconstruction of neuropeptide precursor evolution in ophiuroid echinoderms

Open Biology ◽  
2017 ◽  
Vol 7 (9) ◽  
pp. 170129 ◽  
Author(s):  
Meet Zandawala ◽  
Ismail Moghul ◽  
Luis Alfonso Yañez Guerra ◽  
Jérôme Delroisse ◽  
Nikara Abylkassimova ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Copy ◽  
Signalling Molecules ◽  
Transcriptome Sequence Data ◽  
Neuronal Regulation ◽  
Amphiura Filiformis ◽  
Precursor Proteins ◽  
Multiple Copies ◽  
Intercellular Signalling ◽  
First Time

Neuropeptides are a diverse class of intercellular signalling molecules that mediate neuronal regulation of many physiological and behavioural processes. Recent advances in genome/transcriptome sequencing are enabling identification of neuropeptide precursor proteins in species from a growing variety of animal taxa, providing new insights into the evolution of neuropeptide signalling. Here, detailed analysis of transcriptome sequence data from three brittle star species, Ophionotus victoriae , Amphiura filiformis and Ophiopsila aranea , has enabled the first comprehensive identification of neuropeptide precursors in the class Ophiuroidea of the phylum Echinodermata. Representatives of over 30 bilaterian neuropeptide precursor families were identified, some of which occur as paralogues. Furthermore, homologues of endothelin/CCHamide, eclosion hormone, neuropeptide-F/Y and nucleobinin/nesfatin were discovered here in a deuterostome/echinoderm for the first time. The majority of ophiuroid neuropeptide precursors contain a single copy of a neuropeptide, but several precursors comprise multiple copies of identical or non-identical, but structurally related, neuropeptides. Here, we performed an unprecedented investigation of the evolution of neuropeptide copy number over a period of approximately 270 Myr by analysing sequence data from over 50 ophiuroid species, with reference to a robust phylogeny. Our analysis indicates that the composition of neuropeptide ‘cocktails’ is functionally important, but with plasticity over long evolutionary time scales.

scholarly journals Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy

2021 ◽  
Author(s):  
Wayne Xu ◽  
James R Tucker ◽  
Wubishet A Bekele ◽  
Frank M You ◽  
Yong-Bi Fu ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
Barley Cultivar ◽  
Malting Barley ◽  
Orthologous Genes ◽  
Hordeum Vulgare L ◽  
Chromosome Conformation ◽  
Mate Pair ◽  
Genome Assemblies ◽  
First Time

Abstract Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

Human actin genes are single copy for alpha-skeletal and alpha-cardiac actin but multicopy for beta- and gamma-cytoskeletal genes: 3' untranslated regions are isotype specific but are conserved in evolution

1983 ◽  
Vol 3 (10) ◽  
pp. 1783-1791
Author(s):  
P Ponte ◽  
P Gunning ◽  
H Blau ◽  
L Kedes
Keyword(s):  
Human Genome ◽  
Single Copy ◽  
Untranslated Regions ◽  
Muscle Actin ◽  
Actin Genes ◽  
Hybridization Probes ◽  
Single Exception ◽  
Multiple Copies ◽  
Human Genomic ◽  
Unambiguous Assignment

We have constructed isotype-specific subclones from the 3' untranslated regions of alpha-skeletal, alpha-cardiac, beta-cytoskeletal, and gamma-cytoskeletal actin cDNAs. These clones have been used as hybridization probes to assay the number and organization of these actin isotypes in the human genome. Hybridization of these probes to human genomic actin clones (Engel et al., Proc. Natl. Acad. Sci. U.S.A. 78:4674-4678, 1981; Engel et al., Mol. Cell. Biol. 2:674-684, 1982) has allowed the unambiguous assignment of the genomic clones to isotypically defined actin subfamilies. In addition, only one isotype-specific probe hybridizes to each actin-containing gene, with a single exception. This result suggests that the multiple actin genes in the human genome are not closely linked. Genomic DNA blots probed with these subclones under stringent conditions demonstrate that the alpha-skeletal and alpha-cardiac muscle actin genes are single copy, whereas the cytoskeletal actins, beta and gamma, are present in multiple copies in the human genome. Most of the actin genes of other mammals are cytoplasmic as well. These observations have important implications for the evolution of multigene families.

scholarly journals Sequences of the second internal transcribed spacer of ribosomal DNA for three species of Trichostrongylus (Nematoda: Trichostrongylidae) from sheep in Russia

2007 ◽  
Vol 44 (2) ◽  
pp. 43-46 ◽  
Author(s):  
D. Kuznetsov ◽  
N. Kuznetsova
Keyword(s):  
Dna Sequence ◽  
Intraspecific Variation ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Moscow Region ◽  
Dna Sequence Data ◽  
Interspecific Differences ◽  
Second Internal Transcribed Spacer ◽  
First Time

AbstractFor the first time, DNA sequence data were obtained for three species of Trichostrongylus from Russia. Internal transcribed spacer (ITS-2) of ribosomal DNA was sequenced for T. axei, T. colubriformis and T. probolurus from sheep from the Moscow region. ITS-2 rDNA length was estimated as 238 nucleotides for T. colubriformis and T. probolurus and 237 nucleotides for T. axei. The G+C content of the ITS-2 sequences of T. colubriformis, T. axei and T. probolurus were 31 %, 32 % and 34 % respectively. The level of interspecific differences in ITS-2 of rDNA of T. axei, T. probolurus and T. colubriformis ranged from 3 to 4 %. The ITS-2 sequences from the Russian specimens were compared with those of T. axei, T. probolurus and T. colubriformis from Australia and Germany. Intraspecific variation ranged from 0 % in T. colubriformis to 3.0 % in T. axei.

Clathrosporium retortum, a novel aeroaquatic fungus in the Sordariomycetidae (Ascomycota) from Brazil

Phytotaxa ◽  
2015 ◽  
Vol 239 (1) ◽  
pp. 17
Author(s):  
Larissa Bernardino Moro ◽  
Gregorio Delgado ◽  
Iracema Helena SCHOENLEIN-CRUSIUS
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Molecular Data ◽  
Sao Paulo ◽  
São Paulo ◽  
Present Fungus ◽  
Broad Concept ◽  
Morphological And Molecular Data ◽  
First Time

Clathrosporium retortum sp. nov., collected on submerged mixed leaf litter samples at Ilha do Cardoso State Park, São Paulo state, Brazil, is described based on morphological and molecular data. The fungus is characterized by forming whitish, dense, subglobose to irregular propagules, hyaline to subhyaline when young, subhyaline to dark brown at maturity, that are formed by densely interwoven conidial filaments with each conidial cell repeatedly branching bilaterally or occasionally unilaterally. Phylogenetic analyses using partial LSU nrDNA sequence data suggest that C. retortum belongs in the Sordariomycetes (Ascomycota) where it forms a well-supported clade with Clohesia corticola in the Sordariomycetidae, but its ordinal or familial placement remains unresolved. Its phylogenetic placement confirms the polyphyletic nature of aeroaquatic fungi like Clathrosporium, as it was distantly related to one available sequence in GenBank named as C. intricatum, the type species, which is phylogenetically related to the Helotiales (Leotiomycetes). However, due to lack of authenticity of the identity of this sequence with the type specimen of C. intricatum, a broad concept of Clathrosporium is tentatively adopted here to accommodate the present fungus instead of introducing a new genus. Beverwykella clathrata, Helicoön septatissimum and Peyronelina glomerulata are recorded for the first time from Brazil. Cancellidium applanatum and Candelabrum brocchiatum are new records for the state of São Paulo.

JUXTAPOSING LITERARY AND DOCUMENTARY EVIDENCE: A NEW COPY OF THE SO-CALLED HELIODOROS STELE AND THE CORPUS INSCRIPTIONUM IUDAEAE/PALAESTINAE (CIIP)

2017 ◽  
Vol 60 (1) ◽  
pp. 1-15
Author(s):  
HANNAH M. COTTON-PALTIEL ◽  
AVNER ECKER ◽  
DOV GERA
Keyword(s):  
Documentary Evidence ◽  
High Priest ◽  
The Third ◽  
Multiple Copies ◽  
First Time ◽  
The Temple

Abstract This article was prompted by the recent discovery of two more copies of the so-called ‘Heliodoros Stele’ from Maresha. A second one from Byblos was published in 2015. The third one, re-discovered recently and published here for the first time, also comes from Maresha. The steles bear Seleukos IV's epistolary prostagma from 178 bc to his vizier Heliodoros, and forwarded to other officials with the instruction to display it in public. It contains an appointment of one Olympiodoros to be high priest in Koele Syria and Phoenicia. Both Seleukos IV and Heliodoros also appear in the story of the plundering of the Temple related in II Maccabees 3. The existence of multiple copies, though hardly surprising, made us suspect the king's apologetic tone and identify the ‘reform’ as an attempt to embellish the withdrawal of previously bestowed privileges on the Jews (so Josephus) as well as on others.

Selection and validation of reference genes for quantitative real-time PCR in Artemisia sphaerocephala based on transcriptome sequence data

Gene ◽  
2018 ◽  
Vol 657 ◽  
pp. 39-49 ◽  
Author(s):  
Xiaowei Hu ◽  
Lijing Zhang ◽  
Shuzhen Nan ◽  
Xiumei Miao ◽  
Pengfang Yang ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Reference Genes ◽  
Sequence Data ◽  
Quantitative Real Time Pcr ◽  
Transcriptome Sequence Data ◽  
Artemisia Sphaerocephala

A new Australian record of a Parajapidae (Diplura): a potential pest of wheat

Soil Research ◽  
2018 ◽  
Vol 56 (7) ◽  
pp. 657
Author(s):  
Penelope Greenslade ◽  
Yun-Xia Luan
Keyword(s):  
Sequence Data ◽  
New South ◽  
Agricultural Crops ◽  
Deep Soil ◽  
South Wales ◽  
Potential Pest ◽  
North And South America ◽  
First Time ◽  
North And South

Parajapyx isabellae (Grassi, 1886) is recorded for the first time from Australia. It is a cosmopolitan soil species found in Europe, North and South America and Asia. Womersley last studied Australian Parajapygidae 80 years ago, listing a single endemic species for the genus Parajapyx Silvestri, 1903, sensu stricta. In 2017, an unidentified Parajapyx was found in deep soil under wheat in winter, spring and summer at Harden, New South Wales, in a long-term tillage trial. It was most abundant in the minimum tillage/stubble retained plots in soil below 5 cm but rarely observed in the conventionally tilled/stubble burned plots. The same field experiment was sampled five times using the same methods over 3 years from 1993–95 but no specimens of Diplura were collected. The specimens were identified as P. isabellae using morphology and confirmed with the DNA barcoding sequence data. Most species of Parajapygidae are carnivores feeding on small arthropods but there are records from North America, Europe and Hawaii of P. isabellae feeding on roots of wheat and other agricultural crops. We provide here illustrations of species P. isabellae so that crop scientists in Australia are aware of the potential pest and can identify it. Sequence data indicate that the population may have originated from two sources.

Systematics of the Australian golden trapdoor spiders of the Euoplos variabilis-group (Mygalomorphae : Idiopidae : Euoplini): parapatry and sympatry between closely related species in subtropical Queensland

2021 ◽  
Author(s):  
Jeremy D. Wilson ◽  
Michael G. Rix
Keyword(s):  
Species Delimitation ◽  
Systematic Approach ◽  
Sequence Data ◽  
Future Research ◽  
Populated Area ◽  
Closely Related Species ◽  
Taxonomic Description ◽  
Eastern Australia ◽  
First Time ◽  
Adequate Data

The Australian golden trapdoor spiders of the tribe Euoplini (family Idiopidae) are among the most abundant and diverse of mygalomorph lineages in subtropical eastern Australia. Throughout this highly populated area, species in the monophyletic Euoplos variabilis-group are largely ubiquitous; however, species delimitation has long proven difficult in the group because species are morphologically very similar and have parapatric or even sympatric distributions. We address these challenges in the variabilis-group, and explore the phylogeny and taxonomy of species using an integrative systematic approach. In doing so, we apply a conservative, pragmatic methodology, naming only species for which adequate data are available (namely sequence data and unequivocally linked male specimens), and explicitly stating and mapping material that could not be linked to a species, to aid future research on the group. We describe five new species from south-eastern Queensland –E. booloumba sp. nov., E. jayneae sp. nov., E. raveni sp. nov., E. regalis sp. nov. and E. schmidti sp. nov.; we redescribe two previously named species – E. similaris (Rainbow & Pulleine, 1918) and E. variabilis (Rainbow & Pulleine, 1918); and we reillustrate the recently described E. grandis Wilson & Rix, 2019. The nominate species, E. variabilis, is shown to have a far smaller distribution than previously thought, and E. similaris is given a modern taxonomic description for the first time. A key to adult male specimens is also provided. This study further reveals a case of sympatry between two species within the variabilis-group; both E. raveni sp. nov. and E. schmidti sp. nov. occur in the Brisbane Valley, south of the Brisbane River – a notable result given that closely related mygalomorph species usually occur allopatrically. This work updates what is currently known of the phylogeny and diversity of one of the dominant mygalomorph lineages of subtropical eastern Australia, resolving a complex and highly endemic fauna. http://zoobank.org/urn:lsid:zoobank.org:pub:A4FB92F6-EFFF-4468-B1D8-000D69923996

Structure and expression of the chicken ferritin H-subunit gene

1987 ◽  
Vol 7 (5) ◽  
pp. 1751-1758
Author(s):  
P W Stevens ◽  
J B Dodgson ◽  
J D Engel
Keyword(s):  
Chicken Genome ◽  
Single Copy ◽  
Transcription Unit ◽  
Subunit Gene ◽  
Conserved Sequence ◽  
Coding Regions ◽  
Mature Transcript ◽  
Multiple Copies ◽  
Human Ferritin ◽  
Ferritin H

Although the genomes of many species contain multiple copies of ferritin heavy (H)- and light (L)-chain sequences, the chicken genome contains only a single copy of the H-subunit gene. The primary transcription unit of this gene is 4.6 kilobase pairs and contains four exons which are posttranscriptionally spliced to generate a mature transcript of 869 nucleotides. Chicken and human ferritin H-subunit genomic loci are organized with similar exon-intron boundaries. They exhibit approximately 85% nucleotide identity in coding regions, which yield proteins 93% identical in amino acid sequence. We have identified a sequence of 22 highly conserved nucleotides in the 5' untranslated sequences of chicken, human, and tadpole ferritin H-subunit genes and propose that this conserved sequence may regulate iron-modulated translation of ferritin H-subunit mRNAs.

Sign in / Sign up

Export Citation Format

Share Document