scholarly journals Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae)

2021 ◽  
Vol 8 (9) ◽  
pp. 210474
Author(s):  
Nicolas Straube ◽  
Michaela Preick ◽  
Gavin J. P. Naylor ◽  
Michael Hofreiter
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Resource ◽  
Type Specimen ◽  
Model Organisms ◽  
Sequence Information ◽  
Similar Species ◽  
Dna Library ◽  
Reference Information ◽  
Dna Characteristics ◽  
Archival Dna

After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus , in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi . Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus . As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy.

scholarly journals Models of mitochondrial DNA transmission genetics and evolution in higher eucaryotes

1982 ◽  
Vol 40 (1) ◽  
pp. 41-57 ◽  
Author(s):  
Robert W. Chapman ◽  
J. Claiborne Stephens ◽  
Robert A. Lansman ◽  
John C. Avise
Keyword(s):  
Mitochondrial Dna ◽  
Population Biology ◽  
Sequence Information ◽  
Random Allocation ◽  
Cell Lineages ◽  
Daughter Cells ◽  
Mtdna Sequence ◽  
Population Sizes ◽  
Future Value ◽  
Mtdna Evolution

SUMMARYThe future value of mitochondrial DNA (mtDNA) sequence information to studies in population biology will depend in part on understanding of mtDNA transmission genetics both within cell lineages and between animal generations. A series of stochastic models has been constructed here based on various possibilities concerning this transmission. Several of the models generate predictions inconsistent with available data and, hence, their assumptions are provisionally rejected. Other models cannot yet be falsified. These latter models include assumptions that (1) mtDNA's are sorted through cellular lineages by random allocation to daughter cells in germ cell lineages; (2) the effective intracellular population sizes (nM's) of mtDNA's are small; and (3) sperm may (or may not) provide a low level ‘gene-flow’ bridge between otherwise isolated female lineages. It is hoped that the models have helped to identify and will stimulate further empirical study of various parameters likely to strongly influence mtDNA evolution. In particular, critical experiments or measurements are needed to determine the effective sizes of mtDNA populations in germ (and somatic) cells and to examine possible paternal contributions to zygote mtDNA composition.

scholarly journals A new species of Amphisbaena (Squamata: Amphisbaenidae) from the Orinoquian region of Colombia

2021 ◽  
Vol 71 ◽  
pp. 55-74
Author(s):  
Juan José Torres-Ramírez ◽  
Teddy Angarita-Sierra ◽  
Mario Vargas-Ramírez
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Phylogenetic Analyses ◽  
Similar Species ◽  
General Knowledge ◽  
Southern Brazil ◽  
Base Pairs ◽  
Northern South America ◽  
Great Genetic Distance ◽  
A New Species

In northern South America, amphisbaenians are rarely seen among the herpetofauna.Thus, general knowledge about them is very poor. During a herpetological survey in 2012 at Casanare, Colombia, we found two specimens of an unusual Amphisbaena. A third specimen sharing the same morphotype labeled Amphisbaena sp. from Vichada department was found deposided in an Colombian reptile collection. Based on morphological analyses together with phylogenetic analyses of 1029 base pairs of the mitochondrial DNA (mtDNA), we describe a new species of Amphisbaena that inhabits in the Orinoquian region of Colombia. The new species is part of a phylogenetic clade together with A. mertensii and A. cunhai (central-southern Brazil), exhibiting a great genetic distance (26.1–28.9%) between the newly identified lineage versus those taxa, and versus the sympatric taxa A. alba and A. fuliginosa. Morphologically, this new Amphisbaena can be distinguished from their congeners by characters combination of number of preocloacal pores, absence of malar scale, postgenial scales and body and caudal annuli counts. Amphisbaena gracilis is on morphology grounds the most similar species. However, the new species can be distinguished from it by having higher body annuli counts, angulus ories aliegned with the edges of the ocular scales and center of frontal scales, less number of large middorsal segments of the first and second body annulus, and rostral scale visible from above. The description of this new Amphisbaena species points out the urgent need to increase the knowledge of worm lizards in Colombia

scholarly journals Mitochondrial DNA Survey Reveals the Lack of Accuracy in Maremmano Horse Studbook Records

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 839 ◽  
Author(s):  
Andrea Giontella ◽  
Irene Cardinali ◽  
Hovirag Lancioni ◽  
Samira Giovannini ◽  
Camillo Pieramati ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Resource ◽  
High Variability ◽  
Pedigree Information ◽  
Pedigree Data ◽  
Local Breed ◽  
Ancient Population ◽  
Mitochondrial Haplotypes ◽  
Multiple Sampling ◽  
Genealogical Data

The Maremmano horse is considered one of the most important Italian warmblood breeds which originated from an ancient population. In 1980, the National Association of Maremmano Breeders established the first Studbook that recorded 440 dams and four sire founders. In this study, we selected the most significant maternal lines in terms of offspring (for a total of 74 lineages and 92 Maremmano horses) and analyzed their mitochondrial DNA control regions. We found a high variability, reflecting the importance of this local breed as a genetic resource to be preserved. Through multiple sampling, we then verified the pedigree information for 12 dam lines by matching genealogical data with mitochondrial haplotypes. A complete concordance was demonstrated in nine lineages, while for the other we highlighted a different number of haplotypes for each line (three in Fiorella, two in Nizza I, and two in Pomposina), thus suggesting that the information recorded in the Studbook could be wrong and the samples do not descend from the same maternal founder. Our combined analysis provides the opportunity to confirm the ancestry of animals and could be employed to prevent errors in pedigree data also for other breeds and species.

Insect omics research coming of age1This review is part of a virtual symposium on recent advances in understanding a variety of complex regulatory processes in insect physiology and endocrinology, including development, metabolism, cold hardiness, food intake and digestion, and diuresis, through the use of omics technologies in the postgenomic era.

2012 ◽  
Vol 90 (4) ◽  
pp. 440-455 ◽  
Author(s):  
Bart Boerjan ◽  
Dries Cardoen ◽  
Rik Verdonck ◽  
Jelle Caers ◽  
Liliane Schoofs
Keyword(s):  
Rna Interference ◽  
Cold Hardiness ◽  
Model Organisms ◽  
Sequence Information ◽  
Huge Amount ◽  
Omics Technologies ◽  
Regulatory Processes ◽  
Biological Aspects ◽  
Insect Biology ◽  
Functional Inactivation

As more and more insect genomes are fully sequenced and annotated, omics technologies, including transcriptomic, proteomic, peptidomics, and metobolomic profiling, as well as bioinformatics, can be used to exploit this huge amount of sequence information for the study of different biological aspects of insect model organisms. Omics experiments are an elegant way to deliver candidate genes, the function of which can be further explored by genetic tools for functional inactivation or overexpression of the genes of interest. Such tools include mainly RNA interference and are currently being developed in diverse insect species. In this manuscript, we have reviewed how omics technologies were integrated and applied in insect biology.

Designation of a neotype for the Brazilian porcupine, Coendou prehensilis (Linnaeus, 1758)

Zootaxa ◽  
2011 ◽  
Vol 2791 (1) ◽  
pp. 30 ◽  
Author(s):  
YURI L. R. LEITE ◽  
VILACIO CALDARA JÚNIOR ◽  
ANA CAROLINA LOSS ◽  
LEONORA PIRES COSTA ◽  
ÉVERTON R. A. MELO ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Geographic Distribution ◽  
Related Species ◽  
Taxonomic Revision ◽  
Type Specimen ◽  
Northeastern Brazil ◽  
Closely Related Species ◽  
Geographic Ranges ◽  
Central Brazil ◽  
Shed Light

The Brazilian porcupine was one of several species described and illustrated by the 17 th -century naturalist Georg Marcgrave, whose text was among the primary references upon which Linnaeus based his Hystrix prehensilis. As currently understood, Coendou prehensilis is a wide-ranging polytypic taxon that has never been revised and may represent a complex of closely related species. Given that no name-bearing type specimen of C. prehensilis is believed to be extant, and in order to avoid ambiguous application of this name, we designate a specimen collected at the type locality in Pernambuco, northeastern Brazil, as the neotype for Hystrix prehensilis Linnaeus. The geographic distribution of mitochondrial DNA haplotypes suggests that specimens from west-central Brazil previously identified as “Coendou prehensilis” belong to a different species, but only a comprehensive taxonomic revision of the genus will shed light on species limits and the geographic ranges of C. prehensilis and other congeneric forms.

scholarly journals Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

2020 ◽  
Author(s):  
Michal Levin ◽  
Marion Scheibe ◽  
Falk Butter
Keyword(s):  
Mass Spectrometry ◽  
Bombyx Mori ◽  
Cell Line ◽  
De Novo ◽  
High Resolution Mass Spectrometry ◽  
Gene Annotation ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
Sequence Information ◽  
A Genome

Abstract BackgroundThe process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-Seq or mass spectrometry. While satisfactory annotation has been made feasible for well-studied model organisms through great efforts of big consortia, for most systems this kind of data is either absent or not adequately precise. ResultsCombining in-depth transcriptome sequencing and high resolution mass spectrometry, we here use proteotranscriptomics to improve gene annotation of protein-coding genes in the Bombyx mori cell line BmN4 which is an increasingly used tool for the analysis of piRNA biogenesis and function. Using this approach we provide the exact coding sequence and evidence for more than 6,200 genes on the protein level. Furthermore using spatial proteomics, we establish the subcellular localization of thousands of these proteins. We show that our approach outperforms current Bombyx mori annotation attempts in terms of accuracy and coverage. ConclusionsWe show that proteotranscriptomics is an efficient, cost-effective and accurate approach to improve previous annotations or generate new gene models. As this technique is based on de-novo transcriptome assembly, it provides the possibility to study any species also in the absence of genome sequence information for which proteogenomics would be impossible.

scholarly journals Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis

2020 ◽  
Author(s):  
Nan Dong ◽  
Julia Bandura ◽  
Zhaolei Zhang ◽  
Yan Wang ◽  
Karine Labadie ◽  
...  
Keyword(s):  
Ion Channels ◽  
Reference Genome ◽  
Lymnaea Stagnalis ◽  
De Novo ◽  
Model Organisms ◽  
Sequence Length ◽  
Pond Snail ◽  
Sequence Information ◽  
Functional Domain ◽  
Rna Seq

Abstract Background. The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its CNS. However, its usefulness is restricted by a limited availability of transcriptome data. While sequence information for the L. stagnalis CNS transcripts has been obtained from EST library and a de novo RNA-seq assembly, the quality of these assemblies is limited by a combination of low coverage of EST libraries, the fragmented nature of de novo assemblies, and lack of reference genome. Results. In this study, taking advantage of the recent availability of the L. stagnalis reference genome, we generated an RNA-seq library from the adult L. stagnalis CNS, using a combination of genome-guided and de novo assembly programs to identify 17,832 protein-coding L. stagnalis transcripts. We combined our library with existing resources to produce a transcript set with greater sequence length, completeness, and diversity than previously available ones. Using our assembly and functional domain analysis, we profiled L. stagnalis CNS transcripts encoding ion channels and ionotropic receptors, which are key proteins for CNS function, and compared their sequences to other vertebrate and invertebrate model organisms. Interestingly, L. stagnalis transcripts encoding numerous putative Ca2+ channels showed the most sequence similarity to those of mouse, zebrafish, Xenopus tropicalis, fruit fly, and C. elegans, suggesting that many calcium channel-related signaling pathways may be evolutionarily conserved. Conclusions. Our study provides the most thorough characterization to date of the L. stagnalis transcriptome and provides insights into differences between vertebrates and invertebrates in CNS transcript diversity, according to function and protein class. Furthermore, this study is, to the best of our knowledge, the first to provide a complete characterization of the ion channels of a single species, opening new avenues for future research on fundamental neurobiological processes.

scholarly journals Phylogeography and Phylogenetic Evolution in Tibetan Sheep Based on MT-CYB Sequences

Animals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1177
Author(s):  
Jianbin Liu ◽  
Zengkui Lu ◽  
Chao Yuan ◽  
Fan Wang ◽  
Bohui Yang
Keyword(s):  
Mitochondrial Dna ◽  
Tibetan Plateau ◽  
Clustering Analysis ◽  
Genetic Resource ◽  
Population Studies ◽  
Ovis Aries ◽  
Base Pairs ◽  
Branching Order ◽  
Tibetan Sheep ◽  
Phylogenetic Evolution

To date, molecular genetics and population studies in Tibetan sheep (Ovis aries) have been limited, and little is known about the phylogenetic evolution and phylogeography of Tibetan sheep populations. The aim of the present research was to explore phylogeography and phylogenetic evolution of Tibetan sheep populations, on the basis of mitochondrial DNA (mtDNA) gene MT-CYB (1140 base pairs). Our dataset consisted of 641 MT-CYB sequences from the same amount of animals belonging to 15 populations of Tibetan sheep living in the Qinghai–Tibetan Plateau, China. Haplotype and nucleotide diversities were 0.748 ± 0.010 and 0.003 ± 0.001, respectively. The analysis of phylogeography revealed the presence of two formerly described haplogroups in 15 populations of Tibetan sheep, however only one haplogroup was present in Awang sheep. Moreover, 641 Tibetan sheep were distributed into a minimum of two clusters by clustering analysis. The 15 Tibetan sheep populations and 19 reference populations of 878 individuals were separated into six main groups based on their substitutions per site, from which we constructed a phylogenetic tree. Minor differences in branching order of various taxa between trees acquired from either gene were observed. This study provides insights on the origins and phylogenetic evolution of populations residing in the Qinghai–Tibetan Plateau, which will aid information of future conservation programs aimed at conserving this valuable genetic resource.

Untangling the type collection and recircunscription of Pseudolaelia corcovadensis: a threatened orchid species from Brazilian Atlantic Rain Forest

Phytotaxa ◽  
2020 ◽  
Vol 433 (4) ◽  
pp. 265-276
Author(s):  
MARILIA S. WÄNGLER ◽  
THIAGO E. C. MENEGUZZO ◽  
CÁSSIO VAN DEN BERG ◽  
JOSÉ FERNANDO A. BAUMGRATZ
Keyword(s):  
Geographical Distribution ◽  
Rain Forest ◽  
Type Specimen ◽  
Morphological Description ◽  
Atlantic Rain Forest ◽  
Similar Species ◽  
Careful Study ◽  
Type Collection ◽  
Orchid Species ◽  
Forest Biome

Understanding the composition of the type specimen of Pseudolaelia corcovadensis is very important for establishing its taxonomic circumscription. This specimen, originally collected on the Morro do Corcovado in the municipality of Rio de Janeiro, within the Atlantic Forest biome, were mixed with those of another species of Pseudolaelia. A careful study of the specimens has made it possible to propose the lectotypification of P. corcovadensis and determine the identity of the mixed specimen, which corresponds to P. vellozicola, a similar species. The morphological description and geographical distribution, now more restricted, are presented for P. corcovadensis, and the range of P. vellozicola is established as more extensive than previously understood.

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