Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), Using Multilocus Sanger Sequence and Genomic ddRADseq Data

Abstract BACKGROUND The recent molecular analyses have revealed that central nervous system primitive neuroectodermal tumors (CNS PNETs) those having clusters of small round tumor cells are genetically different tumors. However, the concepts of CNS PNET are complicated, and it is difficult to diagnose them appropriately in clinical field. To overcome this difficulty, we reviewed previous studies associated with CNS PNETs, and carried out several approaches, those are relatively easy access to use in clinics, for our 8 samples of embryonal brain tumors diagnosed CNS PNETs in our institution, initially. METHODS We used in combination with immunohistochemistry (IHC), Sanger sequence, Pyrosequence, polymerase chain reaction (PCR), real time PCR and copy number analysis referring recent reports. RESULTS In terms of the diagnosis three out of 8 cases were changed based on the results in this study from previous diagnoses. CONCLUSION In this review, it seemed that either the histopathological evaluation or molecular analyses would be not enough to make accurate diagnosis of CNS embryonal brain tumors, and it is essential to combine both of them including recent comprehensive analysis methods.

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Sanger sequence data

UQ eSpace ◽

10.14264/f801edd ◽

2021 ◽

Author(s):

Mohamed Cassim Mohamed Zakeel ◽

Akinsanmi Olufemi ◽

Geering Andrew

Keyword(s):

Sequence Data ◽

Sanger Sequence

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Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing

Scientific Reports ◽

10.1038/s41598-021-01749-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Albina Nowak ◽

Omer Murik ◽

Tzvia Mann ◽

David A. Zeevi ◽

Gheona Altarescu

Keyword(s):

Fabry Disease ◽

Copy Number ◽

New Technology ◽

Copy Number Variants ◽

Cost Effective ◽

Nanopore Sequencing ◽

Oxford Nanopore ◽

Long Read ◽

Sanger Sequence ◽

Gla Gene

AbstractMore than 900 variants have been described in the GLA gene. Some intronic variants and copy number variants in GLA can cause Fabry disease but will not be detected by classical Sanger sequence. We aimed to design and validate a method for sequencing the GLA gene using long-read Oxford Nanopore sequencing technology. Twelve Fabry patients were blindly analyzed, both by conventional Sanger sequence and by long-read sequencing of a 13 kb PCR amplicon. We used minimap2 to align the long-read data and Nanopolish and Sniffles to call variants. All the variants detected by Sanger (including a deep intronic variant) were also detected by long-read sequencing. One patient had a deletion that was not detected by Sanger sequencing but was detected by the new technology. Our long-read sequencing-based method was able to detect missense variants and an exonic deletion, with the added advantage of intronic analysis. It can be used as an efficient and cost-effective tool for screening and diagnosing Fabry disease.

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Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)

F1000Research ◽

10.12688/f1000research.38156.1 ◽

2021 ◽

Vol 10 ◽

pp. 289

Author(s):

Xiao Ma ◽

Jeanine L. Olsen ◽

Thorsten B.H. Reusch ◽

Gabriele Procaccini ◽

Dave Kudrna ◽

...

Keyword(s):

Genome Assembly ◽

Zostera Marina ◽

Draft Genome ◽

High Molecular Weight Dna ◽

Protein Coding ◽

New Findings ◽

Long Read ◽

Sanger Sequence ◽

Assembly Pipeline ◽

Chromosome Level

Background: Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding. Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.

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Fleas are parasitic scorpionflies

Palaeoentomology ◽

10.11646/palaeoentomology.3.6.16 ◽

2020 ◽

Vol 3 (6) ◽

pp. 641-653

Author(s):

ERIK TIHELKA ◽

MATTIA GIACOMELLI ◽

DI-YING HUANG ◽

DAVIDE PISANI ◽

PHILIP C. J. DONOGHUE ◽

...

Keyword(s):

Blood Feeding ◽

Morphological Characters ◽

Phylogenetic Position ◽

Murine Typhus ◽

Protein Coding ◽

Important Group ◽

Insect Order ◽

Heterogeneous Models ◽

Sanger Sequence ◽

Molecular Dataset

Fleas (Siphonaptera) are medically important blood-feeding insects responsible for spreading pathogens such as plague, murine typhus, and myxomatosis. The peculiar morphology of fleas resulting from their specialised ectoparasitic lifestyle has meant that the phylogenetic position of this diverse and medically important group has remained one of the most persistent problems in insect evolution. Here we test competing hypotheses on the contentious evolutionary relationships of fleas and antliophoran insects using the largest molecular dataset available to date consisting of over 1,400 protein-coding genes, and a smaller mitogenome and Sanger sequence alignment of 16 genes. By removing ambiguously aligned sequence regions and using site-heterogeneous models, we consistently recover fleas nested within scorpionflies (Mecoptera) as sister to the relictual southern hemisphere family Nannochoristidae. Topology tests accounting for compositional heterogeneity strongly favour the proposed topology over previous hypotheses of antliophoran relationships. This clade is diagnosed by shared morphological characters of the head and sperm pump. Fleas may no longer be regarded as a separate insect order and we propose that Siphonaptera should be treated as an infraorder within Mecoptera, reducing the number of extant holometabolan insect orders to ten.

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A Novel GEMIN4 Variant in a Consanguineous Family Leads to Neurodevelopmental Impairment with Severe Microcephaly, Spastic Quadriplegia, Epilepsy, and Cataracts

Genes ◽

10.3390/genes13010092 ◽

2021 ◽

Vol 13 (1) ◽

pp. 92

Author(s):

Hesham Aldhalaan ◽

Albandary AlBakheet ◽

Sarah AlRuways ◽

Nouf AlMutairi ◽

Maha AlNakiyah ◽

...

Keyword(s):

Clinical Features ◽

Phenotypic Characteristics ◽

Pathogenic Variants ◽

Whole Exome ◽

Spastic Quadriplegia ◽

Novel Variant ◽

Sanger Sequence ◽

Saudi Family ◽

Neurodevelopmental Impairment ◽

Renal Abnormalities

Pathogenic variants in GEMIN4 contribute to a hereditary disorder characterized by neurodevelopmental features, microcephaly, cataracts, and renal abnormalities (known as NEDMCR). To date, only two homoallelic variations have been linked to the disease. Moreover, clinical features associated with the variants have not been fully elucidated yet. Here, we identified a novel variant in GEMIN4 (NM_015721:exon2:c.440A>G:p.His147Arg) in two siblings from a consanguineous Saudi family by using whole exome sequencing followed by Sanger sequence verification. We comprehensively investigated the patients’ clinical features, including brain imaging and electroencephalogram findings, and compared their phenotypic characteristics with those of previously reported cases. In silico prediction and structural modeling support that the p.His147Arg variant is pathogenic.

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Detection of Single Nucleotide and Copy Number Variants in the Fabry Disease-associated GLA Gene Using Nanopore Sequencing

10.21203/rs.3.rs-579267/v1 ◽

2021 ◽

Author(s):

Albina Nowak ◽

Omer Murik ◽

Tzvia Mann ◽

David A. Zeevi ◽

Gheona Altarescu

Keyword(s):

Fabry Disease ◽

Copy Number ◽

New Technology ◽

Copy Number Variants ◽

Cost Effective ◽

Nanopore Sequencing ◽

Oxford Nanopore ◽

Long Read ◽

Sanger Sequence ◽

Gla Gene

Abstract Introduction: More than one thousand variants have been described in the GLA gene. Some intronic variants and copy number variants in GLA can cause Fabry disease but will not be detected by classical Sanger sequence.Aims: We aimed to design and validate a method for sequencing the GLA gene using long read Oxford Nanopore sequencing technology.Methods: Twelve Fabry patients were blindly analyzed, both by conventional Sanger sequence and by long read sequencing of a 13kb PCR amplicon. We used minimap2 to align the long read data and Nanopolish and Sniffles to call variants.Results: All the variants detected by Sanger (including a deep intronic variant) were also detected by long read sequencing. One patient had a deletion that was not detected by Sanger sequencing but was detected by the new technology.Conclusions: Our long read sequencing-based method was able to detect missense variants and an exonic deletion, with the added advantage of intronic analysis. It can be used as an efficient and cost-effective tool for screening and diagnosing Fabry disease.

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Phylogeny of the species-rich Pilea Lindl. (Urticaceae) supports its revised delimitation and infrageneric classification, including the resurrection of Achudemia Blume

10.1101/2020.07.01.180109 ◽

2020 ◽

Author(s):

Long-Fei Fu ◽

Fang Wen ◽

Olivier Maurin ◽

Michele Rodda ◽

Yi-Gang Wei ◽

...

Keyword(s):

Morphological Traits ◽

Sequence Data ◽

Fruit Size ◽

Monophyletic Clade ◽

Infrageneric Classification ◽

Sanger Sequence ◽

Nuclear Regions ◽

First Time ◽

Scientific Questions ◽

Do So

ABSTRACTPilea Lindl., with 933 published names is the largest genus within the Urticaceae. Pilea was last monographed in 1869 and whilst the monophyly of the genus has been proposed by previous authors, this has been based on incomplete taxon sampling and the failure to resolve the position of key taxa. We aimed to generate a robust phylogeny for Pilea and allied genera that could provide a framework for testing the monophyly of Pilea, revising its delimitation and for answering broader scientific questions about this species-rich genus. To do so, we sought to sample taxa representative of previous infrageneric classifications and with anomalous inflorescences or flower configurations and to use the resulting phylogeny to evaluate the delimitation of Pilea and to establish an infrageneric classification. In addition, we included a representative of the Polynesian genus Haroldiella which, morphologically, is very similar to Pilea. Using Sanger sequence data from two plastid and one nuclear regions we constructed a phylogeny using Bayesian Inference, Maximum Likelihood and Maximum Parsiomony approaches. We used our phylogeny to evaluate the informativness of 19 morphological traits and applied both to delimit a monophyletic genus and infrageneric sections. Our results recovered Pilea as paraphyletic with respect to Lecanthus, a consequence of the recovery of a monophyletic clade comprising sections Achudemia and Smithiella, neither of which had been adequately sampled in previous studies. We also recovered Pilea as polyphyletic with respect to Haroldiella. We identified isomery between male and female flowers, flower part number and male sepal arrangement as being phylogenetically informative traits that can be used to delimit two genera, Achudemia, including section Smithiella, recovered as sister to Lecanthus, and Pilea, including Haroldiella, recovered as sister to both. On the basis of our evaluation of both morphological traits and phylogenetic relationships we propose a new infrageneric classification for the genus comprising seven sections, five of which we describe for the first time, § Trimeris Y.G.Wei & A.K.Monro, § Lecanthoides C.J.Chen, § Angulata L.F.Fu & Y.G.Wei, § Tetrameris C.J.Chen, § Verrucosa L.F.Fu & Y.G.Wei, § Plataniflora L.F.Fu & Y.G.Wei and § Leiocarpa L.F.Fu & Y.G.Wei. We also identify a trend of decreasing merism and fruit size, and increasing species-richness as Pilea diverges. In addition, we recover strong geographical structure within our phylogeny, sufficient to propose that Pilea originated in the IndoMalaya biogeographic domain.

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Haplotyping MHC class IIa by high throughput screening in an isolated sheep population

10.1101/2020.07.20.212225 ◽

2020 ◽

Author(s):

K.L. Dicks ◽

J.M. Pemberton ◽

K.T. Ballingall ◽

S.E. Johnston

Keyword(s):

High Throughput Screening ◽

Population Data ◽

Ovis Aries ◽

Island Population ◽

Sheep Population ◽

Soay Sheep ◽

Histocompatibility Complex ◽

Content Variation ◽

Sanger Sequence ◽

Polymorphic Gene

AbstractInvestigating the current evolutionary processes acting on a highly polymorphic gene region, such as the major histocompatibility complex (MHC), requires extensive population data for both genotypes and phenotypes. The MHC consists of several tightly linked loci with both allelic and gene content variation, making it challenging to genotype. Eight class IIa haplotypes have previously been identified in the Soay sheep (Ovis aries) of St. Kilda using Sanger sequencing and cloning, but no single locus is representative of all haplotypes. Here, we exploit the closed nature of the island population of Soay sheep and its limited haplotypic variation to identify a panel of SNPs that enable imputation of MHC haplotypes. We compared MHC class IIa haplotypes determined by Sanger sequence-based genotyping of 135 individuals to their SNP profiles generated using the Ovine Infinium HD BeadChip. A panel of 11 SNPs could reliably determine MHC diplotypes, and two additional SNPs within the DQA1 gene enabled detection of a recombinant SNP haplotype. The panel of 13 SNPs was genotyped in 5951 sheep, of which 5349 passed quality control. Using the Soay sheep pedigree, we were able to trace the origin and inheritance of a recombinant SNP haplotype.

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From metabarcoding to metaphylogeography: separating the wheat from the chaff

10.1101/629535 ◽

2019 ◽

Cited By ~ 5

Author(s):

Xavier Turon ◽

Adrià Antich ◽

Creu Palacín ◽

Kim Præbel ◽

Owen Simon Wangensteen

Keyword(s):

Genetic Variability ◽

Sequence Data ◽

Β Diversity ◽

Haplotype Networks ◽

Main Challenge ◽

Invasion Genetics ◽

Sanger Sequence ◽

Long Time ◽

Codon Positions ◽

Occurrence Patterns

AbstractMetabarcoding is by now a well-established method for biodiversity assessment in terrestrial, freshwater and marine environments. Metabarcoding datasets are usually used for α- and β-diversity estimates, that is, interspecies (or inter-MOTU) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra-MOTU) information - mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding datasets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field which we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra-MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co-occurrence patterns of sequences. Using a dataset of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two-step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole dataset. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between-seas component as well. There were inter-group differences in the amount of variability between and within communities in each sea. For two species the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra- and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.

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