scholarly journals The germline-specific region of the sea lamprey genome plays a key role in spermatogenesis

2021 ◽  
Author(s):  
Tamanna Yasmin ◽  
Phil Grayson ◽  
Margaret F. Docker ◽  
Sara V. Good
Keyword(s):  
Sex Determination ◽  
Genome Rearrangement ◽  
De Novo ◽  
Sequence Data ◽  
Gonad Development ◽  
Sea Lamprey ◽  
Specific Region ◽  
A Genome ◽  
Reproductive Processes

The sea lamprey genome undergoes programmed genome rearrangement (PGR) in which ~20% is jettisoned from somatic cells soon after fertilization. Although the role of PGR in embryonic development has been studied, the role of the germline-specific region (GSR) in gonad development is unknown. We analysed RNA-sequence data from 28 sea lamprey gonads sampled across life-history stages, generated a genome-guided de novo superTransciptome with annotations, and identified genes in the GSR. We found that the 638 genes in the GSR are enriched for reproductive processes, exhibit 36x greater odds of being expressed in testes than ovaries, show little evidence of conserved synteny with other chordates, and most have putative paralogues in the GSR and/or somatic genomes. Further, several of these genes play known roles in sex determination and differentiation in other vertebrates. We conclude that the GSR of sea lamprey plays an important role in testicular differentiation and potentially sex determination.

scholarly journals Role of Alternative Splicing in Sex Determination in Vertebrates

2021 ◽  
pp. 1-11
Author(s):  
Isabel Gómez-Redondo ◽  
Benjamín Planells ◽  
Paula Navarrete ◽  
Alfonso Gutiérrez-Adán
Keyword(s):  
Alternative Splicing ◽  
Sex Determination ◽  
Transcription Initiation ◽  
Time Window ◽  
Gonad Development ◽  
Reproductive Organ ◽  
Mrna Splicing ◽  
Transcriptional Level ◽  
Splicing Regulators

During the process of sex determination, a germ-cell-containing undifferentiated gonad is converted into either a male or a female reproductive organ. Both the composition of sex chromosomes and the environment determine sex in vertebrates. It is assumed that transcription level regulation drives this cascade of mechanisms; however, transcription factors can alter gene expression beyond transcription initiation by controlling pre-mRNA splicing and thereby mRNA isoform production. Using the key time window in sex determination and gonad development in mice, it has been reported that new non-transcriptional events, such as alternative splicing, could play a key role in sex determination in mammals. We know the role of key regulatory factors, like WT1(+/–KTS) or FGFR2(b/c) in pre-mRNA splicing and sex determination, indicating that important steps in the vertebrate sex determination process probably operate at a post-transcriptional level. Here, we discuss the role of pre-mRNA splicing regulators in sex determination in vertebrates, focusing on the new RNA-seq data reported from mice fetal gonadal transcriptome.

scholarly journals Short template switch events explain mutation clusters in the human genome

2016 ◽  
Author(s):  
Ari Löytynoja ◽  
Nick Goldman
Keyword(s):  
Human Genome ◽  
Genome Rearrangement ◽  
Common Ancestor ◽  
De Novo ◽  
Variant Calling ◽  
Template Switching ◽  
Human Genomes ◽  
Switch Mechanism ◽  
Template Switch

AbstractResequencing efforts are uncovering the extent of genetic variation in humans and provide data to study the evolutionary processes shaping our genome. One recurring puzzle in both intra- and inter-species studies is the high frequency of complex mutations comprising multiple nearby base substitutions or insertion-deletions. We devised a generalized mutation model of template switching during replication that extends existing models of genome rearrangement, and used this to study the role of template switch events in the origin of such mutation clusters. Applied to the human genome, our model detects thousands of template switch events during the evolution of human and chimp from their common ancestor, and hundreds of events between two independently sequenced human genomes. While many of these are consistent with the template switch mechanism previously proposed for bacteria but not thought significant in higher organisms, our model also identifies new types of mutations that create short inversions, some flanked by paired inverted repeats. The local template switch process can create numerous complex mutation patterns, including hairpin loop structures, and explains multi-nucleotide mutations and compensatory substitutions without invoking positive selection, complicated and speculative mechanisms, or implausible coincidence. Clustered sequence differences are challenging for mapping and variant calling methods, and we show that detection of mutation clusters with current resequencing methodologies is difficult and many erroneous variant annotations exist in human reference data. Template switch events such as those we have uncovered may have been neglected as an explanation for complex mutations because of biases in commonly used analyses. Incorporation of our model into reference-based analysis pipelines and comparisons of de novo-assembled genomes will lead to improved understanding of genome variation and evolution.

55 Identification of microRNAs associated with sex determination in bovine amniotic fluid and maternal blood plasma

2020 ◽  
Vol 32 (2) ◽  
pp. 153 ◽  
Author(s):  
J. M. Sánchez ◽  
I. Gómez-Redondo ◽  
J. A. Browne ◽  
B. Planells ◽  
A. Gutiérrez-Adán ◽  
...  
Keyword(s):  
Amniotic Fluid ◽  
Sex Determination ◽  
Blood Plasma ◽  
Sex Chromosome ◽  
Gonad Development ◽  
Maternal Blood ◽  
Biological Processes ◽  
Female Embryo ◽  
Male Embryo

In most eutherian mammals, sex determination is the process through which a bipotential gonad (also known as genital ridges) develops into a testis or ovary depending on the sex chromosome content of the embryo, specifically by the presence of the SRY/Sry gene (sex-determining region of the Y chromosome). MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression and are involved in diverse functional roles including development, differentiation, apoptosis, and immunity. We hypothesised that the expression of miRNAs in amniotic fluid (AF) and maternal blood plasma (MP) would be affected by the sex of the embryo around the time of sex determination. Amniotic fluid and MP were collected from 6 crossbred beef pregnant heifers (3 carrying a single male and 3 carrying a single female embryo) following slaughter on Day 39 (when the peak of SRY expression occurs in cattle). All heifers had been synchronized and inseminated with semen from the same beef bull. A total of 12 samples (6 AF and 6 MP) were profiled using the miRCURY LNA miRNA Serum/Plasma Focus PCR Panel (Qiagen; 179 assays targeting relevant miRNAs). Data were analysed by GeneGlobe Data Analysis Center (Qiagen). A threshold cycle cut-off of 35 was applied and data were analysed using an unpaired t-test. Gene ontology enrichment analysis was performed using the WebGestaltR package to explore the possible functions of differentially expressed (DE) miRNAs. In this study, DE miRNAs were identified in male vs. female AF (n=5; 3 upregulated and 2 downregulated; P<0.05) and MP (n=57; 54 upregulated and 3 downregulated; P<0.05). Although no enrichment was detected for DE miRNAs in AF (in either sex) or in MP in heifers carrying a female embryo, 37 biological processes were enriched by DE miRNAs in MP of heifers carrying a male embryo (false discovery rate<0.05). Interestingly, the top five most enriched biological processes were male gonad development, development of primary male sexual characteristics, signal transduction in absence of ligand, actomyosin structure organisation, and male sex differentiation, suggesting a potential role of these miRNAs in reproductive traits. Results from this study highlight unique aspects of sex determination in cattle such as the role of miRNAs in gonad development. Moreover, although it is well known that AF provides a protective space around the developing embryo/fetus that allows its movement and growth; here we provide evidence suggesting that its components may play important roles in fetal development. Finally, miRNAs in MP may offer new opportunities to investigate biomarkers for early prediction of embryo/fetal sex in commercial practice. This research was supported by the Science Foundation Ireland (13/IA/1983) and the European Union H2020 Marie Sklodowska-Curie Innovative Training Network project Biology and Technology of Reproductive Health - REP-BIOTECH - 675526.

scholarly journals Testing pipelines for genome-wide SNP calling from Genotyping-By-Sequencing (GBS) data for Pinus ponderosa

2020 ◽  
Author(s):  
Mengjun Shu ◽  
Emily V. Moran
Keyword(s):  
Genome Sequence ◽  
Loblolly Pine ◽  
Pinus Ponderosa ◽  
Reference Genome ◽  
De Novo ◽  
Sequence Data ◽  
Snp Markers ◽  
Conifer Species ◽  
Snp Calling ◽  
A Genome

Abstract Background Single Nucleotide Polymorphism (SNP) markers have rapidly gained popularity due to their abundance in most genomes and their amenability to high-throughput genotyping techniques. Reduced-representation restriction-enzyme-based sequencing methods (GBS or RADseq) have been demonstrated to be robust and cost-effective genotyping methods. While previous studies have shown that alignment of the short-read fragments to a genome sequence results in better SNP calling than de novo approaches, only a few tree species - and few conifers in particular - have an annotated sequence. While these could be used to align sequence fragments from related species, sequence divergence might result in SNPs being missed if they are in fragments that don't align properly. Producing a new annotated genome sequence for every conifer species before SNP analyses are conducted is still prohibitive, as many conifer genomes are huge (> 19 GB) and include a large proportion of repeat sequences, making assembly difficult. Here we compare four bioinformatics pipelines, two of which require a reference genome (TASSEL-GBS V2 and Stacks), two of which are de novo pipelines (UNEAK and Stacks). We used Illumina sequence data from 94 ponderosa pines, with loblolly pine as the reference genome. Results The number of SNPs called was much lower without a reference genome (62–196 thousand vs. 2.1–2.7 million SNPs). UNEAK was the fastest overall and identified more SNPs than Stacks de novo. Stacks with a reference genome produced the highest number of SNPs with lowest proportion of paralogs, while SNPs identified by TASSEL-GBS V2 exhibited the highest heterozygosity, minor allele frequency, and proportion of paralogs. More SNPs were uniquely identified by Stacks than TASSEL, though there was high overlap between methods. Conclusion The present case study provides a comprehensive comparison between four commonly-used SNP calling pipelines, and identifies the Stacks reference-based approach as the best overall for conifers (or other species with large repetitive genomes) that do not have a published reference genome for the same species. However, all four pipelines had distinct benefits and limitations, with Stacks for instance being less user-friendly than some of the other pipelines. In addition, researchers studying other conifer species using similar approaches should be prepared to analyze very large numbers of SNPs.

scholarly journals Expression of Kisspeptin 1 in the Brain of the Adult Sea Lamprey Petromyzon marinus

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1174
Author(s):  
Daniel Sobrido-Cameán ◽  
Luis Alfonso Yáñez-Guerra ◽  
Alexandre Deber ◽  
María Celina Rodicio ◽  
Antón Barreiro-Iglesias
Keyword(s):  
In Situ Hybridization ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sea Lamprey ◽  
Anatomical Basis ◽  
Sea Lampreys ◽  
Puberty Onset ◽  
The Brain

Kisspeptin peptides play major roles in the regulation of reproduction and puberty onset in mammals. While most mammals only have one kisspeptin gene, other jawed vertebrates present two or three genes. Recent data also revealed the presence of two genes in lampreys (jawless vertebrates). However, apart from gene sequence data, there is almost no information on the kisspeptinergic system of lampreys. Here, we report phylogenetic and cluster-based analyses showing that the duplication of the ancestral kisspeptin gene occurred before the separation of jawless and jawed vertebrates. We also studied the expression of the kisspeptin transcripts in the brain of post-metamorphic juveniles and upstream migrating adult sea lampreys. Our in situ hybridization results revealed expression of kisspeptin 1 in hypothalamic neurons, which indicates that the hypothalamic expression of kisspeptins is an ancestral character in vertebrates. We also observed the presence of kisspeptin 1 expressing neurons in the paratubercular (posterior tubercle) nucleus of the diencephalon. This is the first description of the presence of kisspeptin 1 expressing neurons in this brain region in any vertebrate. We did not detect expression of kisspeptin 2 in the juvenile or adult sea lamprey brain with in situ hybridization. Our data provides an anatomical basis to study the role of kisspeptin 1 in the hypothalamic-pituitary system of lampreys and the contribution of diencephalic kisspeptinergic neurons to different circuits of the lamprey brain.

scholarly journals De-novo chromosome level assembly of plant genomes from long read sequence data

2021 ◽  
Author(s):  
Priyanka Sharma ◽  
Ardashir Kharabian Masouleh ◽  
Bruce Topp ◽  
Agnelo Furtado ◽  
Robert J. Henry
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Genetic Maps ◽  
Sequence Contigs ◽  
Plant Genomes ◽  
Proximity Analysis ◽  
Long Reads ◽  
A Genome ◽  
Long Read ◽  
Chromosome Level

SummaryRecent advances in the sequencing and assembly of plant genomes have allowed the generation of genomes with increasing contiguity and sequence accuracy. The chromosome level assembly of the contigs generated from long read sequencing has involved the use of proximity analysis (Hi-C) or traditional genetic maps to guide the placement of sequence contigs within chromosomes. The development of highly accurate long reads by repeated sequencing of circularized DNA (PacBio HiFi) has greatly increased the size of contigs. We now report the use of HiFiasm to assemble the genome of Macadamia jansenii. a genome that has been used as model to test sequencing and assembly. This achieved almost complete chromosome level assembly from the sequence data alone without the need for higher level chromosome map information. Eight of the 14 chromosomes were represented by a single large contig and the other 6 assembled into 2-4 main contigs. The small number of chromosome breaks appear to be due to highly repetitive regions of ribosomal genes that cannot be assembled by these approaches. De novo assembly of near complete chromosome level plant genomes now seems possible using these sequencing and assembly tools. Further targeted strategies might allow these remaining gaps to be closed.Significance statement (of up to two sentences)De novo assembly of near complete chromosome level plant genomes is now possible using current long read sequencing and assembly tools.

Transcriptome analysis unravels RNAi pathways genes and putative expansion of CYP450 gene family in cotton leafhopper Amrasca biguttula biguttula(Ishida)

2021 ◽  
Author(s):  
Mridula Gupta ◽  
Satnam singh ◽  
Gurmeet Kaur ◽  
Suneet Pandher ◽  
Noorpreet Kaur ◽  
...  
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Indian Subcontinent ◽  
Rnai Pathway ◽  
Functional Categories ◽  
Rnai Machinery ◽  
Data Resource ◽  
Amrasca Biguttula Biguttula ◽  
Important Pest

Abstract Amrasca biguttula biguttula is an important pest of cotton and okra in the Indian subcontinent. Presently limited genomic/ transcriptomic information is available for this insect in any open source databases. To initiate molecular studies in this insect, we report first assembled and annotated de novo transcriptome of cotton leafhopper. Out of 75,551 transcripts, 39613 CDS (Coding Sequence) were predicted with 35282 showing positive blast hits with NCBI nr database . From the Gene ontology (GO) analysis, 7431 CDS were annotated. KEGG pathway analysis categorized CDS into 22 different functional categories. The majority of CDS were annotated in signal transduction and transport catabolism pathways. The sequence data was screened for RNAi pathway genes and presence of 37 transcripts associated with this process confirmed the existence of robust RNAi machinery in this insect. The role of core RNAi machinery genes ( Dicer-2 , Ago-2 , Piwi and Staufen ) has been validated through dsRNA feeding studies. The data resource has also been used to identify potential RNAi targets and genes associated with insecticide detoxification specifically CYP 450 family.

scholarly journals A genome-wide analysis of DNA methylation identifies a novel association signal for Lp(a) concentrations in the LPA promoter

2019 ◽  
Author(s):  
Stefan Coassin ◽  
Natascha Hermann-Kleiter ◽  
Margot Haun ◽  
Simone Wahl ◽  
Rory Wilson ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Major Gene ◽  
Base Change ◽  
Minor Allele ◽  
Tissue Samples ◽  
Total N ◽  
Cpg Site ◽  
A Genome

AbstractLipoprotein(a) [Lp(a)] is a major cardiovascular risk factor, which is largely genetically determined by one major gene locus, the LPA gene. Many aspects of the transcriptional regulation of LPA are poorly understood and the role of epigenetics has not been addressed yet. Therefore, we conducted an epigenome-wide analysis of DNA methylation on Lp(a) levels in two population-based studies (total n=2208). We identified a CpG site in the LPA promoter which was significantly associated with Lp(a) concentrations. Surprisingly, the identified CpG site was found to overlap the SNP rs76735376. We genotyped this SNP de-novo in three studies (total n=7512). The minor allele of rs76735376 (1.1% minor allele frequency) was associated with increased Lp(a) values (p=1.01e-59) and explained 3.5% of the variation of Lp(a). Statistical mediation analysis showed that the effect on Lp(a) is rather originating from the base change itself and is not mediated by DNA methylation levels. This finding is supported by eQTL data from 153 liver tissue samples from the GTEx project, which shows a significant association of the rs76735376 minor allele with increased LPA expression. In summary, our data supports a functional role of rs76735376 in the regulation of LPA expression.

Posttransplant CMV infection and the role of immunosuppression (Sponsor: Novartis Pharma GmbH, Nürnberg)

2016 ◽  
Vol 04 (01) ◽  
pp. 4-10
Keyword(s):  
Lower Incidence ◽  
Paradigm Shift ◽  
Mtor Inhibitor ◽  
De Novo ◽  
Expert Panel ◽  
Risk Of Infection ◽  
Cmv Infection ◽  
Expert Meeting ◽  
Selection Of

AbstractImmunosuppression permits graft survival after transplantation and consequently a longer and better life. On the other hand, it increases the risk of infection, for instance with cytomegalovirus (CMV). However, the various available immunosuppressive therapies differ in this regard. One of the first clinical trials using de novo everolimus after kidney transplantation [1] already revealed a considerably lower incidence of CMV infection in the everolimus arms than in the mycophenolate mofetil (MMF) arm. This result was repeatedly confirmed in later studies [2–4]. Everolimus is now considered a substance with antiviral properties. This article is based on the expert meeting “Posttransplant CMV infection and the role of immunosuppression”. The expert panel called for a paradigm shift: In a CMV prevention strategy the targeted selection of the immunosuppressive therapy is also a key element. For patients with elevated risk of CMV, mTOR inhibitor-based immunosuppression is advantageous as it is associated with a significantly lower incidence of CMV events.

An Unbiased Predictive Model to Detect DNA Methylation Propensity of CpG Islands in the Human Genome

2020 ◽  
Vol 15 ◽  
Author(s):  
Dicle Yalcin ◽  
Hasan H. Otu
Keyword(s):  
Model Building ◽  
De Novo ◽  
Cpg Islands ◽  
Treatment Strategies ◽  
Area Under The Curve ◽  
Global Methylation ◽  
Sequence Features ◽  
A Genome ◽  
Combined Features ◽  
Epigenetic Repression

Background: Epigenetic repression mechanisms play an important role in gene regulation, specifically in cancer development. In many cases, a CpG island’s (CGI) susceptibility or resistance to methylation are shown to be contributed by local DNA sequence features. Objective: To develop unbiased machine learning models–individually and combined for different biological features–that predict the methylation propensity of a CGI. Methods: We developed our model consisting of CGI sequence features on a dataset of 75 sequences (28 prone, 47 resistant) representing a genome-wide methylation structure. We tested our model on two independent datasets that are chromosome (132 sequences) and disease (70 sequences) specific. Results: We provided improvements in prediction accuracy over previous models. Our results indicate that combined features better predict the methylation propensity of a CGI (area under the curve (AUC) ~0.81). Our global methylation classifier performs well on independent datasets reaching an AUC of ~0.82 for the complete model and an AUC of ~0.88 for the model using select sequences that better represent their classes in the training set. We report certain de novo motifs and transcription factor binding site (TFBS) motifs that are consistently better in separating prone and resistant CGIs. Conclusion: Predictive models for the methylation propensity of CGIs lead to a better understanding of disease mechanisms and can be used to classify genes based on their tendency to contain methylation prone CGIs, which may lead to preventative treatment strategies. MATLAB and Python™ scripts used for model building, prediction, and downstream analyses are available at https://github.com/dicleyalcin/methylProp_predictor.

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