Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome

AbstractEntomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the best genome of S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36Mb. The largest scaffold, with 20.9Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this new genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae’s chromosome X to be primarily orthologous to C. elegans’ and P. pacificus’ chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for new comparative genomic and gene expression studies within the Steinernema clade and across the Nematoda phylum.Article SummaryThe insect killing worms Steinernema carpocapsae is a model organism for parasitism and symbiosis. The authors have used long reads and optical mapping to generate substantially contiguous assembly and a new set of gene annotations. They have identified the X chromosome as well as expansions in specific family proteases found in the venom of this worm. A macrosyntenic analysis with C. elegans shows a broad conservation of ancestral chromosomes with the exception of chromosome X. This new assembly will be useful to the Steinernema community and the broader nematode genomics community.

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P–154 The role of the X Chromosome in early human embryo metabolism

Human Reproduction ◽

10.1093/humrep/deab130.153 ◽

2021 ◽

Vol 36 (Supplement_1) ◽

Author(s):

A Groff ◽

A Korkidakis ◽

D Sakkas ◽

D Page

Keyword(s):

Gene Expression ◽

Sex Differences ◽

Electron Transport ◽

X Chromosome ◽

Early Embryo ◽

P Value ◽

Chromosome X ◽

Embryo Metabolism ◽

Early Human

Abstract Study question What role does the X chromosome play in early embryo metabolism? Does X chromosome copy number contribute to sex differences in early embryonic metabolism? Summary answer Chromosome X contains several metabolism-related genes that are expressed prior to X-inactivation, suggesting that their dosage plays a role in sex-biased regulation of embryo metabolism. What is known already Published reports indicate that sex differences in preimplantation embryo metabolism exist across mammalian species, including humans. Two observations supporting this are that male embryos reach blastocyst stage earlier than their female counterparts, and that glucose uptake and processing is thought to be higher in female compared to male embryos. It has been hypothesized that these differences reflect the location of the metabolism gene G6PD, the rate limiting enzyme in the Pentose Phosphate Pathway, on Chromosome X. Study design, size, duration This study is a reanalysis of publicly available RNA-seq data, including 1176 single cells from 59 blastocysts (24 E5, 18 E6, 17 E7) published in one study (Petropoulos et al 2016). Participants/materials, setting, methods Cells were subjected to a digital karyotype inference algorithm and aneuploid samples were removed from the dataset. Sex differential gene expression analyses (DE) were then performed in euploid trophectoderm cells (TE; 233 XY from 16 embryos and 180 XX cells from 12 embryos). Cell numbers from ICM were too sparse to compare. Main results and the role of chance Analysis of XX and XY TE revealed 618 significantly differentially expressed genes (DEGs; 507 upregulated in XX cells, and 111 upregulated in XY cells). These genes are spread across autosomes and sex chromosomes. Interestingly, G6PD is not significantly more highly expressed in XX cells. Gene Ontology (GO) analysis of the XX-biased DEGs revealed a transcriptional sex bias in metabolism-related GO categories, including “mitochondrial ATP synthesis coupled electron transport”, and “respiratory chain complex I”. Gene-level assessment revealed that the drivers of these enrichments are spread across the genome, but 28/64 reside on Chromosome X (hypergeometric p-value = 5.984473e–27), including NDUFA1, NDUFB11, and COX7B (components of the electron transport chain), and SLC25A5 (an ATP/ADP transporter involved in maintaining mitochondrial membrane potential). This indicates a direct role for multiple X-linked genes in sex-biased regulation of embryo metabolism. Metabolic genes that are not sex-biased are distributed across the genome, with no significant enrichment on Chromosome X (76/266, hypergeometric p-value=0.607). Together, these data indicate that GO metabolic term X enrichment is a feature of sex-biased expression and not due to an accumulation of metabolism-related genes on the X. Limitations, reasons for caution This analysis draws on publicly available data, and thus we are unable to perform orthogonal validation of karyotype calls. Additionally, while the initial dataset is large, the quality-filtered dataset (euploid XX and XY TE) is small, and single cell data is infamously variable. Further data collection is required. Wider implications of the findings: Our analysis of sex-biased gene expression in early human embryos suggests a more important role for the X chromosome in modulating sex biases in early embryo metabolism than previously recognized. This study provides insight into the mechanisms underlying the development of metabolic sex differences throughout the lifespan. Trial registration number NA

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Gene expression, chromosome heterogeneity and the fast-X effect in mammals

Biology Letters ◽

10.1098/rsbl.2015.0010 ◽

2015 ◽

Vol 11 (2) ◽

pp. 20150010 ◽

Cited By ~ 10

Author(s):

Linh-Phuong Nguyen ◽

Nicolas Galtier ◽

Benoit Nabholz

Keyword(s):

Gene Expression ◽

X Chromosome ◽

Gc Content ◽

Detectable Effect ◽

Synonymous Substitutions ◽

Expression Levels ◽

Gene Expression Levels

The higher rate of non-synonymous over synonymous substitutions (dN/dS) of the X chromosome compared with autosomes is often interpreted as a consequence of X hemizygosity. However, other factors, such as gene expression, are also known to vary between X and autosomes. Analysing 4800 orthologues in six mammals, we found that gene expression levels, associated with GC content, fully account for the variation in dN/dS between X and autosomes with no detectable effect of hemizygosity. We also report an extensive variance in dN/dS and gene expression between autosomes.

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Characterization of the Escherichia coli Virulent Myophage ST32

Viruses ◽

10.3390/v10110616 ◽

2018 ◽

Vol 10 (11) ◽

pp. 616 ◽

Cited By ~ 7

Author(s):

Honghui Liu ◽

Hany Geagea ◽

Geneviève Rousseau ◽

Simon Labrie ◽

Denise Tremblay ◽

...

Keyword(s):

Escherichia Coli ◽

Phylogenetic Tree ◽

Biological Control Agent ◽

Burst Size ◽

Gc Content ◽

Genomic Analysis ◽

Coli Strain ◽

Comparative Genomic ◽

Wastewater Sample ◽

Range Analysis

The virulent phage ST32 that infects the Escherichia coli strain ST130 was isolated from a wastewater sample in China and analyzed. Morphological observations showed that phage ST32 belongs to the Myoviridae family, as it has an icosahedral capsid and long contractile tail. Host range analysis showed that it exhibits a broad range of hosts including non-pathogenic and pathogenic E. coli strains. Interestingly, phage ST32 had a much larger burst size when amplified at 20 °C as compared to 30 °C or 37 °C. Its double-stranded DNA genome was sequenced and found to contain 53,092 bp with a GC content of 44.14%. Seventy-nine open reading frames (ORFs) were identified and annotated as well as a tRNA-Arg. Only nineteen ORFs were assigned putative functions. A phylogenetic tree using the large terminase subunit revealed a close relatedness with four unclassified Myoviridae phages. A comparative genomic analysis of these phages showed that the Enterobacteria phage phiEcoM-GJ1 is the closest relative to ST32 and shares the same new branch in the phylogenetic tree. Still, these two phages share only 47 of 79 ORFs with more than 90% identity. Phage ST32 has unique characteristics that make it a potential biological control agent under specific conditions.

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CNVkit-RNA: Copy number inference from RNA-Sequencing data

10.1101/408534 ◽

2018 ◽

Cited By ~ 9

Author(s):

Eric Talevich ◽

A. Hunter Shain

Keyword(s):

Gene Expression ◽

Rna Sequencing ◽

Copy Number ◽

Point Mutations ◽

Gc Content ◽

The Cancer Genome Atlas ◽

Comparative Genomic ◽

Sequencing Data ◽

Number Variation ◽

User Friendly

AbstractRNA-sequencing is most commonly used to measure gene expression, but it is possible to extract genotypic information from RNA-sequencing data, too. Point mutations and translocations can be detected when they occur in expressed genes, however, there are few software solutions to infer copy number information from RNA-sequencing data. This is because a gene’s expression is dictated by a number of variables, including, but not limited to, copy number variation. Here, we report new functionalities within the software package CNVkit that enable copy number inference from RNA-sequencing data. First, CNVkit removes technical variation in gene expression associated with GC-content and transcript length. Next, CNVkit assigns a weight, dictated by several variables, to each transcript with the net effect of preferentially inferring copy number from highly and stably expressed genes. We benchmarked our approach on 105 melanomas from The Cancer Genome Atlas project and observed a high degree of concordance (R = 0.739) between our estimates and those from array comparative genomic hybridization (aCGH) on the same samples. After initial configuration, the software requires few inputs, is able to process a batch of up to 100 samples in less than ten minutes, and can be used in conjunction with pre-existing features of CNVkit, including visualization tools. Overall, we present a rapid, user-friendly software solution to infer copy number information from gene expression data.

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Comparative Transcriptomics of heads and tails between Steinernema carpocapsae and Caenorhabditis elegans

10.1101/2020.08.20.259739 ◽

2020 ◽

Author(s):

Isaryhia Maya Rodriguez ◽

Lorrayne Serra Clague ◽

Cassandra Joan McGill ◽

Bryan Rodriguez ◽

Ali Mortazavi

Keyword(s):

Gene Expression ◽

Caenorhabditis Elegans ◽

Neuronal Development ◽

Model Organism ◽

The Body ◽

Steinernema Carpocapsae ◽

Specific Gene ◽

Body Parts ◽

C Elegans

AbstractSteinernema nematodes have been widely studied for insect infection and mutualism, but little is known about the patterns of gene expression along the body of these worms or how these compare to the model organism Caenorhabditis elegans. Here we perform the first comparative analysis between the heads and tail regions of Steinernema carpocapsae and C. elegans Infective Juveniles (IJs)/dauers and young adults using single-worm RNA-seq. While we find overall agreement in gene expression there were several sets of genes with substantial differences between the two species. Gene expression in the S. carpocapsae female compared to the C. elegans hermaphrodite heads and tails revealed differences in metabolism, aging, and determination of lifespan. Young adult male heads and tails showed major differences in developmental related processes such as morphogenesis as well as neuronal development and signaling. We also found head- and tail-specific gene expression differences between S. carpocapsae IJs and C. elegans dauers for genes related to growth and development as well as neuronal signaling and activity. This study is one of the first comparative transcriptomic analyses of body parts between distantly related species of nematodes and provides insight into both the highly conserved and genetically distinctive characteristics of both species.

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X-linked CNV and skewed X-chromosome inactivation

Nauchno-prakticheskii zhurnal «Medicinskaia genetika» ◽

10.25557/2073-7998.2020.03.19-21 ◽

2020 ◽

pp. 19-21

Author(s):

Е.А. Фонова ◽

Е.Н. Толмачева ◽

А.А. Кашеварова ◽

М.Е. Лопаткина ◽

К.А. Павлова ◽

...

Keyword(s):

Cell Proliferation ◽

Intellectual Disability ◽

X Chromosome ◽

Copy Number ◽

Copy Number Variations ◽

X Chromosome Inactivation ◽

Chromosome Inactivation ◽

Chromosome X ◽

Skewed X Chromosome Inactivation

Смещение инактивации Х-хромосомы может быть следствием и маркером нарушения клеточной пролиферации при вариациях числа копий ДНК на Х-хромосоме. Х-сцепленные CNV выявляются как у женщин с невынашиванием беременности и смещением инактивации Х-хромосомы (с частотой 33,3%), так и у пациентов с умственной отсталостью и смещением инактивацией у их матерей (с частотой 40%). A skewed X-chromosome inactivation can be a consequence and a marker of impaired cell proliferation in the presence of copy number variations (CNV) on the X chromosome. X-linked CNVs are detected in women with miscarriages and a skewed X-chromosome inactivation (with a frequency of 33.3%), as well as in patients with intellectual disability and skewed X-chromosome inactivation in their mothers (with a frequency of 40%).

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