scholarly journals Copy number variations with adaptive potential in caribou (Rangifer tarandus): genome architecture and new annotated genome assembly

2021 ◽  
Author(s):  
Julien Prunier ◽  
Alexandra Carrier ◽  
Isabelle Gilbert ◽  
William Poisson ◽  
Vicky Albert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Assembly ◽  
Copy Number ◽  
Rangifer Tarandus ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Copy Number Variations ◽  
Genome Architecture ◽  
Metabolism Regulation ◽  
Genomic Studies

Background: Rangifer tarandus (caribou and reindeer) has experienced recent drastic population size reductions throughout its circumpolar distribution. In efforts aimed at preserving caribou in North America and reindeer in Eurasia, genetic diversity conservation is of utmost importance, particularly the adaptive genetic diversity. To facilitate genomic studies of the caribou population, we improved genome assembly and annotation by combining long-read, linked-read and RNA sequencing technologies. As copy number variations (CNVs) are known to impact phenotype and are therefore likely to play a key role in adaptation, we investigated CNVs among the genomes of individuals representing three ecotypes of caribou (migratory, boreal and mountain). Results: Using de novo transcriptome assembly and similarity with annotated human gene sequences, we identified 17,394 robust gene models embedded in a new highly contiguous genome assembly made of 13,994 scaffolds and presenting the highest N50 reported to date. A BUSCO analysis supported the high accuracy of this assembly, 90% of which being represented by only 131 scaffolds. Genome level comparisons with domestic ruminant species showed high synteny within this clade. A total of 1,698 large CNVs (length > 1kb) were identified, including 332 overlapping coding sequences annotated for functions related to immunity, musculoskeletal development or metabolism regulation and others. While the CNV distribution over the genome revealed 31 CNV hotspots, 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions related to cardiac development, fatty acid regulation, cold responses, locomotory behavior or environmental perception (hearing and sight), that can be related to the expected adaptations. Conclusions: This work includes the first publicly available annotation of the Rangifer tarandus genome and the first genome assembly allowing genome architecture analyses. This robust annotation based on truly expressed sequences showed a distribution overlapping many CNVs that are promising candidates given the annotations supporting their involvement in adaptation. This new highly contiguous assembly will allow relative localization of genetic variations and features and will be a valuable resource for molecular tool development and genomic studies aimed at describing and preserving this species.

scholarly journals CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly

2021 ◽  
Vol 5 (3) ◽  
pp. e202101207
Author(s):  
Julien Prunier ◽  
Alexandra Carrier ◽  
Isabelle Gilbert ◽  
William Poisson ◽  
Vicky Albert ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Rangifer Tarandus ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Copy Number Variations ◽  
Genome Architecture ◽  
Adaptive Potential ◽  
A Genome ◽  
Long Read ◽  
Genomic Studies

Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length > 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here.

scholarly journals The brain transcriptome of the wolf spider, Schizocosa ocreata

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Daniel Stribling ◽  
Peter L. Chang ◽  
Justin E. Dalton ◽  
Christopher A. Conow ◽  
Malcolm Rosenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Wolf Spiders ◽  
Schizocosa Ocreata ◽  
Genomic Studies ◽  
The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

scholarly journals Lessons Learned from CNV Analysis of Major Birth Defects

2020 ◽  
Vol 21 (21) ◽  
pp. 8247
Author(s):  
Alina Christine Hilger ◽  
Gabriel Clemens Dworschak ◽  
Heiko Martin Reutter
Keyword(s):  
Birth Defects ◽  
Copy Number ◽  
Congenital Malformations ◽  
De Novo ◽  
Copy Number Variations ◽  
Lessons Learned ◽  
Organ System ◽  
Molecular Karyotyping ◽  
The Past ◽  
Single Organ

The treatment of major birth defects are key concerns for child health. Hitherto, for the majority of birth defects, the underlying cause remains unknown, likely to be heterogeneous. The implicated mortality and/or reduced fecundity in major birth defects suggest a significant fraction of mutational de novo events among the affected individuals. With the advent of systematic array-based molecular karyotyping, larger cohorts of affected individuals have been screened over the past decade. This review discusses the identification of disease-causing copy-number variations (CNVs) among individuals with different congenital malformations. It highlights the differences in findings depending on the respective congenital malformation. It looks at the differences in findings of CNV analysis in non-isolated complex congenital malformations, associated with central nervous system malformations or intellectual disabilities, compared to isolated single organ-system malformations. We propose that the more complex an organ system is, and the more genes involved during embryonic development, the more likely it is that mutational de novo events, comprising CNVs, will confer to the expression of birth defects of this organ system.

scholarly journals A Case With 4 de Novo Copy Number Variations With Clinical Features That Overlap 1q43q44 Microdeletion and 3q29 Microduplication Syndromes

2018 ◽  
Vol 5 ◽  
pp. 2329048X1879820
Author(s):  
Miriam Kessi ◽  
Jing Peng ◽  
Lifen Yang ◽  
Haolin Duan ◽  
Yulin Tang ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Corpus Callosum ◽  
Copy Number ◽  
De Novo ◽  
Copy Number Variations ◽  
Language Delay ◽  
Global Developmental Delay ◽  
Recurrent Infections ◽  
Dental Anomalies ◽  
Microdeletion Syndrome

1q43q44 microdeletion syndrome is characterized by intellectual disability/global developmental delay, epilepsy, dysmorphic facies, stereotypic movement, language delay, recurrent infections, dental anomalies, and hand and foot anomalies. Microcephaly and corpus callosum dysplasia are present in some cases depending on gene content. 3q29 microduplication syndrome is characterized by intellectual disability, language delay, microcephaly, and dental anomalies. We report the first case with 4 de novo copy number variations with clinical features which overlap 1q43q44 microdeletion and 3q29 microduplication syndromes. Our case presented with global developmental delay, epilepsy, recurrent infections, stereotypic movements, speech delay, microcephaly, facial dysmorphism, bilateral clinodactyly, and small puffy feet with metatarsus varus; however, she had no corpus callosum dysplasia. Our case highlights the role of multiple copy number variations in the occurrence of a certain phenotype. Moreover, it supports the theory that the loss of HNRNPU gene function cannot explain the occurrence of microcephaly and abnormalities of the corpus callosum in 1q43q44 microdeletion syndrome.

scholarly journals Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq

2020 ◽  
Vol 21 (21) ◽  
pp. 7934
Author(s):  
Thiago Mateus Rosa-Santos ◽  
Renan Gonçalves da Silva ◽  
Poornasree Kumar ◽  
Pratibha Kottapalli ◽  
Chiquito Crasto ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Arable Land ◽  
Aluminum Tolerance ◽  
Aluminum Stress ◽  
Physiological Processes ◽  
Aluminum Ions ◽  
Detoxification Mechanism ◽  
Genomic Studies

Some metals are beneficial to plants and contribute to critical physiological processes. Some metals, however, are not. The presence of aluminum ions (Al3+) can be very toxic, especially in acidic soils. Considerable parts of the world’s arable land are acidic in nature; mechanistically elucidating a plant’s response to aluminum stress is critical to mitigating this stress and improving the quality of plants. To identify the genes involved in sugarcane response to aluminum stress, we generated 372 million paired-end RNA sequencing reads from the roots of CTC-2 and RB855453, which are two contrasting cultivars. Data normalization resulted in 162,161 contigs (contiguous sequences) and 97,335 genes from a de novo transcriptome assembly (trinity genes). A total of 4858 and 1307 differently expressed genes (DEGs) for treatment versus control were identified for the CTC-2 and RB855453 cultivars, respectively. The DEGs were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and downregulated in RB855453 (sensitive cultivar). Here, we present the first root transcriptome of sugarcane under aluminum stress. The results and conclusions of this study are a crucial launch pad for future genetic and genomic studies of sugarcane. The transcriptome analysis shows that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with lateral root formation and activation of redox enzymes. We also present a hypothetical model for aluminum tolerance in the CTC-2 cultivar.

scholarly journals Detection and reconstruction of tandemly organized de novo copy number variations

2010 ◽  
Vol 11 (S11) ◽  
Author(s):  
Dan He ◽  
Nicholas Furlotte ◽  
Eleazar Eskin
Keyword(s):  
Copy Number ◽  
De Novo ◽  
Copy Number Variations

scholarly journals Associations between Familial Rates of Psychiatric Disorders and De Novo Genetic Mutations in Autism

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Kyleen Luhrs ◽  
Tracey Ward ◽  
Caitlin M. Hudac ◽  
Jennifer Gerdts ◽  
Holly A. F. Stessman ◽  
...  
Keyword(s):  
Psychiatric Disorders ◽  
Copy Number ◽  
Depressive Disorders ◽  
De Novo ◽  
Familial Risk ◽  
Autism Spectrum ◽  
Copy Number Variations ◽  
Genetic Etiology ◽  
Additive Contribution ◽  
Familial Risk Factors

The purpose of this study was to examine the confluence of genetic and familial risk factors in children with Autism Spectrum Disorder (ASD) with distinct de novo genetic events. We hypothesized that gene-disrupting mutations would be associated with reduced rates of familial psychiatric disorders relative to structural mutations. Participants included families of children with ASD in four groups: de novo duplication copy number variations (DUP, n=62), de novo deletion copy number variations (DEL, n=74), de novo likely gene-disrupting mutations (LGDM, n=267), and children without a known genetic etiology (NON, n=2111). Familial rates of psychiatric disorders were calculated from semistructured interviews. Results indicated overall increased rates of psychiatric disorders in DUP families compared to DEL and LGDM families, specific to paternal psychiatric histories, and particularly evident for depressive disorders. Higher rates of depressive disorders in maternal psychiatric histories were observed overall compared to paternal histories and higher rates of anxiety disorders were observed in paternal histories for LGDM families compared to DUP families. These findings support the notion of an additive contribution of genetic etiology and familial factors are associated with ASD risk and highlight critical need for continued work targeting these relationships.

scholarly journals Increased Frequency of Copy Number Variations Revealed by Array Comparative Genomic Hybridization in the Offspring of Male Mice Exposed to Low Dose-Rate Ionizing Radiation

2021 ◽  
Vol 22 (22) ◽  
pp. 12437
Author(s):  
Keiji Ogura ◽  
Yoshiko Ayabe ◽  
Chihiro Harada ◽  
Ignacia Braga Tanaka ◽  
Satoshi Tanaka ◽  
...  
Keyword(s):  
Ionizing Radiation ◽  
Dose Rate ◽  
Copy Number ◽  
Array Comparative Genomic Hybridization ◽  
Low Dose ◽  
De Novo ◽  
Copy Number Variations ◽  
Comparative Genomic ◽  
Male Mice ◽  
Low Dose Rate

There is very little information on the transgenerational or genetic effects of low dose-rate ionizing radiation. We report the detection of the transgenerational effects of chronic low dose-rate irradiation in mice, at the molecular level in the whole genome, using array comparative genomic hybridization technology. We observed that the number of the mice with de novo copy number variations (specifically, deletions) was significantly increased in the offspring of C57BL/6J male mice exposed to 20 mGy/day gamma-rays for 400 days (total dose: 8000 mGy), as compared to non-irradiated controls. We did not detect any difference in the size of the de novo deletions between the irradiated and the non-irradiated groups. An analysis of the life span of the offspring suggested a possibility that de novo copy-number variations may be associated with shorter life spans.

scholarly journals Multiple de novo copy number variations in two subjects with developmental problems and multiple congenital anomalies

2012 ◽  
Vol 6 (S6) ◽  
Author(s):  
Pengfei Liu ◽  
Klaudia Walter ◽  
Karin Writzl ◽  
Violet Gelowani ◽  
Sarah Lindsay ◽  
...  
Keyword(s):  
Congenital Anomalies ◽  
Copy Number ◽  
De Novo ◽  
Copy Number Variations ◽  
Multiple Congenital Anomalies ◽  
Developmental Problems

scholarly journals De novo and rare inherited copy-number variations in the hemiplegic form of cerebral palsy

2017 ◽  
Vol 20 (2) ◽  
pp. 172-180 ◽  
Author(s):  
Mehdi Zarrei ◽  
Darcy L Fehlings ◽  
Karizma Mawjee ◽  
Lauren Switzer ◽  
Bhooma Thiruvahindrapuram ◽  
...  
Keyword(s):  
Cerebral Palsy ◽  
Copy Number ◽  
De Novo ◽  
Copy Number Variations
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