Deletion of 2.7 kb near <i><scp>HOXD</scp>3</i> in an Arabian horse with occipitoatlantoaxial malformation

Bordbari, Matthew H.; Penedo, M. C. T.; Aleman, Monica R; Valberg, Stephanie J.; Mickelson, James R.; Finno, Carrie J.

doi:10.1111/age.12531

Cited by 16 publications

(12 citation statements)

References 23 publications

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“…Recently, a deletion of a 2.7‐kb segment located 4.4 kb downstream from the end of HOXD4 and 8.2 kb upstream from the start of HOXD3 was identified in 1 Arabian foal with OAAM . The homeobox HOX gene cluster is a region highly conserved across species and involved in the development of the axial and appendicular skeleton .…”

Section: Discussionmentioning

confidence: 99%

“…This disorder is suspected to be transmitted as an autosomal recessive trait . The frequency of a carrier status for the homeobox deletion was determined to be 1.2% from the DNA database in a small population of Arabian horses from the Veterinary Genetics Laboratory at UCD . Affected foals can present with a range of signs from stiffness and abnormal posture to varying grades of ataxia .…”

Section: Discussionmentioning

confidence: 99%

“…1 Recently, a deletion of a 2.7-kb segment located 4.4 kb downstream from the end of HOXD4 and 8.2 kb upstream from the start of HOXD3 was identified in 1 Arabian foal with OAAM. 42 The homeobox HOX gene cluster is a region highly conserved across species and involved in the development of the axial and appendicular skeleton. 42 Occipitoatlantoaxial malformation is a developmental defect in which the first cervical vertebra (atlas) resembles the base of the skull (occiput), and the second vertebra (axis) resembles the atlas.…”

Section: Discussionmentioning

confidence: 99%

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Investigation of Known Genetic Mutations of Arabian Horses in Egyptian Arabian Foals with Juvenile Idiopathic Epilepsy

Aleman

Finno

Weich

et al. 2017

Veterinary Internal Medicne

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BackgroundThe carrier status of lavender foal syndrome (LFS), cerebellar abiotrophy (CA), severe combined immunodeficiency (SCID), and occipitoatlantoaxial malformation (OAAM1) in foals with juvenile idiopathic epilepsy (JIE) is unknown.Hypothesis/ObjectivesTo determine the carrier status of LFS, CA, SCID, and OAAM1 in foals with JIE.AnimalsTen foals with JIE.Materials and MethodsArchived DNA samples were tested for known genetic mutations causing LFS, CA, SCID, and OAAM1. The inclusion criteria consisted of having been diagnosed with JIE by ruling out other causes of seizures in foals and supported by electroencephalographic examination.ResultsTen Egyptian Arabian horses (5 females and 5 males) were phenotyped as foals with JIE by electroencephalography (EEG). All foals were negative for the genetic mutations that cause LFS, CA, SCID, and OAAM1 except for 1 foal that was a carrier of CA.Conclusions and Clinical ImportanceJuvenile idiopathic epilepsy of Egyptian Arabian foals and LFS appear to be phenotypically and genetically distinct disorders. There was no apparent association between JIE and LFS, CA, SCID, and OAAM1.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Investigation of Known Genetic Mutations of Arabian Horses in Egyptian Arabian Foals with Juvenile Idiopathic Epilepsy

Aleman

Finno

Weich

et al. 2017

Veterinary Internal Medicne

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“…Making raw sequence data available is key for the experimental reproducibility (Stodden, Seiler & Ma, 2018), a pillar of scientific endeavor. SRA database has been recurrently used to support new research, such as: the evaluation of single nucleotide polymorphisms and deletions (Bordbari et al, 2017), the test of new bioinformatics pieces of software (Simpson et al, 2009;Langmead & Salzberg, 2012;Bolger, Lohse & Usadel, 2014), and also to evaluate the impacts of common procedures on data, such as trimming (Del Fabbro et al, 2013), among other studies (Kayal et al, 2015;Bernstein, Doan & Dewey, 2017;Linard et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Peer Review #2 of "Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data (v0.1)"

2019

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The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the "no budget mitogenomics" approach ideal for comprehensive molecular studies, especially for

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“…Making raw sequence data available is key for the experimental reproducibility, a pillar of scientific endeavor. SRA database has been recurrently used to support new research, such as: the evaluation of single nucleotide polymorphisms and deletions (Bordbari et al, 2017), the test of new bioinformatics software (Simpson et al, 2009;Langmead & Salzberg, 2012;Bolger, Lohse & Usadel, 2014), and also to evaluate the impacts of common procedures on data, such as trimming (Del Fabbro et al, 2013), among many other studies.…”

Section: Introductionmentioning

confidence: 99%

No budget mitogenomics: Assembling 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

Vieira

Prosdocimi

2018

Preprint

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The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genome data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formcidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the “no budget mitogenomics” approach ideal for comprehensive molecular studies, especially for subsampled taxa.

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Deletion of 2.7 kb near HOXD3 in an Arabian horse with occipitoatlantoaxial malformation

Cited by 16 publications

References 23 publications

Investigation of Known Genetic Mutations of Arabian Horses in Egyptian Arabian Foals with Juvenile Idiopathic Epilepsy

Investigation of Known Genetic Mutations of Arabian Horses in Egyptian Arabian Foals with Juvenile Idiopathic Epilepsy

Peer Review #2 of "Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data (v0.1)"

No budget mitogenomics: Assembling 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

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