Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes.
Jan E. Janecka,Brian W. Davis,Sharmila Ghosh,Nandina Paria,P. J. Das,Ludovic Orlando,Ludovic Orlando,Mikkel Schubert,Martin K. Nielsen,Tom A.E. Stout,Wesley A. Brashear,Gang Li,Charles D. Johnson,Richard P. Metz,Al Muatasim Al Zadjali,Charles C. Love,Dickson D. Varner,Daniel W. Bellott,William J. Murphy,Bhanu P. Chowdhary,Bhanu P. Chowdhary,Terje Raudsepp +21 more
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TLDR
This study presents an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates and provides a reference sequence for improved understanding of equine male development and fertility.Abstract:
Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes The eMSY gene density approaches that of autosomes with the highest number of retained X-Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion fertility A novel testis-expressed XY ampliconic sequence class, ETSTY7, is shared with the parasite Parascaris genome, providing evidence for eukaryotic horizontal transfer and inter-chromosomal mobility Our study highlights the dynamic nature of the Y and provides a reference sequence for improved understanding of equine male development and fertilityread more
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Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators
Jennifer F. Hughes,Helen Skaletsky,Laura G. Brown,Tatyana Pyntikova,Ting-Jan Cho,Natalia Koutseva,Sara Zaghlul,Tina Graves,Susie Rock,Colin Kremitzki,Robert S. Fulton,Shannon Dugan,Yan Ding,Donna Morton,Ziad Khan,Lora Lewis,Christian J. Buhay,Qiaoyan Wang,Jennifer Watt,Michael Holder,Sandy Lee,Lynne V. Nazareth,Jessica Alföldi,Steve Rozen,Donna M. Muzny,Wesley C. Warren,Richard A. Gibbs,Rick K. Wilson,Daniel W. Bellott,David C. Page +29 more
TL;DR: This article reconstructed the evolution of the Y chromosome across eight mammals to identify biases in gene content and the selective pressures that preserved the surviving ancestral genes, and concluded that the gene content of Y chromosome became specialized through selection to maintain the ancestral dosage of homologous X-Y gene pairs that function as broadly expressed regulators of transcription, translation and protein stability.
Isodicentric Y Chromosomes and Sex Disorders as Byproducts of Homologous Recombination that Maintains Palindromes
Julian Lange,Helen Skaletsky,Saskia K.M. van Daalen,Stephanie L. Embry,Cindy M. Korver,Laura G. Brown,Robert D. Oates,Sherman J. Silber,Sjoerd Repping,David C. Page +9 more
TL;DR: It is proposed that intrapalindrome sequence identity is maintained via noncrossover pathways of homologous recombination, exposing an Achilles' heel in the mechanism that preserves palindrome-borne genes.
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Photoelectrochemical water splitting: a road from stable metal oxides to protected thin film solar cells
TL;DR: In this paper, a detailed analysis of photoelectrochemical (PEC) devices from metal oxide electrodes forming a semiconductor-liquid junction to protected and catalyst-decorated third generation solar cells adapted into photo-electrodes is presented.
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Data denoising with transfer learning in single-cell transcriptomics.
TL;DR: It is shown that transfer learning across datasets remarkably improves data quality and SAVER-X trains a deep neural network for transfer learning that improves the quality of scRNA-seq data using prior information learnt from existing public studies.
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Intercalation and exfoliation chemistries of transition metal dichalcogenides
TL;DR: In this paper, the authors provide a comprehensive summary about the intercalation and exfoliation processes of layered materials as well as their properties and applications, and the applications of 2D TMDs fabricated from exfoliations are also introduced.
References
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TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
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Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
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