Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50)

Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well annotated, reference sequence for the water buffalo is an important prerequisite for studying the biology of this species, and necessary to manage genetic diversity and to use modern breeding and genomic selection techniques. However, no such genome assembly has been previously reported. There are two species of domestic water buffalo, the river (2n = 50) and the swamp (2n = 48) buffalo. Here we describe a draft quality reference sequence for the river buffalo created from Illumina GA and Roche 454 short read sequences using the MaSuRCA assembler. The assembled sequence is 2.83 Gb, consisting of 366,983 scaffolds with a scaffold N50 of 1.41 Mb and contig N50 of 21,398 bp. Annotation of the genome was supported by transcriptome data from 30 tissues, and identified 21,711 predicted protein coding genes. Searches for complete mammalian BUSCO gene groups found 98.6% of curated single copy orthologs present among predicted genes, which suggests a high level of completeness of the genome. The annotated sequence is available from NCBI at accession GCA_000471725.1.John L. Williams, Daniela Iamartino, Kim D. Pruitt, Tad Sonstegard, Timothy P.L. Smith, Wai Yee Low, Tommaso Biagini, Lorenzo Bomba, Stefano Capomaccio, Bianca Castiglioni, Angelo Coletta, Federica Corrado, Fabrizio Ferré, Leopoldo Iannuzzi, Cynthia Lawley, Nicolò Macciotta, Matthew McClure, Giordano Mancini, Donato Matassino, Raffaele Mazza, Marco Milanesi, Bianca Moioli, Nicola Morandi, Luigi Ramunno, Vincenzo Peretti, Fabio Pilla, Paola Ramelli, Steven Schroeder, Francesco Strozzi, Francoise Thibaud-Nissen, Luigi Zicarelli, Paolo Ajmone-Marsan, Alessio Valentini, Giovanni Chillemi, and Aleksey Zimi

Haplotype Affinities Resolve a Major Component of Goat (Capra hircus) MtDNA D-Loop Diversity and Reveal Specific Features of the Sardinian Stock

Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using Bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity

Rapid innovation in sequencing technologies and improvement in assembly algorithms have enabled the creation of highly contiguous mammalian genomes. Here we report a chromosome-level assembly of the water buffalo (Bubalus bubalis) genome using single-molecule sequencing and chromatin conformation capture data. PacBio Sequel reads, with a mean length of 11.5 kb, helped to resolve repetitive elements and generate sequence contiguity. All five B. bubalis sub-metacentric chromosomes were correctly scaffolded with centromeres spanned. Although the index animal was partly inbred, 58% of the genome was haplotype-phased by FALCON-Unzip. This new reference genome improves the contig N50 of the previous short-read based buffalo assembly more than a thousand-fold and contains only 383 gaps. It surpasses the human and goat references in sequence contiguity and facilitates the annotation of hard to assemble gene clusters such as the major histocompatibility complex (MHC)

AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow

The Affymetrix Axiom genotyping standard and 'best practice' workflow for Linux and Mac users consists of three stand-alone executable programs (Affymetrix Power Tools) and an R package (SNPolisher). Currently, SNP analysis has to be performed in a step-by-step procedure. Manual intervention and/or programming skills by the user is required at each intermediate point, as Affymetrix Power Tools programs do not produce input files for the program next-in-line. An additional problem is that the output format of genotypes is not compatible with most analysis software currently available. AffyPipe solves all the above problems, by automating both standard and 'best practice' workflows for any species genotyped with the Axiom technology. AffyPipe does not require programming skills and performs all the steps necessary to obtain a final genotype file. Furthermore, users can directly edit SNP probes and export genotypes in PLINK format.https://github.com/nicolazzie/AffyPipe.git.Ezequiel L. Nicolazzi, Daniela Iamartino and John L. William

Errors: Communication and its Discontents

Errors are examples of behavior which deviate from a perceived norm. They may be prompted by misjudgements or ignorance of norms, and perceived as more or less ‘serious’. In a relatively stable society, or one that aspires to be so, norms have a gatekeeping function, and errors need to be ‘corrected’ as a consequence. This extends to all aspects of human endeavour (errare humanum est), and particularly to human communication systems in which errors are traditionally labeled as cultural, pragmatic or linguistic, and where a prescriptive approach to language teaching (whether it calls itself ‘communicative’ or not) implies investing considerable resources in error correction. In keeping with the rationale of the series, this volume intends to look at the notion of error with particular reference to communication in the 21st century. The global economy, the migratory flows which fuel it, and the new methods of real time communication which support it, have all contributed to real change in language use. This is particularly true for English, the world’s lingua franca, most speakers of which are non native, whose numbers now exceed 2 billion (Crystal 2003), and who are likely to influence the future development of the language. The speed of change may lead to a sense of bewilderment for people professionally involved with language, such as teachers and translators, and a concern about shifting or declining standards, accelerated by the growth of real time communication through texting and social media, uncomfortably poised as it is between spoken and written channels. This phenomenon has prompted a range of best selling publications advocating the observance of established (native speaker) norms of spelling, punctuation, etc. Conversely, the growth of intercultural, international communication (not necessarily in English) can also empower non native speakers and writers with a sense of opportunity and the chance to experiment and to find a voice in a language which is not the mother tongue, implying the adoption of new norms (of lexis, syntax, etc.) This volume however is not confined just to a consideration of opposing views on language change. Rather, it is intended to offer a range of perspectives on language-related errors – social, cultural, psychological, linguistic – which, because of their diversity of approach can together shed useful light on what happens when human beings attempt to communicate with another, and why communication sometimes breaks down – perhaps more often than we realize

Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle

This study sought to characterize differences in gene content, regulation and structure between taurine cattle and river buffalo (one subspecies of domestic water buffalo) using the extensively annotated UMD3.1 cattle reference genome as a basis for comparisons. We identified 127 deletion CNV regions in river buffalo representing 5 annotated cattle genes. We also characterized 583 merged mobile element insertion (MEI) events within the upstream regions of annotated cattle genes. Transcriptome analysis in various tissue types on river buffalo confirmed the absence of four cattle genes. Four genes which may be related to phenotypic differences in meat quality and color, had upstream MEI predictions and were found to have significantly elevated expression in river buffalo compared with cattle. Our comparative alignment approach and gene expression analyses suggested a functional role for many genomic structural variations, which may contribute to the unique phenotypes of river buffalo.Wenli Li, Derek M. Bickhart, Luigi Ramunno, Daniela Iamartino, John L. Williams, George E. Li