Variation of DNA methylation and phenotypic traits following unilateral sexual polyploidization in Medicago

Sexual hybridization is an important generator of biodiversity and a powerful breeding tool. Hybridization can also overcome ploidy barriers when it involves 2n gametes, as in the case of unilateral sexual polyploidization (USP) that has been utilized in several crops, among which alfalfa. This research was aimed at gaining insights into the effects of USP on genome methylation and on phenotypic traits in alfalfa, an important forage species. The Methylation-Sensi- tive Amplified Polymorphism technique was used to estimate the cytosine methylation changes occurring in a tetraploid (2n = 4x = 32) USP progeny from crosses between a diploid Medicago sativa subsp. falcata genotype that produces 2n eggs and a cultivated tetraploid Medicago sativa subsp. sativa variety. De novo methylation or demethylation in the USP progeny were observed for 13% of the detected genomic sites, indicating that methylation changes can be relevant. USP plants showed larger surface area of the leaf epidermis cells than both parents, but this did not result in larger leaf size or higher plant biomass. They displayed significant higher ovule sterility than the tetraploid parent, but normal fertility was observed in crosses with unrelated male testers. We conclude that hybridization and sexual polyploidization resulted in novel variation in terms of remodeling of the methylation landscape as well as changes in phenotypic traits in alfalfa

PANEV: an R package for a pathway-based network visualization

BACKGROUND: During the last decade, with the aim to solve the challenge of post-genomic and transcriptomic data mining, a plethora of tools have been developed to create, edit and analyze metabolic pathways. In particular, when a complex phenomenon is considered, the creation of a network of multiple interconnected pathways of interest could be useful to investigate the underlying biology and ultimately identify functional candidate genes affecting the trait under investigation. RESULTS: PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on information available on KEGG, it visualizes genes within a network of multiple levels (from 1 to n) of interconnected upstream and downstream pathways. The network graph visualization helps to interpret functional profiles of a cluster of genes. CONCLUSIONS: The suite has no species constraints and it is ready to analyze genomic or transcriptomic outcomes. Users need to supply the list of candidate genes, specify the target pathway(s) and the number of interconnected downstream and upstream pathways (levels) required for the investigation. The package is available at https://github.com/vpalombo/PANEV

Long-read RNA Sequencing Improves the Annotation of the Equine Transcriptome

A high-quality reference genome assembly, a biobank of diverse equine tissues from the Functional Annotation of the Animal Genome (FAANG) initiative, and incorporation of long-read sequencing technologies, have enabled efforts to build a comprehensive and tissue-specific equine transcriptome. The equine FAANG transcriptome reported here provides up to 45% improvement in transcriptome completeness across tissue types when compared to either RefSeq or Ensembl transcriptomes. This transcriptome also provides major improvements in the identification of alternatively spliced isoforms, novel noncoding genes, and 3’ transcription termination site (TTS) annotations. The equine FAANG transcriptome will empower future functional studies of important equine traits while providing future opportunities to identify allele-specific expression and differentially expressed genes across tissues

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

Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

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