The Complete Nucleotide Sequence of Barley Yellow Dwarf Virus-PAV from Wheat in Turkey

We report the sequence of an assembled genome of Barley yellow dwarf virus-PAV (BYDV-PAV) from Turkey. This 5,672 nucleotide RNA encodes seven known open reading frames and a possible eighth. This genome from wheat is closely related to BYDV-PAVs in Pakistan, Brazil, and Australia, including one sequenced 34 years ago.Scientific and Technological Research Council of Turkey, International Postdoctoral Research Scholarship Program (TUBITAK-BIDEB); Tekirdag Namik Kemal University, The Scientific Research Projects Coordination Unit (NKU-BAP) [NKUBAP.03.GA.21.289]; Iowa State University Plant Sciences Institute; DARPA Insect Allies Program; Iowa Agriculture and Home Economics Experiment Station, Ames, IA - Hatch Act [4308]; State of Iowa fundsThis study was funded by the Scientific and Technological Research Council of Turkey, International Postdoctoral Research Scholarship Program (TUBITAK-BIDEB), and Tekirdag Namik Kemal University, The Scientific Research Projects Coordination Unit (NKU-BAP, Project No: NKUBAP.03.GA.21.289) to H.I., and the Iowa State University Plant Sciences Institute and the DARPA Insect Allies Program funding to W.A.M. This paper of the Iowa Agriculture and Home Economics Experiment Station, Ames, IA, Project No. 4308 was supported in part by Hatch Act and State of Iowa funds

CenH3 evolution in diploids and polyploids of three angiosperm genera

BACKGROUND: Centromeric DNA sequences alone are neither necessary nor sufficient for centromere specification. The centromere specific histone, CenH3, evolves rapidly in many species, perhaps as a coevolutionary response to rapidly evolving centromeric DNA. To gain insight into CenH3 evolution, we characterized patterns of nucleotide and protein diversity among diploids and allopolyploids within three diverse angiosperm genera, Brassica, Oryza, and Gossypium (cotton), with a focus on evidence for diversifying selection in the various domains of the CenH3 gene. In addition, we compare expression profiles and alternative splicing patterns for CenH3 in representatives of each genus. RESULTS: All three genera retain both duplicated CenH3 copies, while Brassica and Gossypium exhibit pronounced homoeologous expression level bias. Comparisons among genera reveal shared and unique aspects of CenH3 evolution, variable levels of diversifying selection in different CenH3 domains, and that alternative splicing contributes significantly to CenH3 diversity. CONCLUSIONS: Since the N terminus is subject to diversifying selection but the DNA binding domains do not appear to be, rapidly evolving centromere sequences are unlikely to be the primary driver of CenH3 sequence diversification. At present, the functional explanation for the diversity generated by both conventional protein evolution in the N terminal domain, as well as alternative splicing, remains unexplained. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-014-0383-3) contains supplementary material, which is available to authorized users

The Complete Genome Sequence of Clade B, Wheat Streak Mosaic Virus Isolate from Turkey

Wheat streak mosaic virus is one of the most widespread viruses in cereal crops, causing severe losses, dramatically affecting worldwide wheat production. Currently, four distinct clades of WSMV have been grouped and named: A (Mexico), B (Europe, Asia, Russia), C (Iran), and D (United States, Argentina, Brazil, Australia, Canada, Turkey). Each of these groups is based on genome-wide variability, emphasizing the CP. Previously reported Turkish wheat isolates of WSMV clustered within both clades D and B. However, the placement of the Turkish WMSV into clade B is only based on a partial genome sequence. Here, we used high throughput sequencing to assemble the complete genome sequence of WSMV type B isolate collected from wheat found in the European part of Turkey. Excluding the poly(A) tail, the genome of isolate S34Edirne (Genbank no. MZ405098) consists of 9,360 nucleotides and contains a single large open reading frame encoding a polyprotein of 3,033 amino acids. The characteristic lack of a GAG (Gly2761) codon within the CP of the polyprotein is typical for the clade B, WSMV-ΔE isolates, which are widely found throughout the European continent. However, two American isolates were recently placed in this group. Sequence comparisons revealed that WSMV Turkish wheat isolate is the most closely related to Czech isolate, with highly similar nucleotide and amino acid identities at 98.83-99.13%, respectively. The result of this study indicates that the WSMV full-length genome of S34Edirne isolate should be placed into clade B of the European WSMV-ΔE isolates.This preprint is made available through Research Square at doi:10.21203/rs.3.rs-3151096/v1. Posted with permission. This work is licensed under a Creative Commons Attribution 4.0 International License

The Complete Nucleotide Sequence of Barley Yellow Dwarf Virus-PAV from Wheat in Turkey

We report the sequence of an assembled genome of Barley yellow dwarf virus-PAV (BYDV-PAV) from Turkey. This 5,672 nucleotide RNA encodes seven known open reading frames and a possible eighth. This genome from wheat is closely related to BYDV-PAVs in Pakistan, Brazil, and Australia, including one sequenced 34 years ago.This article is published as Ilbağı, Havva, Rick E. Masonbrink, and W. Allen Miller. "The Complete Nucleotide Sequence of Barley Yellow Dwarf Virus-PAV from Wheat in Turkey." Microbiology Resource Announcements 11, no. 10 (2022): e00745-22. doi:10.1128/mra.00745-22. Posted with permission.This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International license

The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5

Plant-parasitic nematodes are a major, and in some cases a dominant, threat to crop production in all agricultural systems. The relative scarcity of classical resistance genes highlights a pressing need to identify new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major stages of the interaction. This novel approach enabled the analysis of the hologenome of the infection site, to identify metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that the highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is critically important for parasitism. Knockout of either the plant-encoded or the now nematode-encoded steps in the pathway blocks parasitism. Our experiments establish a reference for cyst nematodes, use this platform to further our fundamental understanding of the evolution of plant-parasitism by nematodes, and show that understanding congruent differential expression of metabolic pathways represents a new way to find nematode susceptibility genes, and thereby, targets for future genome editing-mediated generation of nematode-resistant crops.This article is published as Siddique, Shahid, Zoran S. Radakovic, Clarissa Hiltl, Clement Pellegrin, Thomas J. Baum, Helen Beasley, Oliver Chitambo et al. "The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B." bioRxiv (2021). DOI: 10.1101/2021.10.01.462558. Copyright 2021 The Authors. Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). Posted with permission

Shared Data Science Infrastructure for Genomics Data

Background Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant data. Shared data science infrastructures like Boag is needed to efficiently process and parse data contained in large data repositories. The main features of Boag are inspired from existing languages for data intensive computing and can easily integrate data from biological data repositories. Results As a proof of concept, Boa for genomics, Boag, has been implemented to analyze RefSeq’s 153,848 annotation (GFF) and assembly (FASTA) file metadata. Boag provides a massive improvement from existing solutions like Python and MongoDB, by utilizing a domain-specific language that uses Hadoop infrastructure for a smaller storage footprint that scales well and requires fewer lines of code. We execute scripts through Boag to answer questions about the genomes in RefSeq. We identify the largest and smallest genomes deposited, explore exon frequencies for assemblies after 2016, identify the most commonly used bacterial genome assembly program, and address how animal genome assemblies have improved since 2016. Boag databases provide a significant reduction in required storage of the raw data and a significant speed up in its ability to query large datasets due to automated parallelization and distribution of Hadoop infrastructure during computations. Conclusions In order to keep pace with our ability to produce biological data, innovative methods are required. The Shared Data Science Infrastructure, Boag, provides researchers a greater access to researchers to efficiently explore data in new ways. We demonstrate the potential of a the domain specific language Boag using the RefSeq database to explore how deposited genome assemblies and annotations are changing over time. This is a small example of how Boag could be used with large biological datasets.This article is published as Bagheri, Hamid, Usha Muppirala, Rick E. Masonbrink, Andrew J. Severin, and Hridesh Rajan. "Shared data science infrastructure for genomics data." BMC Bioinformatics 20, no. 1 (2019): 1-13. DOI: 10.1186/s12859-019-2967-2. Copyright 2020 The Author(s). Attribution 4.0 International (CC BY 4.0). Posted with permission