Delineating the Elusive BaMMV Resistance Gene rym15 in Barley by Medium-Resolution Mapping

Abstract Barley mild mosaic virus (BaMMV), transmitted by the soil-borne protist Polymyxa graminis, has a serious impact on winter barley production. Previously, the BaMMV resistance gene rym15 was mapped on chromosome 6HS, but the order of flanking markers was non-collinear between different maps. To resolve the position of the flanking markers and to enable map-based cloning of rym15, two medium-resolution mapping populations Igri (susceptible) × Chikurin Ibaraki 1 (resistant) (I×C) and Chikurin Ibaraki 1 × Uschi (susceptible) (C×U), consisting of 342 and 180 F2 plants, respectively, were developed. Efficiency of the mechanical inoculation at susceptible standards varied from 87.5–100% and in F2 populations from 90.56–93.23%. Phenotyping of F2 plants and corresponding F3 families revealed segregation ratios of 250s:92r (I×C, χ2 = 0.659) and 140s:40r (C×U, χ2 = 0.741), suggesting the presence of a single recessive resistance gene. Eight KASP assays, developed after screening the parents with the 50K Infinium chip and anchoring corresponding SNPs to the barley reference genome, were used to remap the gene. Newly constructed maps revealed a collinear order of markers, thereby allowing the identification of high throughput flanking markers. This study demonstrates how construction of medium-resolution mapping populations in combination with robust phenotyping can efficiently resolve conflicting marker ordering and reduce the size of the target interval. In an era of reference genomes and high throughput marker platforms, medium-resolution mapping will help accelerate candidate gene identification for traits where phenotyping is difficult.

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Delineating the elusive BaMMV resistance gene rym15 in barley by medium-resolution mapping

Molecular Breeding ◽

10.1007/s11032-021-01270-9 ◽

2021 ◽

Vol 41 (12) ◽

Author(s):

Yaping Wang ◽

Antje Habekuß ◽

Rod J. Snowdon ◽

Frank Ordon ◽

Dragan Perovic

Keyword(s):

Resistance Gene ◽

Reference Genome ◽

Gene Identification ◽

Polymyxa Graminis ◽

Genome Wide ◽

Medium Resolution ◽

Segregation Ratios ◽

Resolution Mapping ◽

Mild Mosaic Virus ◽

Mapping Populations

Abstract Barley mild mosaic virus (BaMMV), transmitted by the soil-borne protist Polymyxa graminis, has a serious impact on winter barley production. Previously, the BaMMV resistance gene rym15 was mapped on chromosome 6HS, but the order of flanking markers was non-collinear between different maps. To resolve the position of the flanking markers and to enable map-based cloning of rym15, two medium-resolution mapping populations Igri (susceptible) × Chikurin Ibaraki 1 (resistant) (I × C) and Chikurin Ibaraki 1 × Uschi (susceptible) (C × U), consisting of 342 and 180 F2 plants, respectively, were developed. Efficiency of the mechanical inoculation of susceptible standards varied from 87.5 to 100% and in F2 populations from 90.56 to 93.23%. Phenotyping of F2 plants and corresponding F3 families revealed segregation ratios of 250 s:92r (I × C, χ2 = 0.659) and 140 s:40r (C × U, χ2 = 0.741), suggesting the presence of a single recessive resistance gene. After screening the parents with the 50 K Infinium chip and anchoring corresponding SNPs to the barley reference genome, 8 KASP assays were developed and used to remap the gene. Newly constructed maps revealed a collinear order of markers, thereby allowing the identification of high throughput flanking markers. This study demonstrates how construction of medium-resolution mapping populations in combination with robust phenotyping can efficiently resolve conflicting marker ordering and reduce the size of the target interval. In the reference genome era and genome-wide genotyping era, medium-resolution mapping will help accelerate candidate gene identification for traits where phenotyping is difficult.

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One is not enough: on the effects of reference genome for the mapping and subsequent analyses of short-reads

10.1101/2020.04.14.041004 ◽

2020 ◽

Author(s):

Carlos Valiente-Mullor ◽

Beatriz Beamud ◽

Iván Ansari ◽

Carlos Francés-Cuesta ◽

Neris García-González ◽

...

Keyword(s):

High Throughput ◽

Legionella Pneumophila ◽

Phylogenetic Trees ◽

High Throughput Sequencing ◽

Reference Genome ◽

Bacterial Species ◽

Genomic Diversity ◽

Reference Sequence ◽

The Impact ◽

Reference Genomes

AbstractMapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species were selected as reference sequences, and read alignment statistics, SNP calling, recombination rates, dN/dS ratios, and phylogenetic trees were evaluated depending on the mapping reference. The choice of different reference genomes proved to have an impact on almost all the parameters considered in the five species. In addition, these biases had potential epidemiological implications such as including/excluding isolates of particular clades and the estimation of genetic distances. These findings suggest that the single reference approach might introduce systematic errors during mapping that affect subsequent analyses, particularly for data sets with isolates from genetically diverse backgrounds. In any case, exploring the effects of different references on the final conclusions is highly recommended.Author summaryMapping consists in the alignment of reads (i.e., DNA fragments) obtained through high-throughput genome sequencing to a previously assembled reference sequence. It is a common practice in genomic studies to use a single reference for mapping, usually the ‘reference genome’ of a species —a high-quality assembly. However, the selection of an optimal reference is hindered by intrinsic intra-species genetic variability, particularly in bacteria. Biases/errors due to reference choice for mapping in bacteria have been identified. These are mainly originated in alignment errors due to genetic differences between the reference genome and the read sequences. Eventually, they could lead to misidentification of variants and biased reconstruction of phylogenetic trees (which reflect ancestry between different bacterial lineages). However, a systematic work on the effects of reference choice in different bacterial species is still missing, particularly regarding its impact on phylogenies. This work intended to fill that gap. The impact of reference choice has proved to be pervasive in the five bacterial species that we have studied and, in some cases, alterations in phylogenetic trees could lead to incorrect epidemiological inferences. Hence, the use of different reference genomes may be prescriptive to assess the potential biases of mapping.

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Faculty Opinions recommendation of High-Throughput, High-Resolution Mapping of Protein Localization in Mammalian Brain by In Vivo Genome Editing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.726346764.793519161 ◽

2016 ◽

Author(s):

Vijay Tiwari ◽

Amitava Basu

Keyword(s):

High Resolution ◽

Genome Editing ◽

High Throughput ◽

Protein Localization ◽

Mammalian Brain ◽

High Resolution Mapping ◽

Resolution Mapping

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Reference flow: reducing reference bias using multiple population genomes

Genome Biology ◽

10.1186/s13059-020-02229-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Nae-Chyun Chen ◽

Brad Solomon ◽

Taher Mun ◽

Sheila Iyer ◽

Ben Langmead

Keyword(s):

Genetic Variation ◽

Reference Genome ◽

Alignment Method ◽

Sequencing Data ◽

Computational Overhead ◽

Reference Flow ◽

Multiple Population ◽

Reference Bias ◽

Flow Alignment ◽

Reference Genomes

AbstractMost sequencing data analyses start by aligning sequencing reads to a linear reference genome, but failure to account for genetic variation leads to reference bias and confounding of results downstream. Other approaches replace the linear reference with structures like graphs that can include genetic variation, incurring major computational overhead. We propose the reference flow alignment method that uses multiple population reference genomes to improve alignment accuracy and reduce reference bias. Compared to the graph aligner vg, reference flow achieves a similar level of accuracy and bias avoidance but with 14% of the memory footprint and 5.5 times the speed.

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Mapping and candidate gene screening of Cladosporium fulvum resistance gene Cf‐12 in tomato ( Solanum lycopersicum ) by high‐throughput sequencing

Plant Breeding ◽

10.1111/pbr.12852 ◽

2020 ◽

Vol 139 (5) ◽

pp. 977-987

Author(s):

Xinfeng Chai ◽

Xiangyang XU ◽

Dong Wang ◽

Dongqi Xue ◽

Jingfu Li

Keyword(s):

Candidate Gene ◽

Solanum Lycopersicum ◽

Resistance Gene ◽

High Throughput ◽

High Throughput Sequencing ◽

Cladosporium Fulvum ◽

Gene Screening

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High-resolution mapping of the brown planthopper resistance gene Bph6 in rice and characterizing its resistance in the 9311 and Nipponbare near isogenic backgrounds

Theoretical and Applied Genetics ◽

10.1007/s00122-010-1413-7 ◽

2010 ◽

Vol 121 (8) ◽

pp. 1601-1611 ◽

Cited By ~ 59

Author(s):

Yongfu Qiu ◽

Jianping Guo ◽

Shengli Jing ◽

Lili Zhu ◽

Guangcun He

Keyword(s):

High Resolution ◽

Resistance Gene ◽

Brown Planthopper ◽

High Resolution Mapping ◽

Resolution Mapping ◽

Brown Planthopper Resistance

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AStrap: identification of alternative splicing from transcript sequences without a reference genome

Bioinformatics ◽

10.1093/bioinformatics/bty1008 ◽

2018 ◽

Vol 35 (15) ◽

pp. 2654-2656 ◽

Cited By ~ 5

Author(s):

Guoli Ji ◽

Wenbin Ye ◽

Yaru Su ◽

Moliang Chen ◽

Guangzao Huang ◽

...

Keyword(s):

Machine Learning ◽

Alternative Splicing ◽

Single Molecule ◽

Reference Genome ◽

De Novo ◽

Supplementary Information ◽

Model Organisms ◽

Sequencing Data ◽

Extensive Evaluation ◽

Reference Genomes

Abstract Summary Alternative splicing (AS) is a well-established mechanism for increasing transcriptome and proteome diversity, however, detecting AS events and distinguishing among AS types in organisms without available reference genomes remains challenging. We developed a de novo approach called AStrap for AS analysis without using a reference genome. AStrap identifies AS events by extensive pair-wise alignments of transcript sequences and predicts AS types by a machine-learning model integrating more than 500 assembled features. We evaluated AStrap using collected AS events from reference genomes of rice and human as well as single-molecule real-time sequencing data from Amborella trichopoda. Results show that AStrap can identify much more AS events with comparable or higher accuracy than the competing method. AStrap also possesses a unique feature of predicting AS types, which achieves an overall accuracy of ∼0.87 for different species. Extensive evaluation of AStrap using different parameters, sample sizes and machine-learning models on different species also demonstrates the robustness and flexibility of AStrap. AStrap could be a valuable addition to the community for the study of AS in non-model organisms with limited genetic resources. Availability and implementation AStrap is available for download at https://github.com/BMILAB/AStrap. Supplementary information Supplementary data are available at Bioinformatics online.

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Trehalose-6-phosphate synthase from the cat flea Ctenocephalides felis and Drosophila melanogaster: gene identification, cloning, heterologous functional expression and identification of inhibitors by high throughput screening

Insect Molecular Biology ◽

10.1111/j.1365-2583.2012.01151.x ◽

2012 ◽

Vol 21 (4) ◽

pp. 456-471 ◽

Cited By ~ 16

Author(s):

C. Kern ◽

C. Wolf ◽

F. Bender ◽

M. Berger ◽

S. Noack ◽

...

Keyword(s):

Drosophila Melanogaster ◽

High Throughput ◽

High Throughput Screening ◽

Functional Expression ◽

Ctenocephalides Felis ◽

Gene Identification ◽

Cat Flea ◽

Phosphate Synthase

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benchNGS : An approach to benchmark short reads alignment tools

10.7287/peerj.preprints.1007v1 ◽

2015 ◽

Author(s):

Farzana Rahman ◽

Mehedi Hassan ◽

Alona Kryshchenko ◽

Inna Dubchak ◽

Tatiana V Tatarinova ◽

...

Keyword(s):

Reference Genome ◽

Global Alignment ◽

Short Report ◽

Related Genome ◽

Genome Sequences ◽

Short Reads ◽

Relevant Reference ◽

Next Generation Sequencing Ngs ◽

Reference Genomes ◽

Generation Sequencing

In the last decade a number of algorithms and associated software were developed to align next generation sequencing (NGS) reads to relevant reference genomes. The results of these programs may vary significantly, especially when the NGS reads are contain mutations not found in the reference genome. Yet there is no standard way to compare these programs and assess their biological relevance. We propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. In this paper we outline the method and also present a short report of an experiment performed on five popular alignment tools .

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