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Ecology and Epidemiology of Wheat Curl Mite and Mite-Transmissible Viruses in Colorado and Insights into the Wheat Virome

10 Aug 2020-bioRxiv (Cold Spring Harbor Laboratory)-

TL;DR: Variation in WSMV resistance among wheat varieties; however a variety that harbored dual resistance to mite and W SMV had lower virus titer compared to varieties that contained single resistance gene, which suggests that pyramiding genes will ensure improved and durable resistance.

AbstractThe wheat curl mite (WCM)-transmissible wheat streak disease complex is the most serious disease of wheat in the U.S. Great Plains. In the current study, we determined the genetic variability in WCM and mite-transmitted viruses in Colorado and identified sources of resistance in Colorado wheat germplasm to wheat streak disease complex. We identified two distinct genotypes of WCM, Type 1 and Type 2 based on the ribosomal ITS1 region. Both genotypes were found to co-exist throughout the wheat producing regions of Colorado. Analysis of the whole genome and partial coat protein sequences revealed rich diversity of wheat streak mosaic virus (WSMV) and High Plains wheat mosaic virus (HPWMoV) isolates collected from Colorado, whereas triticum mosaic virus (TriMV) showed low sequence variability. Analysis of WSMV isolates revealed two novel isolates and one that was 100% similar to a new variant of WSMV from Kansas. Interestingly, between 2-4 genotypes of all 8 RNA segments of HPWMoV were identified, which suggests new variants of emaraviruses and co-occurrence of multiple strains within host populations. Several novel viruses including mycoviruses were identified for the first time in Colorado. We found variation in WSMV resistance among wheat varieties; however a variety that harbored dual resistance to mite and WSMV had lower virus titer compared to varieties that contained single resistance gene. This suggests that pyramiding genes will ensure improved and durable resistance. Future research may be aimed at elucidating the dynamics, diversity, and distribution of the new WSMV and HPWMoV isolates and their responses to wheat genotypes.

Summary (2 min read)

Wheat Curl Mite and Plant Tissue Collection

  • Plants were examined using a dissecting microscope for the presence of WCMs.
  • Plants were grown in gallon pots with 2-3 plants per pot in Promix HP © soil.
  • Additionally, leaf tissues were tested for presence of WSMV, TriMV and HPWMoV.

Virus Detection and Quantification

  • Total RNA was extracted from approximately 40 mg homogenized leaf tissues obtained from various sources described above, lysed in Trisure® (Bioline Meridian Bioscience) using Direct-zol® RNA Purification Kit (Zymo Research, CA, USA) according to the manufacturer's recommendations.
  • The quantity of RNA was approximated using a NanoDrop One spectrophotometer (Thermo Fisher Scientific, MA, USA) and stored at -80°C until virus quantification.
  • To detect and quantify WSMV and TriMV, approximately 50 ng of RNA was used in a previously published qRT-PCR duplex assay (Price et al. 2010) with the TaqMan® RNA-to-Ct™ 1-step kit (Applied Biosystems™, ThermoFisher Scientific) on a QuantStudio™3 Real-Time PCR system (Applied Biosystems™, ThermoFisher Scientific).
  • Field samples with CQ values above the lower detection limit, as defined by the standard curves described below, were considered to be positive for the specified virus.
  • To detect HPWMoV, complementary DNA (cDNA) was synthesized from 1 μg of total RNA using the Verso® cDNA Synthesis Kit (ThermoFisher Scientific).

Wheat Virome Analysis

  • Four leaf tissue samples that previously tested positive for WSMV from Larimer county., positive for WSMV and TriMV from Bent county., positive for WSMV and HPWMoV from Phillips county., and positive for WSMV and TriMV from Kit Carson county.
  • After all filtering operations, an average of 0.25x10 6 reads (3%) remained per dataset.
  • Then, analysis of SNPs for the viruses from assembled virome data were performed using the Tablet software program to determine genetic diversity.
  • Lastly, the raw sequence data was deposited in the NCBI Sequence Read Archive (SRA) repository under submission number SUB7870854.
  • Phylogenetic analysis of the complete sequences of the nucleoprotein encoding RNA3 segments of members of both groups of HPWMoV and three variants all from the Phillips county sample, shows version Colorado RNA3C (MT762120) is similar to isolates from OH/TX or group A (Fig. 5 ).

Wheat Germplasm and Virulence Test

  • A natural infection of wheat streak mosaic virus was observed in the Colorado State University Irrigated Variety Performance Trial (IVPT) at Burlington, CO, in 2019.
  • The trial included 24 different genotypes (released varieties and experimental lines), planted in a randomized complete block design with three replications.
  • To quantify virus titer in wheat varieties, 10 leaf samples were collected on June 21, 2019.
  • All ten leaves were stacked, and a small section of tissue was cut from the center of the stack.

Virus Occurence in Colorado

  • Survey of WCM-transmitted viruses revealed the presence of all three economicallyimportant viruses in Colorado, WSMV, TriMV and HPWMoV (Fig. 2 ).
  • Of the 40 symptomatic samples tested, 38 were positive for one or more WCM-transmitted viruses.
  • WSMV was found in all surveyed counties (Fig. 2.

Identification of Virus Genotypes

  • To determine the genetic variability among WSMV isolates in Colorado, the authors sequenced a portion of the WSMV-NIb region and performed phylogenetic analyses with isolates from other wheat producing states in the U.S. and other regions of the world.
  • Interestingly, an isolate, Larimer county 1, was 100% similar to a Kansas isolate (MK318278) that was collected from a wheat variety carrying the Wsm2 virus resistance gene that is known to confer resistance to WSMV (Fellers et al. 2019) .
  • The isolate Larimer county 2 collected from same location as the Larimer county 1 isolate, appeared to be genetically distinct from other isolates in the U.S.
  • In contrast, to the genetic diversity in WSMV isolates, there was limited variability in TriMV isolates collected in Colorado compared to that of other sequenced isolates.
  • Phylogenetic analysis reveals two distinct groups of the HPWMoV isolates among available HPWMoV nucleoprotein sequences as observed by previous studies (Stewart 2016) .

Virus Resistance in Variety Trial

  • Wheat varieity trial included a combination of 24 public and private varieties and experimental lines.
  • Seed companies with entries in the variety trials included AgriMaxx Wheat, AgriPro Syngenta, Dyna-Gro Seed, Limagrain Cereal Seeds, and WestBred Bayer.
  • The gerplasm included varieties with no known resistance, a single resistance marker to either WCM (WCM6D) or WSMV (Wsm2), and one variety, Guardian, with both resistance markers, WCM6D and Wsm2 (Table 4 ).

Discussion

  • Mite-vectored wheat viruses continue to cause significant yield losses in Colorado.
  • Wheat virome analysis confirmed the presence of known viruses such as WSMV, TriMV and HPWMoV, but also revealed presence of several mycoviruses and a novel Ixeridium yellow mottle virus 2 from Colorado wheat samples.
  • The genetic diversity of WSMV has been evaluated among various isolates in the U.S. and from around the world by sequencing the coat protein (CP) (Robinson and Murray 2013) and more recent whole genome sequencing (Schubert et al. 2015) .
  • There have been reports of increasing mite populations and virus infection in resistant varieties (Tatineni and Hein 2018) .

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1
Ecology and Epidemiology of Wheat Curl Mite and Mite-Transmissible Viruses in 1
Colorado and Insights into the Wheat Virome 2
3
Tessa Albrecht
1
, Samantha White
1
, Marylee Layton
2
, Mark Stenglein
2
, Scott Haley
3
4
and Punya Nachappa
1
5
1
Department of Agricultural Biology, Colorado State University, 307 University Ave, Fort 6
Collins, CO 80523 7
2
Department of Microbiology, Immunology, and Pathology, College of Veterinary 8
Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, 9
U.S.A. 10
3
Department of Soil and Crop Sciences, Colorado State University, 307 University Ave, 11
Fort Collins, CO 80523 12
13
Corresponding author: Punya Nachappa; E-mail: punya.nachappa@colostate.edu 14
Keywords: wheat curl mite, wheat streak mosaic virus, triticum mosaic virus, High 15
Plains wheat mosaic virus, resistance, virome 16
Funding: Colorado Wheat Research Foundation, Colorado Wheat Administrative 17
Committee 18
19
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 10, 2020. ; https://doi.org/10.1101/2020.08.10.244806doi: bioRxiv preprint

2
Abstract 20
The wheat curl mite (WCM)-transmissible wheat streak disease complex is the most serious 21
disease of wheat in the U.S. Great Plains. In the current study, we determined the genetic 22
variability in WCM and mite-transmitted viruses in Colorado and identified sources of resistance 23
in Colorado wheat germplasm to wheat streak disease complex. We identified two distinct 24
genotypes of WCM, Type 1 and Type 2 based on the ribosomal ITS1 region. Both genotypes 25
were found to co-exist throughout the wheat producing regions of Colorado. Analysis of the 26
whole genome and partial coat protein sequences revealed rich diversity of wheat streak mosaic 27
virus (WSMV) and High Plains wheat mosaic virus (HPWMoV) isolates collected from 28
Colorado, whereas triticum mosaic virus (TriMV) showed low sequence variability. Analysis of 29
WSMV isolates revealed two novel isolates and one that was 100% similar to a new variant of 30
WSMV from Kansas. Interestingly, between 2-4 genotypes of all 8 RNA segments of HPWMoV 31
were identified, which suggests new variants of emaraviruses and co-occurrence of multiple 32
strains within host populations. Several novel viruses including mycoviruses were identified for 33
the first time in Colorado. We found variation in WSMV resistance among wheat varieties; 34
however a variety that harbored dual resistance to mite and WSMV had lower virus titer 35
compared to varieties that contained single resistance gene. This suggests that pyramiding genes 36
will ensure improved and durable resistance. Future research may be aimed at elucidating the 37
dynamics, diversity, and distribution of the new WSMV and HPWMoV isolates and their 38
responses to wheat genotypes. 39
40
Keywords: wheat curl mite, wheat streak mosaic virus, triticum mosaic virus, high plains wheat 41
mosaic virus, resistance, virome42
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 10, 2020. ; https://doi.org/10.1101/2020.08.10.244806doi: bioRxiv preprint

3
Wheat (Triticum aestivum L.) is considered the most important crop in the 21
st
century as it 43
serves as a nutritional source of calories and protein in the human diet worldwide (Arzani and 44
Ashraf 2017; Curtis and Halford 2014). In the United States, wheat ranks third among field 45
crops in planted acreage, production, and gross farm receipts, behind corn and soybeans (USDA-46
ERS 2019). Among the top 10 wheat growing states, Colorado ranked 6
th
in 2019 with 2,150,000 47
acres being planted and a yield of 49 bushels per acre resulting in total production of 98,000,000 48
bushels valued at $387,100,000 (USDA-NASS 2019). The wheat curl mite (WCM), Aceria 49
tosichella Keifer (Acari: Eriophyidae) is a globally important pest affecting wheat production in 50
the Americas, Europe, and Asia (Skoracka et al. 2018). The mite causes direct damage by 51
feeding, which can reduce cereal yield (Harvey et al. 2000). But more importantly, WCM-52
transmitted viruses including wheat streak mosaic virus (family Potyviridae/genus Tritimovirus; 53
acronym WSMV) (Slykhuis 1955), triticum mosaic virus (Potyviridae/Poacevirus; TriMV) 54
(Seifers et al. 2009) and High plains wheat mosaic virus (Fimoviridae/Emaravirus; HPWMoV) 55
(Seifers et al. 1997) are among the most significant viruses in U.S. agriculture, responsible for 56
yield losses in wheat, barley, oats and rye (Burrows et al. 2009; Navia et al. 2013). Average 57
yield losses from the WCM-WSMV complex range from 5 to 7% in the US Great Plains, but 58
100% yield losses may occur in some fields (Appel et al. 2015). 59
Worldwide, the WCM has been found to be a diverse species complex with numerous 60
genetic lineages (Skoracka et al. 2018). In North America however, only two genetically distinct 61
genotypes of WCM have been characterized based on ribosomal ITS1 and mitochondrial 62
Cytochrome oxidase I/II partial sequences: Type 1, initially identified from South Dakota, 63
Kansas, Montana, Nebraska and Texas, and Type 2, from Nebraska (Hein et al. 2012). Both 64
genotypes occur in mixed populations in wheat-producing areas of the U.S. Great Plains. The 65
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 10, 2020. ; https://doi.org/10.1101/2020.08.10.244806doi: bioRxiv preprint

4
two distinct genotypes demonstrate different responses to curl mite colonization (Cmc) genes; 66
Cmc1, Cmc2, Cmc3 and Cmc4 (Dhakal et al. 2017; Harvey et al. 1999) and differential viral 67
transmission efficiencies (Hein et al. 2012; McMechan et al. 2014; Seifers et al. 2002; Wosula 68
et al. 2016). For example, Type 2 is more virulent and makes wheat lines carrying the 1AL.1RS 69
(Cmc3 resistance gene) susceptible (Dhakal et al., 2017) and Type 2 mites transmit WSMV at 70
higher rates compared to Type 1 mites (Wosula et al., 2016). 71
The WSMV populations are complex as well with numerous genotypes (Robinson and 72
Murray 2013; Schubert et al. 2015), although different genotypes rarely occur in the same plant 73
(McNeil et al. 1996). In the U.S., there are two WSMV isolates, Sidney 81 and Type, sharing 74
97.6% nucleotide sequence identity, and produce similar symptoms in wheat (Choi et al. 2001; 75
Hall et al. 2001). A third isolate, El Batán, from Mexico has diverged from the American strains 76
and has 79% nucleotide sequence identity to Sidney 81 and Type (Choi et al. 2001). In contrast, 77
TriMV field populations showed minimal amounts of sequence variation suggesting that the 78
populations are very homogenous (Fuentes-Bueno et al. 2011). There is little information about 79
the phylogenetic relationships between HPWMoV isolates. There appears to be two distinct 80
groups of HPWMoV isolates within the U.S. (Stewart 2016). Currently there are three sources of 81
host resistance to WSMV - Wsm1, Wsm2, and Wsm3 (Liu et al. 2011; Lu et al. 2011; Triebe et 82
al. 1991). However, some of these resistance alleles are temperature sensitive and do not prevent 83
virus infection and replication above 18°C (Fahim et al. 2012). More recently, a novel QTL was 84
identified on wheat chromosome 6DS from the wheat cultivar, TAM112, which provides WCM 85
resistance and moderate WSMV resistance (Dhakal et al. 2018). Genes for resistance to TriMV 86
and HPWMoV have not been identified. 87
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 10, 2020. ; https://doi.org/10.1101/2020.08.10.244806doi: bioRxiv preprint

5
One of the most effective ways of controlling WCM-virus complex is by planting mite 88
and disease resistant varieties; however, knowledge of mite and virus genotypes occurring in a 89
given area is critical because these genetic differences correspond to biological responses at the 90
phenotypic level (Hein et al. 2012). While Colorado is a major wheat producing state, there is no 91
information about the WCM-virus complex in the region. Moreover, little is known about 92
emerging and/or novel viruses of wheat in Colorado. Next generation sequencing is a powerful 93
tool that allows researchers to detect and characterize novel viruses (and bacterial and fungal 94
pathogens) and explore their diversity and pathogenicity in agricultural crops (Villamor et al. 95
2019). NGS is finding increased applications in revealing the viromes that contribute to the 96
disease phenotype. The term “virome” is defined as the genomes of all the viruses inhabiting a 97
specific organism or environment. In the current study, we determined the genetic variability in 98
WCM and mite-transmitted viruses in Colorado and identified sources of resistance in Colorado 99
wheat germplasm to WSMV and TriMV. In addition, we investigated the viromes of wheat from 100
four different locations in Colorado. To our knowledge, our study is among the first to report on 101
the wheat virome in the U.S. 102
103
Materials and Methods 104
Wheat Curl Mite and Plant Tissue Collection 105
Symptomatic wheat leaf tissues were collected across eastern Colorado by researchers, extension 106
agents and producers and delivered to our laboratory at Colorado State University. Plants were 107
examined using a dissecting microscope for the presence of WCMs. If present, mites were 108
transferred to healthy wheat plants of susceptible wheat varieties, Pronghorn or Hatcher at the 109
four-leaf stage or older. Plants were grown in gallon pots with 2-3 plants per pot in Promix HP
©
110
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 10, 2020. ; https://doi.org/10.1101/2020.08.10.244806doi: bioRxiv preprint

Figures (10)
Citations
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TL;DR: This report integrates the current state of knowledge of WCM–virus-plant interactions and addresses knowledge gaps regarding the mechanisms driving WCM infestation, viral epidemics, and plant responses.
Abstract: Wheat production and sustainability are steadily threatened by pests and pathogens in both wealthy and developing countries. This review is focused on the wheat curl mite (WCM), Aceria tosichella, and its relationship with wheat. WCM is a major pest of wheat and other cereals and a vector of at least four damaging plant viruses (Wheat streak mosaic virus, High plains wheat mosaic virus, Brome streak mosaic virus, and Triticum mosaic virus). The WCM–virus pathosystem causes considerable yield losses worldwide and its severity increases significantly when mixed-virus infections occur. Chemical control strategies are largely ineffective because WCM occupies secluded niches on the plant, e.g., leaf sheaths or curled leaves in the whorl. The challenge of effectively managing this pest–virus complex is exacerbated by the existence of divergent WCM lineages that differ in host-colonization and virus-transmission abilities. We highlight research progress in mite ecology and virus epidemiology that affect management and development of cereal cultivars with WCM- and virus-resistance genes. We also address the challenge of avoiding both agronomically deleterious side effects and selection for field populations of WCM that can overcome these resistance genes. This report integrates the current state of knowledge of WCM–virus-plant interactions and addresses knowledge gaps regarding the mechanisms driving WCM infestation, viral epidemics, and plant responses. We discuss the potential application of molecular methods (e.g., transcriptomics, epigenetics, and whole-genome sequencing) to understand the chemical and cellular interface between the wheat plant and WCM–virus complexes.

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TL;DR: Genome sequencing will be critical to fully characterize the genetic diversity in WCM and WSMV populations to better understand the occurrence of WCM-transmitted viruses and to evaluate the potential stability of resistance genes.
Abstract: Wheat curl mite (WCM) is the only known arthropod vector of four wheat viruses, the most important of which is Wheat streak mosaic virus (WSMV). Host resistance to WCM and WSMV is limited to a small number of loci, most of which are introgressed from wild relatives and are often associated with linkage drag and temperature sensitivity. Reports of virulent WCM populations and potential resistance-breaking WSMV isolates highlight the need for more diverse sources of resistance. Genome sequencing will be critical to fully characterize the genetic diversity in WCM and WSMV populations to better understand the incidence of WCM-transmitted viruses and to evaluate the potential stability of resistance genes. Characterizing host resistance genes will help build a mechanistic understanding of wheat-WCM-WSMV interactions and inform strategies to identify and engineer more durable resistance sources.

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References
More filters

Journal ArticleDOI
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Abstract: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straight-forward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.

81,150 citations


"Ecology and Epidemiology of Wheat C..." refers methods in this paper

  • ...Contigs and non-assembling reads were taxonomically categorized first by nucleotide-level alignment to the NCBI nucleotide (nt) database using BLASTN, and then by protein-level alignment to the NCBI protein (nr) database using the diamond aligner (Altschul et al. 1990; Buchfink et al. 2015)....

    [...]


Journal ArticleDOI
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Abstract: As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

27,973 citations


"Ecology and Epidemiology of Wheat C..." refers methods in this paper

  • ...Host (wheat)-derived reads were removed by bowtie2 alignment (Langmead and Salzberg 2012) to the Triticum aestivum reference genome (assembly accession GCA_900519105....

    [...]


Journal ArticleDOI
TL;DR: The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
Abstract: When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/

13,576 citations


"Ecology and Epidemiology of Wheat C..." refers methods in this paper

  • ...Low quality and adapter sequences were removed using cutadapt software (Martin 2011), leaving an average of 8.3×106 sequences remaining per dataset (93%)....

    [...]


Journal ArticleDOI
TL;DR: SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies.
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.

12,399 citations


"Ecology and Epidemiology of Wheat C..." refers methods in this paper

  • ...Remaining non-host reads were assembled into contigs using the Spades assembler (Bankevich et al. 2012)....

    [...]


Journal ArticleDOI
TL;DR: The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine and has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses.
Abstract: The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

11,718 citations


"Ecology and Epidemiology of Wheat C..." refers methods in this paper

  • ...Sequence alignments were generated using ClustalW in MEGA X (Kumar et al. 2018) followed by phylogenetic analyses based on the Maximum Likelihood method with 1000 replications....

    [...]