Comparison of two Near-Isogenic Lines of Bell Pepper (Capsicum annuum): One Endornavirus-Infected and the Other Endornavirus-Free
01 Jan 2017-
About: The article was published on 2017-01-01 and is currently open access. It has received 5 citations till now. The article focuses on the topics: Pepper & Horticulture.
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
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.
10,124 citations
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01 Apr 2004
TL;DR: In this article, the authors define marketing as "the process through which organizations develop and distribute products and services that satisfy the needs of customers." Customer satisfaction is critical to the profitable operations and growth of organizations and is an integral component of modern-day marketing.
Abstract: Rapidly increasing global competition, emergence of new markets, and technological advancements make today’s marketplace a highly dynamic and challenging environment for companies. Effective marketing is therefore crucial for organizations to survive and prosper in such an environment. Marketing is the process through which organizations develop and distribute products and services that satisfy the needs of customers. Customer satisfaction is critical to the profitable operations and growth of organizations and, as such, an integral component of modern-day marketing.
240 citations
01 Jan 2019
TL;DR: This chapter discusses aphid transmitted viruses, their biology, and management, and the feeding feeding potential of MelanAPHIS SACCHARI in TRANSMITTING SORGHUM MOSAIC VIRUS to SorGHUM.
Abstract: ..............................................................................................................................v CHAPTER 1: GENERAL INTRODUCTION .............................................................................1 1.1. References ........................................................................................................................4 CHAPTER 2: LITERATURE REVIEW .....................................................................................7 2.1. Biology and life cycle of aphids ........................................................................................7 2.2. Aphid transmitted viruses, their biology, and management .............................................. 10 2.3. Why aphids are efficient virus vectors? ........................................................................... 16 2.4. Effects of plant viruses on behavior and performance of vectors and non-vectors ............ 17 2.5. Use of electrical penetration graph for study of vector feeding behavior .......................... 20 2.6. Study systems ................................................................................................................. 22 2.7. References ...................................................................................................................... 33 CHAPTER 3: THE FEEDING BEHAVIOR AND VECTOR POTENTIAL OF MELANAPHIS SACCHARI IN TRANSMITTING SORGHUM MOSAIC VIRUS TO SORGHUM .................... 50 3.
5 citations
TL;DR: In this paper , two near-isogenic lines (NILs) of Bell pepper cv. Marengo have been developed; one BPEV-infected and the other BPEv-free.
Abstract: Bell peppers (Capsicum annuum L) are native plants to the Mesoamerican region, whose domestication likely began in the northeast and east central Mexico (Pickersgill, 1989; Kraft et al., 2013). Among other pepper types, bell peppers are the most commonly cultivated in the United States and worldwide (Pickersgill, 1997; 1989; Eshbaugh, 1993; DeWitt and Bosland, 1996). Plant viruses can be grouped as acute or persistent (Roossinck, 2010). Acute viruses cause symptoms, move from cell-to-cell and systemically, and are transmitted vertically and horizontally. In contrast, persistent plant viruses do not cause symptoms, lack cell-to-cell movement, and are transmitted only vertically via gametes. Bell pepper endornavirus (BPEV) is a persistent virus in the family Endornaviridae with a genome of approximately 14.7 kb (Okada et al., 2011). BPEV has been reported worldwide, and in the United States, BPEV has been detected in all tested commercial cultivars of bell pepper (Valverde et al., 1990; Okada et al., 2011; Escalante, 2017; Safari and Roossinck, 2018). Like other persistent viruses, BPEV does not cause symptoms in peppers (Fukuhara and Gibbs, 2012). Many acute viruses infect bell pepper, causing severe loses of fruit yield and quality. The acute virus pepper mild mottle virus (PMMoV) is a species of the genus Tobamovirus with worldwide distribution, causing economically important diseases of pepper (Pernezny, 2003). This virus is abundant and ubiquitous in nature, and it is transmitted mechanically, through seed, and agricultural tools. Transcript analysis is one of the most advanced strategies used to determine the flexibility of gene expression as a response to any external or internal stimulus (Dunwell et al., 2001; Mutz et al., 2013). Taking advantage of this technique, identifying genes involved in important traits provides the basis for new progress in the genetic improvement of cultivated plant species (Dunwell et al., 2001). RNA sequencing (RNA-seq) has helped to elucidate different physiological responses of the host plant under infection by plant viruses and abiotic stresses (Li et al., 2016; 2015; Jiao et al., 2020). Using the backcross breeding method, two near-isogenic lines (NILs) of bell pepper cv. Marengo have been developed; one BPEV-infected and the other BPEV-free (Harlan and Pope, 1922; Escalante and Valverde, 2019). The advantage of using these NILs is that we can associate changes in gene expression with the presence of BPEV and not with the genetics of the host. Therefore, we used these NILs of bell pepper to analyze their transcriptome before and after inoculation with OPEN ACCESS
References
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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.
37,898 citations
"Comparison of two Near-Isogenic Lin..." refers background in this paper
...2, mapping and reconstruction with Bowtie2, and elongation and redundancy of contigs with the sequence assembly program CAP3 (Huang and Madan, 1999; Langmead and Salzberg, 2012; Bankevich et al., 2012)....
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TL;DR: A simplified scoring system is proposed that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length.
Abstract: A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homologous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
12,003 citations
"Comparison of two Near-Isogenic Lin..." refers methods in this paper
...Sequence alignments, including the unidentified virus were performed using the MAFFT online tool (http://mafft.cbrc.jp/alignment/server/) (Katoh et al., 2002) using the G-INS-i format....
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
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.
10,124 citations
TL;DR: The third generation of the CAP sequence assembly program is described, which has a capability to clip 5' and 3' low-quality regions of reads and uses forward-reverse constraints to correct assembly errors and link contigs.
Abstract: The shotgun sequencing strategy has been used widely in genome sequencing projects. A major phase in this strategy is to assemble short reads into long sequences. A number of DNA sequence assembly programs have been developed (Staden 1980; Peltola et al. 1984; Huang 1992; Smith et al. 1993; Gleizes and Henaut 1994; Lawrence et al. 1994; Kececioglu and Myers 1995; Sutton et al. 1995; Green 1996). The FAKII program provides a library of routines for each phase of the assembly process (Larson et al. 1996). The GAP4 program has a number of useful interactive features (Bonfield et al. 1995). The PHRAP program clips 5′ and 3′ low-quality regions of reads and uses base quality values in evaluation of overlaps and generation of contig sequences (Green 1996). TIGR Assembler has been used in a number of megabase microbial genome projects (Sutton et al. 1995). Continued development and improvement of sequence assembly programs are required to meet the challenges of the human, mouse, and maize genome projects.
We have developed the third generation of the CAP sequence assembly program (Huang 1992). The CAP3 program includes a number of improvements and new features. A capability to clip 5′ and 3′ low-quality regions of reads is included in the CAP3 program. Base quality values produced by PHRED (Ewing et al. 1998) are used in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. Efficient algorithms are employed to identify and compute overlaps between reads. Forward–reverse constraints are used to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward–reverse constraints.
An unusual feature of CAP3 is the use of forward–reverse constraints in the construction of contigs. A forward–reverse constraint is often produced by sequencing of both ends of a subclone. A forward–reverse constraint specifies that the two reads should be on the opposite strands of the DNA molecule within a specified range of distance. By sequencing both ends of each subclone, a large number of forward–reverse constraints are produced for a cosmid or BAC data set. A difficulty with use of forward–reverse constraints in assembly is that some of the forward–reverse constraints are incorrect because of errors in lane tracking and cloning. Our strategy for dealing with this difficulty is based on the observation that a majority of the constraints are correct and wrong constraints usually occur randomly. Thus, a few unsatisfied constraints in a contig may not be sufficient to indicate an assembly error in the contig. However, if a sufficient number of constraints are all inconsistent with a join in a contig and all support an alternative join, it is likely that the current join is an error, and the alternative join should be made.
5,074 citations
"Comparison of two Near-Isogenic Lin..." refers background in this paper
...2, mapping and reconstruction with Bowtie2, and elongation and redundancy of contigs with the sequence assembly program CAP3 (Huang and Madan, 1999; Langmead and Salzberg, 2012; Bankevich et al., 2012)....
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01 Jan 2005
4,979 citations