scholarly journals Insights Into the Etiology of Polerovirus-Induced Pepper Yellows Disease

2017 ◽  
Vol 107 (12) ◽  
pp. 1567-1576 ◽  
Author(s):  
Leonidas Lotos ◽  
Antonio Olmos ◽  
Chrysoula Orfanidou ◽  
Konstantinos Efthimiou ◽  
Apostolos Avgelis ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Full Genome Sequence ◽  
Yellow Leaf ◽  
Common Ancestry ◽  
Full Genome ◽  
Small Interfering Rnas ◽  
The Common ◽  
Leaf Curl Virus ◽  
Pepper Vein Yellows Virus ◽  
Generation Sequencing

The study of an emerging yellows disease of pepper crops (pepper yellows disease [PYD]) in Greece led to the identification of a polerovirus closely related to Pepper vein yellows virus (PeVYV). Recovery of its full genome sequence by next-generation sequencing of small interfering RNAs allowed its characterization as a new poleroviruses, which was provisionally named Pepper yellows virus (PeYV). Transmission experiments revealed its association with the disease. Sequence similarity and phylogenetic analysis highlighted the common ancestry of the three poleroviruses (PeVYV, PeYV, and Pepper yellow leaf curl virus [PYLCV]) currently reported to be associated with PYD, even though significant genetic differences were identified among them, especially in the C-terminal region of P5 and the 3′ noncoding region. Most of the differences observed can be attributed to a modular type of evolution, which produces mosaic-like variants giving rise to these different poleroviruses Overall, similar to other polerovirus-related diseases, PYD is caused by at least three species (PeVYV, PeYV, and PYLCV) belonging to this group of closely related pepper-infecting viruses.

scholarly journals A New Geminivirus Associated with a Yellow Leaf Curl Disease of Pepper in Thailand

Plant Disease ◽  
2000 ◽  
Vol 84 (9) ◽  
pp. 1047-1047 ◽  
Author(s):  
K. Samretwanich ◽  
P. Chiemsombat ◽  
K. Kittipakorn ◽  
M. Ikegami
Keyword(s):  
Sequence Similarity ◽  
Yellow Leaf ◽  
Degenerate Primers ◽  
Stem Loop ◽  
Loop Region ◽  
Tomato Leaf Curl ◽  
Leaf Curl Virus ◽  
Leaf Curl Disease ◽  
Pepper Plants ◽  
Leaf Curl

Pepper (Capsicum anuum) plants affected with yellow leaf curl disease were observed at Kanchanaburi in central Thailand in 1995. Three naturally infected pepper plants showing yellow leaf curl were collected and virus cultures maintained in pepper plants. Transmission experiments were carried out with the whitefly vector (Bemisia tabaci Genn.). Acquisition and inoculation threshold periods were 1 h and 30 min, respectively. The latent period was 10 h. Symptoms in cultured plants were the same as those observed in field plants. DNA was extracted from these cultured plants and amplified using polymerase chain reaction (PCR) with geminivirus-specific degenerate primers (1). A PCR product of 2.7 kbp was amplified and cloned. Three independent clones were sequenced and analyzed, and an identical 32-base stem loop region and the unique sequence (TGGGGTC) of putative Rep binding site were found in the intergenic region (IR). The B component could not be detected. The nucleotide sequence of the coat protein gene was compared with 28 well-studied whitefly-transmitted geminiviruses. Our geminivirus showed the highest sequence similarity (85%) with Tomato leaf curl virus from Taiwan (TwToLCV: GeneBank accession number U88692), suggesting that it is a new geminivirus. Therefore, it is designated Pepper yellow leaf curl virus. Reference: (1) M. R. Rojas et al. Plant Dis. 77: 340, 1993.

scholarly journals First Report of Pepper Vein Yellows Virus and Pepper Yellow Leaf Curl Virus Infecting Chilli Pepper (Capsicum annuum) in Malaysia

Plant Disease ◽  
2020 ◽  
Vol 104 (7) ◽  
pp. 2037-2037
Author(s):  
A. R. Sau ◽  
N. M. F. Nazmie ◽  
M. S. M. Yusop ◽  
M. A. Akbar ◽  
M. F. M Saad ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Yellow Leaf ◽  
Chilli Pepper ◽  
First Report ◽  
Leaf Curl Virus ◽  
Pepper Vein Yellows Virus ◽  
Leaf Curl

scholarly journals Complete Genome Sequence of Lleida Bat Lyssavirus

2017 ◽  
Vol 5 (2) ◽  
Author(s):  
Denise A. Marston ◽  
Richard J. Ellis ◽  
Emma L. Wise ◽  
Nidia Aréchiga-Ceballos ◽  
Conrad M. Freuling ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Next Generation ◽  
Generation Sequencing

ABSTRACT All lyssaviruses (family Rhabdoviridae) cause the disease rabies, an acute progressive encephalitis for which, once symptoms occur, there is no effective cure. Using next-generation sequencing, the full-genome sequence for a novel lyssavirus, Lleida bat lyssavirus (LLEBV), from the original brain of a common bent-winged bat has been confirmed.

Control of the Bemisia tabaci/Tomato yellow leaf curl virus complex on protected tomato crops in Algarve (Portugal)*

EPPO Bulletin ◽  
2002 ◽  
Vol 32 (1) ◽  
pp. 31-35
Author(s):  
A. F. Arsenio ◽  
E. Neto ◽  
N. Ramos ◽  
S. Mangerico ◽  
E. Fortunato ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
Tomato Yellow Leaf ◽  
Yellow Leaf ◽  
Virus Complex ◽  
Leaf Curl Virus ◽  
Leaf Curl

Study of a collection of tomato hybrids with genetic resistance to the yellow leaf curl virus in Southern Russia

2020 ◽  
pp. 30-34
Author(s):  
С.Ф. Гавриш ◽  
Т.А. Редичкина ◽  
А.В. Буц ◽  
Г.М. Артемьева
Keyword(s):  
Resistance Genes ◽  
Molecular Genetic Analysis ◽  
Tomato Yellow Leaf ◽  
Tomato Mosaic Virus ◽  
Average Weight ◽  
Yellow Leaf ◽  
The South ◽  
Economically Valuable Traits ◽  
Leaf Curl Virus ◽  
Leaf Curl

Дана информация об изучении коллекции гибридов F1томата (Solanum lycopersicum L.) зарубежной селекции различных фирм-оригинаторов, рекомендованных производителями семян как толерантные к вирусу желтой курчавости листьев томата. Все гибриды обладали комплексом хозяйственно ценных признаков и набором генов устойчивости к основным заболеваниям томата, в том числе к новому для юга России опасному патогену с максимальным потенциальным риском – вирусу желтой курчавости листьев томата (Tomato yellow leaf curl virus — TYLCV). Исследования проведены в 2017-2018 годах в лаборатории пасленовых культур ООО «НИИСОК» и в лаборатории молекулярной диагностики растений ООО «Семеновод». Всего было протестировано 34 гибрида F1 томата. Гибриды оценивали по совокупности хозяйственно ценных признаков, также проводили молекулярно-генетический анализ на наличие и аллельное состояние основных генов устойчивости: к вирусу табачной мозаики (Tm2а), фузариозному увяданию (I2), вертициллезному увяданию (Ve), к кладоспориозу (Cf9), нематодам (Mi1.2), вирусу бронзовости томата (Sw5), вирусу желтой курчавости листьев томата (Ty3a). Установлено, что все проанализированные гибриды томата с заявленной оригинаторами семян устойчивостью к вирусу желтой курчавости листьев были гетерозиготны по гену Ty3a. На основании проведенных исследований и с учетом требований рынка разработаны модели гибридов F1 томата юга России. Перспективный гибрид томата должен обладать индетерминантным типом роста с укороченными междоузлиями (4,5-5 см) а также хорошей облиственностью. Плоды томата должны быть с красной равномерной окраской без зеленого пятна у плодоножки, с плоскоокруглой или округлой формой плода и со средней массой 220-270 г. Для повышения транспортабельности томатов необходимо, чтобы плоды отличались высокой прочностью и характеризовались хорошей лежкостью. Урожайность гибрида томата должна быть более 30 кг/м2, а товарность - не менее 85%. Гибрид томата должен обладать следующим набором генов устойчивости в гетерозиготном состоянии: Ty3a, Mi1.2, Cf-9, а также в гомозиготном состоянии: Tm2a, I2, Ve. The article provides information on the study of the collection of F1 tomato hybrids (Solanum lycopersicumL.) of foreign breeding from various firms-originators recommended for cultivation in regions with a strong spread of tomato yellow leaf curl virus. All hybrids had a complex of economically valuable traits and a set of genes for resistance to the main diseases of tomato, including a new dangerous pathogen for the South of Russia with a maximum potential risk — the tomato yellow leaf curl virus (TYLCV). The studies were carried out in 2017-2018 in the Solanaceae Laboratory of LLC NIISOK and in the Molecular Diagnostics Laboratory of Plants of LLC Semenovod. A total of 34 F1 tomato hybrids were tested. The hybrids were assessed by a set of economically valuable traits. Molecular genetic analysis was also carried out for the presence and allelic state of the main resistance genes: Tomato mosaic virus (Tm2a), Fusarium wilt (I2), Werticillium wilt (Ve), Cladosporium fulvum (Cf9), Nematodes (Mi1.2), Tomato spotted wilt virus (Sw5), Tomato yellow leaf curl virus (Ty3a). It was found that all the analyzed tomato hybrids with the declared by seed originators resistance to yellow leaf curl virus were heterozygous for the Ty3a gene. Based on the conducted research and taking into account the market requirements, models of F1 tomato hybrids for protected ground for the South of Russia have been developed. A promising tomato hybrid should have an indeterminate growth type with shortened internodes (4.5-5 cm) and good foliage. Tomato fruits should have a uniform red color without green shoulders, with a flat-round or round shape of the fruit and with an average weight of 220-270 g. To increase the transportability of tomatoes, it is necessary that the fruits are highly firm and characterized by good shelf life. The yield of tomato hybrid should be more than 30 kg/m2, and marketability should be at least 85%. The tomato hybrid should have the following set of resistance genes in a heterozygous state: Ty3a, Mi1.2, Cf-9, and also in a homozygous state: Tm2a, I2, Ve.

IsoDetect: Detection of splice isoforms from third generation long reads based on short feature sequences

2020 ◽  
Vol 15 ◽  
Author(s):  
Hongdong Li ◽  
Wenjing Zhang ◽  
Yuwen Luo ◽  
Jianxin Wang
Keyword(s):  
Sequence Similarity ◽  
Detection Methods ◽  
Sequence Information ◽  
Third Generation ◽  
Sequencing Data ◽  
Splice Isoforms ◽  
Third Generation Sequencing ◽  
Long Reads ◽  
Feature Sequence ◽  
Generation Sequencing

Aims: Accurately detect isoforms from third generation sequencing data. Background: Transcriptome annotation is the basis for the analysis of gene expression and regulation. The transcriptome annotation of many organisms such as humans is far from incomplete, due partly to the challenge in the identification of isoforms that are produced from the same gene through alternative splicing. Third generation sequencing (TGS) reads provide unprecedented opportunity for detecting isoforms due to their long length that exceeds the length of most isoforms. One limitation of current TGS reads-based isoform detection methods is that they are exclusively based on sequence reads, without incorporating the sequence information of known isoforms. Objective: Develop an efficient method for isoform detection. Method: Based on annotated isoforms, we propose a splice isoform detection method called IsoDetect. First, the sequence at exon-exon junction is extracted from annotated isoforms as the “short feature sequence”, which is used to distinguish different splice isoforms. Second, we aligned these feature sequences to long reads and divided long reads into groups that contain the same set of feature sequences, thereby avoiding the pair-wise comparison among the large number of long reads. Third, clustering and consensus generation are carried out based on sequence similarity. For the long reads that do not contain any short feature sequence, clustering analysis based on sequence similarity is performed to identify isoforms. Result: Tested on two datasets from Calypte Anna and Zebra Finch, IsoDetect showed higher speed and compelling accuracy compared with four existing methods. Conclusion: IsoDetect is a promising method for isoform detection. Other: This paper was accepted by the CBC2019 conference.

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