scholarly journals First report of begomoviruses infecting Cucumis sativus L. in North America and identification of a proposed new begomovirus species

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9245
Author(s):  
Sarahi Sanchez-Chavez ◽  
Carlos Fernando Regla-Marquez ◽  
Zugey Elizabeth Cardenas-Conejo ◽  
Daniel Alejandro Garcia-Rodriguez ◽  
Sara Centeno-Leija ◽  
...  
Keyword(s):  
New Species ◽  
North America ◽  
High Throughput Sequencing ◽  
Evolutionary Relationship ◽  
Small Sample ◽  
Begomovirus Species ◽  
Economic Losses ◽  
Bipartite Begomovirus ◽  
First Report ◽  
Squash Leaf Curl Virus

Background Members of the Begomovirus genus are phytopathogens that infect dicotyledonous plants, producing economic losses in tropical and subtropical regions. To date, only seven species of begomoviruses (BGVs) infecting cucumber have been described. Most cucumber infections were reported in South Asia. In the Americas, begomoviral infections affecting cucumber are scarce; just one report of begomovirus has been described in South America. The presence of whitefly and typical symptoms of viral infections observed in a cucumber field in Colima, Mexico, suggested that plants in this field were affected by BGVs. Methods To identify the BGVs infecting cucumber, we performed a high-throughput sequencing and compared the assembled contigs against the GenBank nucleic acid sequence database. To confirm the presence of viruses in cucumber samples, we performed a PCR detection using specific oligonucleotides. We cloned and sequenced by Sanger method the complete genome of a potential new begomovirus. Begomovirus species demarcation was performed according to the International Committee on Taxonomy of Viruses. The evolutionary relationship of the new virus was inferred using phylogenetic and recombination analyses. Results We identified five species of begomovirus infecting plants in a field. None of these have been previously reported infecting cucumber. One of the five species of viruses here reported is a new begomovirus species. Cucumber chlorotic leaf virus, the new species, is a bipartite begomovirus that has distinctive features of viruses belonging to the squash leaf curl virus clade. Conclusions The findings here described represent the first report of begomoviral infection affecting cucumber plants in North America. Previous to this report, only seven begomovirus species have been reported in the world, here we found five species infecting cucumber plants in a small sample suggesting that cucumber is vulnerable to BGVs. One of these viruses is a new species of begomovirus which is the first begomovirus originally isolated from the cucumber. The findings of this report could help to develop strategies to fight the begomoviral infections that affect cucumber crops.

scholarly journals Identification of the Begomoviruses Squash Leaf Curl Virus and Watermelon Chlorotic Stunt Virus in Various Plant Samples in North America

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 810
Author(s):  
Rafaela S. Fontenele ◽  
Amulya Bhaskara ◽  
Ilaria N. Cobb ◽  
Lucas C. Majure ◽  
Andrew M. Salywon ◽  
...  
Keyword(s):  
North America ◽  
High Throughput Sequencing ◽  
Essential Feature ◽  
Native Vegetation ◽  
Bipartite Begomovirus ◽  
Squash Leaf Curl Virus ◽  
The Usa ◽  
Leaf Curl Virus ◽  
Watermelon Chlorotic Stunt Virus ◽  
Leaf Curl

Geminiviruses are a group of plant-infecting viruses with single-stranded DNA genomes. Within this family, viruses in the genus Begomovirus are known to have a worldwide distribution causing a range of severe diseases in a multitude of dicotyledonous plant species. Begomoviruses are transmitted by the whitefly Bemisia tabaci, and their ssDNA genomes can be either monopartite or bipartite. As part of a viral survey, various plants including those in the families Alliaceae, Amaranthaceae, Apiaceae, Asteraceae, Brassicaceae, Cactaceae, Cucurbitaceae, Lamiaceae, Lauraceae, Malvaceae, Oleaceae and Solanaceae were sampled and screened for begomoviruses using both a high-throughput sequencing and a begomovirus-specific primer pair approach. Based on the sequences derived using these approaches, the full-length genome of various begomoviruses were amplified from plants using abutting primers. Squash leaf curl virus (SLCV) and watermelon chlorotic stunt virus (WCSV) were identified in Cactaceae (n = 25), Solanaceae (n = 7), Cucurbitaceae (n = 2) and Lamiaceae (n = 1) samples. WCSV is an Old World bipartite begomovirus that has only recently been discovered infecting watermelons in the Americas. Our discovery of WCSV in the USA is the first indication that it has reached this country and indicates that this virus might be widespread throughout North America. Phylogenetic analysis suggests WCSV was introduced to the New World twice. The detection of begomoviruses in cactus plants suggests possible spillover events from agricultural areas into native vegetation. Since WCSV and SLCV have previously been found in mixed infections, pseudo-recombination infection experiments were conducted. We demonstrate that WCSV DNA-B is successfully trans-replicated by SLCV DNA-A despite very low degree of similarity between the replication-associated iterative sequences present in their common region, an essential feature for binding of the replication associated protein. This study highlights the importance of viral surveys for the detection of spillover events into native vegetation, but also suggests the need for more surveillance of WCSV in the USA, as this virus is a serious threat to watermelon cultivation in the Middle East.

Middle Cambrian of Avalonian Massachusetts: Stratigraphy and correlation of the Braintree trilobites

2001 ◽  
Vol 75 (1) ◽  
pp. 116-135 ◽  
Author(s):  
Gerd Geyer ◽  
Ed Landing
Keyword(s):  
New Species ◽  
North America ◽  
Early Cambrian ◽  
Middle Cambrian ◽  
First Report ◽  
Senior Synonym ◽  
Low Diversity ◽  
Eastern Massachusetts

Although Middle Cambrian trilobites of the Braintree Member in eastern Massachusetts were among the first published on in North America, re-examination of this fauna has led to wholesale taxonomic and biostratigraphic re-evaluation. This low diversity fauna now includes at least seven species, with the first report of agnostoids (three poorly preserved taxa) and the ellipsocephalid Kingaspis avalonensis new species. Paradoxides (Acadoparadoxides) harlani Green emend., a senior synonym of P. (A.) haywardi Raymond, allows correlation into the lowest Middle Cambrian elsewhere in Avalon. However, all the polymeroid species are endemic, and this precludes a highly resolved correlation into other Cambrian paleocontinents. A breakdown of provincial barriers in the late Early Cambrian as western Gondwana passed from equatorial to the higher south latitudes of Avalon led to faunal exchanges between these continents. Paradoxides (Acadoparadoxides) and Kingaspis of the Braintree fauna are shared with western Gondwana, while Braintreella and “Agraulos” quadrangularis are closest to genera known from the Spanish, Moroccan, and Perunican (Bohemian) margins of Gondwana.

Chloromyxum pristiophori, a New Species of Myxosporidia Parasitic in the Gall-Bladder of Pristiophorus cirratus (Saw-Shark)

Parasitology ◽  
1936 ◽  
Vol 28 (1) ◽  
pp. 72-78 ◽  
Author(s):  
Violet Woolcock
Keyword(s):  
New Species ◽  
North America ◽  
Gall Bladder ◽  
First Record ◽  
First Report ◽  
The Subject ◽  
A New Species

Within recent years a considerable amount of work has been done on the Myxosporidia, especially, as pointed out by Kudo (1919), in North America, Asia, and to a lesser degree in Japan (Fugita, 1912, 1913, 1925). Few investigations, however, have been carried out in Australia, and consequently very little is known concerning the distribution of the group in this country. There appear to be as yet only two contributions to the subject, papers by T. Harvey Johnston and M. J. Bancroft (1918, 1919). As far as can be ascertained, my paper is the first report concerning Myxosporidia from fishes of Southern Australian waters, and contains the first record of a species of Chloromyxum from Australia.

First report of grapevine polerovirus 1 from a grapevine in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Xiaoling Sai ◽  
Zhen Liu ◽  
Xuemeng Ma ◽  
Yinying Zheng
Keyword(s):  
High Throughput Sequencing ◽  
Rna Extraction ◽  
Economic Losses ◽  
Cabernet Sauvignon ◽  
National Bureau ◽  
Coding Region ◽  
Rt Pcr ◽  
First Report ◽  
Increased Risk ◽  
Blastn Analysis

Xinjiang Uygur Autonomous Region is the largest grape-producing area in China, with a grape output of 3.05 million tons in 2020, accounting for nearly 20% of the total grape output in China (National Bureau of Statistics, 2021). Viral disease is a major factor threatening the grape industry and results in large economic losses by affecting the quality of grapes and wines. Actually, nearly 80 different viruses have been recorded in grapevine (Fuchs, 2020). To identify viruses that infect grapevine in Xinjiang, leaves of four vines of cultivar Cabernet Sauvignon with symptoms of chlorotic spots and crinkling were collected from a vineyard at Shihezi University in Shihezi City in May 2019 and pooled for total RNA extraction (Invitrogen™ PureLink ® Plant RNA Reagent, USA). After ribodepletion, a cDNA library was prepared using the Ribo-ZeroTM Kit (Illumina, San Diego, USA) and subjected to high-throughput sequencing (HTS) on the Illumina NovaSeq 6000 platform (Novogene, China). In total, 41,799,420 paired-end reads (150 nt × 2) were obtained after performing quality control using Trimmomatic version 0.39 (Bolger et al., 2014). These reads were de novo assembled into 154,716 contigs using the rnaSPAdes method in SPAdes software with default parameters (Bankevich et al., 2012). BLASTn analysis of these contigs led to the identification of 59 viral-related contigs from 248 -18476 bp. These contigs belonged to six positive-stranded RNA viruses, namely, grapevine polerovirus 1 (GPoV-1; 2 contigs), grapevine berry inner necrosis virus (GBINV; 4 contigs), grapevine leafroll-associated virus 3 (GLRaV-3; 2 contigs), grapevine Pinot gris virus (GPGV; 3 contigs), grapevine rupestris stem pitting-associated virus (GRSPaV; 4 contigs), and grapevine fleck virus (GFkV; 17 contigs); one DNA virus, grapevine geminivirus A (GGVA; 2 contigs); and one viroid, Australian grapevine viroid (AGVd; 1 contig). Among them, GPoV-1 is a newly discovered grape-infecting virus that has recently been reported from Japan and France (Candresse et al., 2020; Chiaki and Ito, 2020). The two contigs of GPoV-1 were assembled manually into a 5627-nt scaffold that covers 99.6% of the genome of the reference GPoV-1 isolate (MT008025). The scaffold shared 98.5% and 98.2% nucleotide (nt) sequence identities with the French GPoV-1 isolate KT (MT008025) and the Japanese GPoV-1 isolate KC (LC505098), respectively. To confirm the GPoV-1 infection of the grapevines used for HTS analysis, we designed a primer pair targeting the coding region of the P1 protein GP30F (5′-CCTCTTTCGCTGCCATAGGC-3′) and GP2180R (5′-CCTGGAGCCTTAAGCTGGTG-3′) and applied them in revere transcription (RT)-PCR using a PrimeScriptTM One Step RT–PCR Kit (Takara, China) to detect GPoV-1. The expected 2151-bp fragment was amplified from one of the four grapevine samples. The amplicon was cloned into the pMD19-T vector (TaKaRa, China) and Sanger sequenced. BLASTn analysis showed that the sequence of the amplicon (GenBank accession no. OK574336) shared 98% identity with the scaffold obtained from HTS and shared 98.5% and 97.4% identity with the GPoV-1 isolates KT and KC, respectively. To determine the occurrence of GPoV-1 in the vineyard, 8 and 20 leaves were randomly collected from grapevines of cvs. Black Monukka and Cabernet Sauvignon, respectively. We designed a primer pair of GPoV4264F (5′-ACTGCACAGACTCTCACACG-3′) and GPoV4657R (5′- TCCTTCGCGCAGTCACTATC-3′), which target the coding region of the P3-P5 fusion protein. An expected 394-bp amplicon was detected in 2 out of the 8 Black Monukka and 7 out of the 20 Cabernet Sauvignon leaf samples. Sanger sequencing confirmed the GPoV-1 identity of the amplicons. Although all the samples used for HTS analysis displayed symptoms, 4 of 9 samples in which GPoV-1 infection was detected were asymptomatic, suggesting that GPoV-1 may be latent, as reported previously (Candresse et al., 2020). To the best of our knowledge, this is the first report of GPoV-1 infection of grapevine in China. Although most members of the genus Polerovirus (family Solemoviridae) are transmitted by aphids, how GPoV is transmitted remains unknown, representing an increased risk for its spread. Therefore, attention should be given to reducing the prevalence of GPoV-1 in grape-producing areas in China, especially in Xinjiang.

scholarly journals First Report of the Detection of ‘Candidatus Liberibacter’ Species in Zebra Chip Disease-Infected Potato Plants in the United States

Plant Disease ◽  
2009 ◽  
Vol 93 (1) ◽  
pp. 108-108 ◽  
Author(s):  
J. A. Abad ◽  
M. Bandla ◽  
R. D. French-Monar ◽  
L. W. Liefting ◽  
G. R. G. Clover
Keyword(s):  
United States ◽  
New Species ◽  
New Zealand ◽  
16S Rdna ◽  
The United States ◽  
Economic Losses ◽  
Zebra Chip ◽  
First Report ◽  
Potato Plants ◽  
A New Species

Zebra chip (ZC), an emerging disease causing economic losses to the potato chip industry, has been reported since the early 1990s in Central America and Mexico and in Texas during 2000 (4). ZC was subsequently found in Nebraska, Colorado, New Mexico, Arizona, Nevada, California, and Kansas (3). Severe losses to potato crops were reported in the last few years in Mexico, Guatemala, and Texas (4). Foliar symptoms include purple top, shortened internodes, small leaves, enlargement of the stems, swollen axillary buds, and aerial tubers. Chips made from infected tubers exhibit dark stripes that become markedly more visible upon frying, and hence, are unacceptable to manufacturers. Infected tubers may or may not produce plants when planted. The causal agent of ZC is not known and has been the subject of increased investigation. The pathogen is believed to be transmitted by the potato psyllid, Bactericera cockerelli, and the association of the vector with the disease is well documented (3). Following the report of a potential new liberibacter species in solanaceous crops in New Zealand, we sought to identify this liberibacter species in plants with symptoms of the ZC disease. Six potato plants (cv. Russet Norkota) exhibiting typical ZC symptoms were collected in Olton, TX in June of 2008. DNA was extracted from roots, stems, midribs, and petioles of the infected plants using a FastDNA Spin Kit and the FastPrep Instrument (Qbiogene, Inc., Carlsbad, CA). Negative controls from known healthy potato plants were included. PCR amplification was carried out with ‘Candidatus L. asiaticus’ omp primers (1), 16S rDNA primers specific for ‘Ca. L. asiaticus’, ‘Ca. L. africanus’, and ‘Ca. L. americanus’ (1), and 16S rDNA primers OA2 (GenBank Accession No. EU834130) and OI2c (2). Amplicons from 12 samples were directly sequenced in both orientations (McLab, San Francisco CA). PCR amplifications using species-specific primers for the citrus huanglongbing liberibacter were negative. However, 1.1- and 1.8-kb amplicons were obtained with the OA2/OI2C and omp primers, respectively. The sequences for the rDNA were submitted to NCBI GenBank (Accession Nos. EU884128 and EU884129). BLASTN alignment of the 16S rDNA sequences obtained with primers OA2 and OI2c revealed 99.7% identity with a new species of ‘Ca. Liberibacter’ identified in New Zealand affecting potato (GenBank Accession No. EU849020) and tomato (GenBank Accession No. EU834130), 97% identity with ‘Ca. L. asiaticus’, and 94% with ‘Ca. L. africanus’ and ‘Ca. L. americanus’. The neighbor-joining phylogenetic tree constructed using the 16S rDNA fragments delineated four clusters corresponding to each of the liberibacter species. These results confirm that ‘Ca. Liberibacter’ spp. DNA sequences were obtained from potatoes showing ZC-like symptoms, suggesting that a new species of this genus may be involved in causing ZC disease. To our knowledge, this is the first report of the detection of ‘Ca. Liberibacter’ spp. in potatoes showing ZC disease in the United States. References: (1) C. Bastianel et al. Appl. Environ. Microbiol. 71:6473, 2005. (2) S. Jagoueix et al. Mol. Cell. Probes 10:43, 1996. (3) J. E. Munyaneza et al. J. Econ. Entomol. 100:656, 2007. (4) G. A. Secor and V. V. Rivera-Varas. Rev. Latinoamericana de la Papa (suppl.)1:1, 2004.

Expanding horizons... The first report of the genus Mysmena (Araneae, Mysmenidae) from continental North America, with the description of a new species

Zootaxa ◽  
2008 ◽  
Vol 1718 (1) ◽  
pp. 36 ◽  
Author(s):  
LARA LOPARDO ◽  
NADINE DUPÉRRÉ ◽  
PIERRE PAQUIN
Keyword(s):  
New Species ◽  
North America ◽  
National Park ◽  
First Report ◽  
The Family ◽  
First Occurrence ◽  
Inventory Survey ◽  
A New Species

Mysmena quebecana, a new species of the spider family Mysmenidae is here described. Mysmena quebecana was discovered in a spider bio-inventory survey of the Yamaska National Park (Québec, Canada). We therefore report the first occurrence of the family in this province, as well as the first member of the genus Mysmena for continental North America.

Cladosporium species associated with disease symptoms on Passiflora edulis and other crops in Brazil, with descriptions of two new species

Phytotaxa ◽  
2019 ◽  
Vol 409 (5) ◽  
pp. 239-260 ◽  
Author(s):  
ANDRÉ W. C. ROSADO ◽  
FÁBIO A. CUSTÓDIO ◽  
DANILO B. PINHO ◽  
ANA PAULA S. FERREIRA ◽  
OLINTO L. PEREIRA
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Plant Diseases ◽  
Economic Losses ◽  
Passiflora Edulis ◽  
Disease Symptoms ◽  
First Report ◽  
Leaf Spots ◽  
Taxonomic Novelties ◽  
Postharvest Rot

Fungi belonging to the genus Cladosporium are cosmopolitan occurring in various substrate or hosts. Cladosporium spp. are responsible for economic losses in numerous agricultural crops, causing leaf spots, scab, postharvest rots and other disease symptoms. The etiology of many diseases associated with these symptoms is still uncertain. The aim of this research was to determine the identity of Cladosporium isolates associated with passionfruit scab and some postharvest rots on different crops in Brazil, based on phylogenetic and morphological analyses. The phylogenetic analyses indicated that all samples belong to the C. cladosporioides complex. Three previously described Cladosporium species were identified: Cladosporium pseudocladosporioides (on kiwi, passionfruit and taro), C. subuliforme (on passionfruit) and C. tenuissimum (on cashew fruit, papaya and passionfruit). In addition, four putative new species were found: Cladosporium passiflorae sp. nov., C. passifloricola sp. nov., Cladosporium sp. 1 and Cladosporium sp. 2, all occurring on passionfruit. This study is the first report of the presence of seven different species of Cladosporium associated with diseased passionfruit. Moreover, this paper represents the first report of C. pseudocladosporioides associated with postharvest rot on kiwi and taro and C. tenuissimum on cashew fruit in Brazil. This study contributes with several taxonomic novelties for the knowledge about the diversity of Cladosporium cladosporioides complex, especially those associated with plant diseases.

Report of Cladorhiza bathycrinoides Koltun (Demospongiae) from North America and a new species of Farrea (Hexactinellida) among sponges from Cordell Bank, California

Zootaxa ◽  
2020 ◽  
Vol 4747 (3) ◽  
pp. 562-574
Author(s):  
HENRY M. REISWIG
Keyword(s):  
New Species ◽  
North America ◽  
Pacific Coast ◽  
The Other ◽  
First Report ◽  
North East ◽  
East Pacific ◽  
Small Collection ◽  
A New Species ◽  
Depth Distributions

A small collection of five Sponges made by E/V Nautilus on Cordell Bank National Marine Sanctuary, California, include the first report of the crinorhyzid Cladorhiza bathycrinoides Koltun off North America and a new species of Hexactinellida, Farrea. cordelli n. sp. The other three sponges in the collection are known to occur off the surrounding North-East Pacific coast, but new geographic or depth distributions are reported for these. 

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