bluuebunny/crossref_metadata_2025 huggingface dataset:
First Report of Bois Noir Phytoplasma in Grapevine in Canada
Authors: Rott M. , Johnson R. , Masters C. , Green M.
Published: November 2007

During the summer and fall of 2006, a survey was done to detect European phytoplasmas of quarantine significance in Canadian vineyards. This survey was developed as one of the 2006 import requirements for grapevine nursery stock from Europe. This addresses the increased concerns regarding inadvertent phytoplasma introductions. Grapevines imported in 2006 and established grapevines were observed for symptoms typical of those associated with diseases caused by phytoplasmas on grapevine. Samples were tested from 155 grapevines. One plant, located in the lower Okanagan Valley, British Columbia, tested positive by a modified real-time PCR assay and TaqMan probe targeting the 16S region of the ribosomal RNA gene (1), which detects a wide variety of known phytoplasmas. The sample was further analyzed and found to be positive by conventional PCR with the phytoplasma-specific primers, P1/P7 (3), and Stolbur specific primers, STOL11f2/r1 (2). Additional PCR tests with primers specific to flavescence doree (FD9f/r) (2) and western X disease (P1/W INT) (3) were negative. These phytoplasmas are also known to infect grapevine. The approximate 1,800-bp fragment obtained with P1/P7 was sequenced (GenBank Accession No. EU086529) and found to have 99.7% nucleotide sequence identity to the Stolbur STOL #11 isolate (GenBank Accession No. AF248959) originally isolated from eastern Europe. This was the highest match to any available phytoplasma sequence obtained and indicates that the phytoplasma in the British Columbian sample is an isolate of bois noir, a pest of quarantine significance to Canada. Additional phylogenetic analysis using CLUSTAL W (Lasergene; DNASTAR, Madison, WI) confirmed this result. The presence and identity of the phytoplasma was confirmed from a second tissue sample that was analyzed by PCR and sequenced using the same test procedures as for the first sample, with identical results. The bois noir phytoplasma belongs to the stolbur group (16SrVII) with the principal vector being a cixiid planthopper. Stolbur phytoplasmas cause diseases in other crops, but bois noir disease is caused by a specific member of that group and is the only stolbur phytoplasma known to infect grapevines in Europe. The infected grapevine was from a lot of 1,965 plants of Grenache clone 70 on rootstock 3309 clone 143 that was imported from Europe in 2006. All plants in this importation have been destroyed. This phytoplasma has not been detected in any other grapevines in Canada. Additional import conditions requiring hot water treatment of European vines have been implemented for 2007. Further survey work for phytoplasma in grapevine will continue.

References: (1) N. M. Christensen et al. Mol. Plant-Microbe Interact. 17:1175, 2004. (2) X. D. Daire et al. Eur. J. Plant Pathol. 103:507, 1997. (3) C. D. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996.
Detection of Tomato spotted wilt virus in Tomato in the Baja California Peninsula of Mexico
Authors: Holguín-Peña R. J. , Rueda-Puente E. O.
Published: November 2007

In 2005, serological screening by ELISA of 24 tomato (Solanum lycopersicon Mill.) plants with virus-like foliar symptoms (locally known as “marchitez manchada” [spotted wilt] disease) was done for a variety of RNA viruses: Tomato spotted wilt virus (TSWV; family Bunyaviridae, genus Tospovirus) was specifically detected. The symptomatic plants testing positive were from the most important tomato areas in San Quintin, in the north of Baja California. Symptoms characteristic of TSWV (4), including chlorosis, malformation of apical leaves, stunting, and ringspot lesions, were observed in this region and throughout the peninsula. In 2006, 42 symptomatic tomato plants from La Paz, in the south of Baja California, were analyzed for TSWV by double-antibody sandwich (DAS)-ELISA with a commercially available kit (TSWV ImmunoStrip Kit; Agdia Inc., Elkhart, IN). Total nucleic acids of the TSWV ELISA-positive samples (16 of 42 = 38%) were extracted and preserved on FTA cards (Whatman, Brentford, U.K.) and processed according to the manufacturer's protocol. The positive TSWV samples were verified by reverse transcription (RT)-PCR with primers specific to the TSWV nucleocapsid protein gene, 5′-ATGTCTAAGGTTAAGCTC-3′ and 5′-TTAAGCAAGTTCTGTGAG-3′ (2). Amplicons of the expected size (approximately 800 bp) were obtained from all 16 positive samples but not in the ELISA-negative samples. The spotted wilt disease was mechanically transmitted to tomato (cv. Rutgers) and Nicotiana glauca seedlings. Symptoms on leaves consisting of chlorotic ring patterns and necrotic lesions were observed in tomato, and slightly concentric chlorotic lesions were observed in N. glauca. All symptomatic plants from San Quintin and La Paz were positive for TSWV in the DAS-ELISA and RT-PCR tests and none were positive for the tobamoviruses, Tomato mosaic virus (ToMV) and Tobacco mosaic virus (TMV). TSWV was not detected in symptomless tomato plants used as negative controls. TSWV was detected in Mexico in tomatillo (Physalis ixocarpa), tobacco (Nicotiana tabacum), jimsonweed (Datura stramonium) (3), and recently, in tomato and pepper in the Central Plateau of Mexico (1). Although spotted wilt disease has been previously observed in San Quintin tomato-producing areas, to our knowledge, this is the first confirmation of TSWV in the Baja Peninsula. The role of weed hosts as a natural reservoir and the role of species of thrips in the epidemiology of the disease are currently unknown, although the incidence of the virus in these regions has risen to destructive levels in tomato.

References: (1) R. De La Torre-Almaráz et al. Agrociencia 36:211, 2002. (2). R. K. Jain et al. Plant Dis. 82:900, 1998. (3) M. E. Llamas-Llamas et al. Plant Pathol. 47:341, 1998. (4) G. Marchoux et al. Plant Pathol. 40:347, 1991.
First Report of Apium virus Y in Celery in New Zealand
Authors: Tang J. , Clover G. R. G. , Alexander B. J. R.
Published: November 2007

Apium virus Y (ApVY) has been detected for the first time in New Zealand. In January 2006, leaf mosaic and vein-banding symptoms were observed on cultivated celery (Apium graveolens cv. Tongo) in Wanganui, New Zealand. Symptoms were widespread and seen in several paddocks. Similar symptoms were also observed in poison hemlock (Conium maculatum), a weed commonly found growing along the edges of the crop. Chenopodium amaranticolor and C. quinoa plants inoculated with leaf sap from a single, symptomatic celery or hemlock plant developed necrotic local spots after 9 and 12 days, respectively. Six Nicotiana spp. did not develop symptoms and were not tested further. Electron microscopy of sap from the celery, hemlock, and C. quinoa plants revealed the presence of elongated flexuous virus particles, 650 to 850 nm long. Symptomatic plants of these three species were tested for ApVY by reverse transcription (RT)-PCR using novel forward (5′-ATGATGCGTGGTTTGAAGG-3′) and reverse (5′-CTTGGTGCGTGAGTTCTTG-3′) primers specific to the coat protein gene (GenBank Accession No. AF203529). Amplicons of the expected size (approximately 425 bp) were obtained from all samples, and an amplicon from celery was sequenced (GenBank Accession No. EU127499). Comparison with ApVY sequences in GenBank confirmed the identity of the product, which had 97 to 99% nucleotide identity with GenBank Accession Nos. AF 203529, AF207594, and AY049716. The effect of ApVY on celery is unknown. ApVY has recently been described and infects three species of Apiaceae in Australia (2). In this study, diseased celery, but not the hemlock plants, were found to be coinfected with Celery mosaic virus (CeMV) by enzyme-linked immunsorbent assays with CeMV-specific antibodies (Loewe Biochemica GmbH, Sauerlach, Germany). Therefore, the symptoms observed in celery may be induced by ApVY or CeMV. CeMV is a serious disease of celery in New Zealand (1) and CeMV symptoms may mask the presence of ApVY.

References: (1) P. R. Fry and C. H. Procter. N. Z. Commer. Grower 24:23, 1968. (2) J. Moran et al. Arch. Virol. 147:1855, 2002.
First Report of the Nematode, Tylenchulus palustris, Parasitizing Peach in Virginia
Authors: Eisenback J. D. , Reaver D. , Ashley J. E.
Published: November 2007

In the fall of 2005 during routine sampling for plant-parasitic nematodes in a nematicide evaluation trial, juveniles of Tylenchulus palustris Inserra, Vovlas, O'Bannon & Esser, 1988 (1) were recovered by semi-automatic elutriation and centrifugation. Mature, sedentary females were hand picked from infected root tissues. The nematodes were parasitizing peach (Prunus persica (L.) Batsch.) at Crown Orchards Purvis Farm (37°51.638′N 78°43.062′W, elevation 230 m.) on U.S. Highway 29S near Faber, VA. Twelve of eighty samples contained the nematode with a density that varied from 10 to 70 nematodes per 500 ml3 of soil. Such low numbers may have been due to the severe state of decline of the 30+-year-old peach orchard; the stunted and nearly dead trees were being removed at the time of sampling. Ironically, this nematode was discovered by the first author more than 20 years ago in this same location before it was described as a new species; however, additional research is necessary to determine the role that this nematode played in the decline of this orchard. Identification was based on morphology of the female including the postvulval body terminus and morphometrics of 15 second-stage juveniles. Voucher specimens were placed in the Virginia Tech Nematode Collection and voucher cultures are maintained in the Virginia Tech Nematode Culture Collection. T. palustris was originally found in Florida parasitizing Carolina ash (Fraxinus caroliniana Mill.) and saltbush (Baccharis halimifolia L.) (1). This nematode has been reported previously on peach in Alabama, Arkansas, and Georgia (2).

References: (1) R. N. Inserra et al. J. Nematol. 20:266, 1988. (2) R. N. Inserra et al. J. Nematol. 22:45, 1990.
Identification of New Alternative Weed Hosts for Iris yellow spot virus in the Pacific Northwest
Authors: Sampangi R. K. , Mohan S. K. , Pappu H. R.
Published: November 2007

Iris yellow spot virus (IYSV; family Bunyaviridae, genus Tospovirus) is an economically important viral pathogen of onion bulb and seed crops in several parts of the United States and the world (1). IYSV is primarily transmitted by onion thrips (Thrips tabaci) and there is no evidence of seed transmission (1). However, susceptible cultivated and weed species could serve as reservoirs of inoculum from which thrips could acquire the virus to introduce and spread it in onion fields. Samples from asymptomatic and symptomatic volunteer onion plants in some of the commonly cultivated crops in the region (corn, wheat, grapes, mint, carrot, alfalfa, and sugar beets) and several common weeds in and around onion bulb and seed fields with a history of IYSV in Idaho and Washington were collected during the months of July, August, September and October of 2006. More than 175 samples from 35 plant species were analyzed for IYSV by a commercially available ELISA kit (Agdia Inc., Elkhart, IN). With the exception of a few volunteer onions, none of the other plant species had any symptoms of virus infection. Symptoms on volunteer onions included characteristic diamond-shaped lesions. To confirm the presence of IYSV in the ELISA-positive samples, total nucleic acids were extracted (2) and used in a reverse transcription (RT)-PCR assay (3). The primer pair consisted of 5′-TAA AAC AAA CAT TCA AAC AA-3′ and 5′-CTC TTA AAC ACA TTT AAC AAG CAC-3′. This primer pair flanks the nucleocapsid (N) gene of IYSV and generates an approximate 1.2-kb amplicon (3) that includes the complete N gene. An amplicon of expected size was obtained from each IYSV-positive sample. The amplicons were cloned and sequenced. There was a 95% sequence identity with known IYSV sequences. While several weed species gave ELISA values that suggested the presence of IYSV, results of RT-PCR assays failed to confirm the presence of the virus. This discrepancy between ELISA and RT-PCR results could be due to nonspecific reaction in ELISA (4) or difficulty associated with obtaining RT-PCR-quality templates for amplification. Only volunteer onions and the following weeds tested positive for IYSV by ELISA and RT-PCR: redroot pigweed (Amaranthus retroflexus), puncturevine (Tribulus terrestris), kochia (Kochia scoparia), prickly lettuce (Lactuca serriola), and common lambsquarters (Chenopodium album). Of these, redroot pigweed was recently reported to be ELISA-positive for IYSV (1). This information on the wider natural host range of IYSV, including potential alternative hosts that could serve as virus reservoirs, is useful for a better understanding of the disease epidemiology and in developing an integrated management strategy for reducing the impact of this disease.

References: (1) D. Gent et al. Plant Dis. 90:1468, 2006. (2) H. R. Pappu et al. HortScience 40:697, 2005. (3) H. R. Pappu et al. Arch. Virol. 151:1015, 2006. (4) T. N. Smith et al. Plant Dis. 90:729, 2006.
First Report of Powdery Mildew on Greenhouse Tomatoes Caused by Oidium neolycopersici in Michoacan, Mexico
Authors: Rodríguez-Alvarado G. , García-López J. , Rodríguez-Fernández R. , Fernández-Pavía S. P. , Garay-Serrano E.
Published: November 2007

During June and July of 2007, powdery mildew-infected tomato (Lycopersicum esculentum Mill. cv. Reserve) plants were observed in a commercial greenhouse with an open hydroponic system in Morelia County. Disease incidence increased from 0.5% to more than 90% in 1 month. Infected plants showed leaves with irregular areas of dense, white mycelium covering most of the upper surface. Microscopic analysis showed hyaline, septate hyphae with lobed appressoria. Conidia were ellipsoid to ovoid and 30 to 45 (38) μm × 15 to 20 (16) μm. Conidiophores were erect, 80 to 120 (103) μm, consisted of a foot cell 42 to 67 (56) μm, and two to three short cells. Conidia were produced singly. On the basis of the observed morphological characteristics, the fungus was identified as Oidium neolycopersici L. Kiss (1). Pathogenicity tests were conducted on fourth true-leaf tomato seedlings cv. Reserve under greenhouse conditions (22 ± 5°C). Inoculation was performed by transferring conidia from infected leaves to the leaves of uninfected tomato seedlings with a single-edged razor blade. Powdery mildew symptoms began to develop 7 days after inoculation. Symptoms and morphological characteristics were similar to those observed in the commercial greenhouse. Noninoculated plants remained healthy throughout the experiments. To our knowledge, this is the first report of O. neolycopersici causing powdery mildew on tomato in Michoacan, Mexico. This disease has been reported from Canada, Europe, Japan, the United States (2), and Venezuela (3) on greenhouse and field tomato crops. The observed high incidence and severe infection indicates that this disease may become an important problem in greenhouse tomatoes in Mexico.

References: (1) L. Kiss et al. Mycol. Res. 105:684, 2001. (2) L. Kiss et al. Plant Dis. 89:491, 2005. (3) J. O. Montilla et al. Plant Dis. 91:910, 2007.
First Report of Dothichiza caroliniana Causing Double Spot on Highbush Blueberry in South America
Authors: Baino O. , Ramallo A. C. , Hongn S. , Ramallo J. C.
Published: November 2007

A foliar disease affecting Jewell, Emerald, and O'Neal cultivars of highbush blueberry (Vaccinium corymbosum L.) was observed in commercial plantings in Tucuman, Argentina during February 2007. Typical symptoms were circular leaf spots that were 10 to 15 mm in diameter, light to dark brown with dark reddish borders, and frequently exhibiting a secondary necrotic area around the original spot. The final appearance was a large necrotic area surrounding a pale, smaller spot. On the abaxial leaf surfaces, white mycelia grew from the border of the initial or enlarged spots toward the healthy tissues. Frequently, black pycnidia bearing an amber rubbery cirrhi were observed. Fewer pycnidia were observed on the adaxial leaf lesions. The fungus was isolated by transferring cirrhi from affected leaves onto petri plates containing potato dextrose agar (PDA). Plates were incubated in darkness at 27°C and light brown concentric colonies with an aerial, effuse, white mycelium developed. After 5 days, dark brown cirrhi emerged from pycnidia in culture. Pycnidiospores were obtuse, hyaline, 1-celled (7 × 2 μm), and grew from the base of pycnidia on short conidiophores. Pycnidia were black, conical, obovoid, averaged 110 × 70 μm wide, and were lightly immersed in the mycelium. Pathogenicity tests were performed by spraying a 106 conidia/ml suspension on leaves of nine blueberry plants (cv. Jewell). Plants were incubated in a moist chamber at 25 to 29°C with a 12-h photoperiod. After 5 weeks, all inoculated leaves had foliar symptoms similar to the lesions previously observed in the field. Reisolation of the fungus completed Koch's postulates. Noninoculated leaves did not develop foliar symptoms. Morphological and cultural characteristics of the fungus conformed to the descriptions of Dothichiza caroliniana (Demaree & M.S. Wilcox) reported to cause “double spot” in blueberry (1,2). Symptoms were consistent with those described for double spot disease (2). To our knowledge, this is the first report of D. caroliniana on blueberry in South America.

References: (1) J. B. Demaree and M. Wilcox. Phytopathology, 37:490, 1947. (2) R. D. Milholland. Double spot. Page 17 in: Compendium of Blueberry and Cranberry Diseases. F. L. Caruso and D. C. Ramsdell, eds. The American Phytopathological Society, St. Paul, MN 1995.
First Report of Five Sooty Blotch and Flyspeck Fungi on Prunus americana in the United States
Authors: Latinović J. , Batzer J. C. , Duttweiler K. B. , Gleason M. L. , Sun G.
Published: November 2007

The sooty blotch and flyspeck (SBFS) complex includes more than 30 fungi that blemish the cuticle of apple fruit, causing economic losses in humid regions worldwide (1). In August 2005, we sampled SBFS-infested wild plum (Prunus americana) fruit growing in hedgerows in Iowa. Colonies were categorized according to mycelial type (1), and isolates were made from representative colonies onto acidified water agar (AWA). Plum skins with SBFS signs were excised, pressed, and photographed. DNA was obtained from purified isolates and also from mycelium and fruiting bodies scraped directly from plum fruit skins. Extracted DNA was amplified using primer pair ITS1-F/Myc1-R (ACTCGTCGAAGGAGCTACG) and PCR products were sequenced using primer pair ITS-1F/ITS4. Six sequences were obtained from pure cultures and seven from colonies on plum fruit skin. BLAST analysis of the 470-bp sequences showed 100% homology to five known species in the SBFS complex: Zygophiala cryptogama, Zygophiala wisconsinensis, Pseudocercosporella sp. RH1, and Stomiopeltis spp. RS1 and RS2 (GenBank Accession Nos. AY598854, AY598853, AY5988645, AY598882, and AY598883, respectively). Observations of colony and fruiting structure morphology from cultures on potato dextrose agar (PDA) and colonies on plums confirmed species identity. A modified version of Koch's postulates was conducted to verify that these fungi caused the signs observed on plum and could also infest apple fruit. In June 2006, 1-month-old cultures on PDA were pulverized in a blender with sterile distilled water, passed through four layers of sterile cheesecloth, and transferred to sterile jars. Each isolate was inoculated onto 20 fruit on plum trees (P. americana) on the Iowa State University (ISU) campus and 20 fruit on cv. Golden Delicious apple trees at the ISU Research Station, Gilbert, IA. Each fruit was disinfested with 70% ethanol, air dried, swabbed with inoculum, and covered with a Fuji bag. At harvest, fungal colonies on fruit were reisolated onto AWA. DNA was extracted from pure cultures; when isolations on agar were unsuccessful, DNA was extracted directly from colonies on fruit. PCR was conducted using ITS1-F/Myc1-R, and PCR products were sequenced using ITS1-F/ITS4. All five species were reisolated and sequenced from apple. Pseudocercosporella sp. RH1 and Stomiopeltis sp. RS1 were sequenced from inoculated plums. Although flyspeck, presumably caused by Schizothyrium pomi, was reported on Japanese plum (P. salicina) in Japan (2) and black cherry (P. serotina) in the United States (3), to our knowledge this is the first report of SBFS fungi on plum in the United States and the first confirmation that fungi from plum can produce SBFS signs on apple fruit. Wild plum may therefore act as a reservoir host, providing inoculum for SBFS infestations on apple.

References: (1) J. Batzer et al. Mycologia 97:1268, 2005. (2) H. Nasu and H. Kunoh. Plant Dis. 71:361, 1987. (3) T. B. Sutton. Plant Dis. 72:801, 1988.
First Report of Dolabra nepheliae on Rambutan and Litchi in Hawaii and Puerto Rico
Authors: Rossman A. Y. , Goenaga R. , Keith L.
Published: November 2007

A stem canker disease on rambutan (Nephelium lappaceum L.) and litchi (Litchi chinensis Sonn. (Sapindaceae) was found in plants in Hawaii and Puerto Rico. A fungus associated with cankers was identified as Dolabra nepheliae C. Booth & Ting (1). Numerous black, stipitate, elongate ascomata were produced within cracks of cankers. These ascomata contain elongate, bitunicate asci amid unbranched, interthecial elements and thin, cylindrical, hyaline ascospores measuring 96 to 136 × 2.5 to 3.5 μm. This fungus was originally described from Malaysia on N. lappaceum (1) and is also known on pulasan (N. mutabile Blume) in Australia (2). Classified by the Food and Agriculture Organization as a ‘minor disease’, the canker appears to be relatively common in Hawaii and was most likely introduced into Puerto Rico on imported germplasm. Nevertheless, efforts are underway to study the potential damage of this disease as well as mechanisms of control, including introduction of disease resistant clones. Specimens have been deposited at the U.S. National Fungus Collections (Hawaii on Nephelium BPI 878189, Puerto Rico (PR) on Nephelium BPI 878188, and PR on Litchi BPI 878190). Although a specimen of D. nepheliae on L. chinensis was collected from Hawaii in 1984 by G. Wong and C. Hodges and deposited as BPI 626373, this fungus was not known on Nephelium spp. in Hawaii and was not previously known from Puerto Rico on either host.

References: (1) C. Booth and W. P. Ting. Trans. Brit. Mycol. Soc. 47:235, 1964. (2) T. K. Lim and Y. Diczbalis. Rambutan. Page 306 in: The New Rural Industries. Online publication. Rural Industries Research and Development Corporation, Australia, 1997.
First Report in Myanmar of Xanthomonas axonopodis pv. mangiferaeindicae Causing Mango Bacterial Canker on Mangifera indica
Authors: Ah-You N. , Gagnevin L. , Pruvost O. , Myint N. T. , Johnson G. I.
Published: November 2007

Bacterial canker of mango (or bacterial black spot) caused by Xanthomonas axonopodis pv. mangiferaeindicae (1) is a disease of economic importance in tropical and subtropical producing areas. X. axonopodis pv. mangiferaeindicae can cause severe infection in a wide range of mango cultivars and induces raised, angular, black leaf lesions, sometimes with a chlorotic halo. Several months after infection, leaf lesions dry and turn light brown or ash gray. Severe leaf infection may result in abscission. Fruit symptoms appear as small, water-soaked spots on the lenticels. These spots later become star shaped, erumpent, and exude an infectious gum. Often, a “tear stain” infection pattern is observed on the fruit. Severe fruit infections will cause premature fruit drop. Twig cankers are potential sources of inoculum and weaken branch resistance to winds (2). Suspected leaf lesions of bacterial canker were collected from mango nursery stock cv. Yin Kwe at a nursery in Yangon, Myanmar during March 2007. Nonpigmented Xanthomonas-like bacterial colonies were isolated on KC and NCTM3 semiselective agar media (4). Amplified fragment length polymorphism analysis was performed on three isolates from Myanmar and additional reference isolates of xanthomonads originating from Anacardiaceae (X. axonopodis pv. anacardii, X. axonopodis pv. mangiferaeindicae, X. axonopodis pv. spondiae, and X. translucens strains from pistachio) using SacI/MspI and four primer pairs (unlabeled MspI + 1 [A, C, T, or G] primers and 5′-labeled - SacI + C primer for the selective amplification step) (1). On the basis of multidimensional scaling (1), the Myanmar isolates were identified as X. axonopodis pv. mangiferaeindicae and were most closely related to group B strains that were isolated from mango in India and Eastern Asia (2). Mango cv. Maison Rouge leaves, inoculated as previously reported (1) with the Myanmar isolates, showed typical symptoms of bacterial canker 1 week after inoculation. One month after inoculation, mean X. axonopodis pv. mangiferaeindicae population sizes ranging from 5 × 106 to 8 × 106 CFU per lesion were recovered from leaf lesions, typical of a compatible interaction (1). Mangifera indica L. probably evolved in the area that includes northwestern Myanmar (3) and to our knowledge, this is the first confirmed detection of X. axonopodis pv. mangiferaeindicae from Myanmar. Further surveys and strain collection will be necessary to evaluate its geographic distribution and prevalence in the country.

References: (1) N. Ah-You et al. Phytopathology 97:1568, 2007. (2) L. Gagnevin and O. Pruvost. Plant Dis. 85:928, 2001. (3) S. K. Mukherjee. Page 1 in: The Mango, Botany, Production and Uses. R. E. Litz, ed. CAB International, Wallingford, UK, 1997. (4) O. Pruvost et al. J. Appl. Microbiol. 99:803, 2005.
First Report of Sweet potato virus G and Sweet potato virus 2 Infecting Sweet Potato in Spain
Authors: Trenado H. P. , Lozano G. , Valverde R. A. , Navas-Castillo J.
Published: November 2007

Sweet potato feathery mottle virus (SPFMV), Sweet potato virus G (SPVG), and Sweet potato virus 2 (SPV2) (also known as Ipomoea vein mosaic virus (2) and Sweet potato virus Y) are members of the genus Potyvirus (family Potyviridae), which can synergistically interact with Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus, family Closteroviridae), increasing symptom severity on sweet potato (Ipomoea batatas (L.) Lam.) (1,2,3). During 2002, 2006, and 2007, vine cuttings from sweet potato plants were collected in Malaga (southern Spain), Tenerife, and Lanzarote (Canary Islands, Spain) to be tested for the presence of viruses. Sampled plants ranged from asymptomatic to severely affected by symptoms of sweet potato virus disease (SPVD), caused by dual infection with SPFMV or other potyviruses with SPCSV. Scions collected during 2002 were grafted to the indicator host I. setosa. Foliar samples from I. setosa were used for nitrocellulose membrane (NCM)-ELISA testing with antisera specific to SPVG or SPV2 (provided by C. A. Clark, Louisiana State University) following described procedures (2). NCM-ELISA testing indicated that SPVG was present in samples from Malaga, Tenerife, and Lanzarote, whereas SPV2 was only found in samples from Malaga. Reverse-transcription (RT)-PCR was performed on RNA extracts from sweet potato or I. setosa leaves using primer pairs MA541 (5′-AACAATTCCAGATAGTAGAGGGGTTG-3′)/MA542(5′-TGTGGGGACAGCATGATCCAATAG-3′) and MA540 (5′-AACCCCAACACCAGCAAAATCAGTTAAG-3′)/MA542 corresponding to the capsid protein (CP) genes of SPVG and SPV2, respectively. Thirteen of 47 samples from Malaga and 4 of 30 from the Canary Islands yielded the expected 483-bp DNA fragment with the primers for SPVG. Fifteen of 47 samples from Malaga yielded the expected 627-bp DNA fragment with primers for SPV2. Two RT-PCR amplicons of SPVG, one from Malaga and one from Tenerife, were sequenced. Their nucleotide sequences (GenBank Accession Nos. EF577438 and EF577439, respectively) showed 98% identity to SPVG isolates from Louisiana (2) and China. Sequencing of one RT-PCR amplicon of SPV2 from Malaga resulted in a nucleotide sequence (GenBank Accession No. EF577437) with 99% identity to SPV2 from Lousiana and Australia (3). The presence of SPVG and SPV2 increases the already existing risk of SPVD, since the main viruses involved in the synergism, SPFMV and SPCSV, are present in Spain (4). SPCSV was also detected in some of the plants infected with SPVG or SPV2, in some cases, in coinfection with SPFMV.

References: (1) C. D. Kokkinos and C. A. Clark. Plant Dis. 90:1347, 2006. (2) E. R. Souto et al. Plant Dis. 87:1226, 2003. (3) F. Tairo et al. Plant Dis. 90:1120, 2006. (4) R. A. Valverde et al. Plant Dis. 88:428, 2004.
Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
Authors: Heger Andreas , Ponting Chris P.
Published: November 2007

The newly sequenced genome sequences of 11 Drosophila species provide the first opportunity to investigate variations in evolutionary rates across a clade of closely related species. Protein-coding genes were predicted using established Drosophila melanogaster genes as templates, with recovery rates ranging from 81%–97% depending on species divergence and on genome assembly quality. Orthology and paralogy assignments were shown to be self-consistent among the different Drosophila species and to be consistent with regions of conserved gene order (synteny blocks). Next, we investigated the rates of diversification among these species’ gene repertoires with respect to amino acid substitutions and to gene duplications. Constraints on amino acid sequences appear to have been most pronounced on D. ananassae and least pronounced on D. simulans and D. erecta terminal lineages. Codons predicted to have been subject to positive selection were found to be significantly over-represented among genes with roles in immune response and RNA metabolism, with the latter category including each subunit of the Dicer-2/r2d2 heterodimer. The vast majority of gene duplications (96.5%) and synteny rearrangements were found to occur, as expected, within single Müller elements. We show that the rate of ancient gene duplications was relatively uniform. However, gene duplications in terminal lineages are strongly skewed toward very recent events, consistent with either a rapid-birth and rapid-death model or the presence of large proportions of copy number variable genes in these Drosophila populations. Duplications were significantly more frequent among trypsin-like proteases and DM8 putative lipid-binding domain proteins.
Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase
Authors: Villasante Alfredo , Abad José P. , Planelló Rosario , Méndez-Lago María , Celniker Susan E. , de Pablos Beatriz
Published: November 2007

Drosophila telomeres do not have arrays of simple telomerase-generated G-rich repeats. Instead, Drosophila maintains its telomeres by occasional transposition of specific non-long terminal repeat (non-LTR) retrotransposons to chromosome ends. The genus Drosophila provides a superb model system for comparative telomere analysis. Here we present an evolutionary study of Drosophila telomeric elements to ascertain the significance of telomeric retrotransposons (TRs) in the maintenance of Drosophila telomeres. PCR and in silico surveys in the sibling species of Drosophila melanogaster and in more distantly related species show that multiple TRs maintain telomeres in Drosophila. In addition to TRs with two open reading frames (ORFs) capable of autonomous transposition, there are deleted telomeric retrotransposons that have lost their ORF2, which we refer to as half telomeric-retrotransposons (HTRs). The phylogenetic relationship among these telomeric elements is congruent with the phylogeny of the species, suggesting that they have been vertically inherited from a common ancestor. Our results suggest that an existing non-LTR retrotransposon was recruited to perform the cellular function of telomere maintenance.
Sequence variation within the rRNA gene loci of 12 Drosophila species
Authors: Stage Deborah E. , Eickbush Thomas H.
Published: November 2007

Concerted evolution maintains at near identity the hundreds of tandemly arrayed ribosomal RNA (rRNA) genes and their spacers present in any eukaryote. Few comprehensive attempts have been made to directly measure the identity between the rDNA units. We used the original sequencing reads (trace archives) available through the whole-genome shotgun sequencing projects of 12 Drosophila species to locate the sequence variants within the 7.8–8.2 kb transcribed portions of the rDNA units. Three to 18 variants were identified in >3% of the total rDNA units from 11 species. Species where the rDNA units are present on multiple chromosomes exhibited only minor increases in sequence variation. Variants were 10–20 times more abundant in the noncoding compared with the coding regions of the rDNA unit. Within the coding regions, variants were three to eight times more abundant in the expansion compared with the conserved core regions. The distribution of variants was largely consistent with models of concerted evolution in which there is uniform recombination across the transcribed portion of the unit with the frequency of standing variants dependent upon the selection pressure to preserve that sequence. However, the 28S gene was found to contain fewer variants than the 18S gene despite evolving 2.5-fold faster. We postulate that the fewer variants in the 28S gene is due to localized gene conversion or DNA repair triggered by the activity of retrotransposable elements that are specialized for insertion into the 28S genes of these species.
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
Authors: Stark Alexander , Kheradpour Pouya , Parts Leopold , Brennecke Julius , Hodges Emily , Hannon Gregory J. , Kellis Manolis
Published: November 2007

MicroRNAs (miRNAs) are short regulatory RNAs that inhibit target genes by complementary binding in 3′ untranslated regions (3′ UTRs). They are one of the most abundant classes of regulators, targeting a large fraction of all genes, making their comprehensive study a requirement for understanding regulation and development. Here we use 12 Drosophila genomes to define structural and evolutionary signatures of miRNA hairpins, which we use for their de novo discovery. We predict >41 novel miRNA genes, which encompass many unique families, and 28 of which are validated experimentally. We also define signals for the precise start position of mature miRNAs, which suggest corrections of previously known miRNAs, often leading to drastic changes in their predicted target spectrum. We show that miRNA discovery power scales with the number and divergence of species compared, suggesting that such approaches can be successful in human as dozens of mammalian genomes become available. Interestingly, for some miRNAs sense and anti-sense hairpins score highly and mature miRNAs from both strands can indeed be found in vivo. Similarly, miRNAs with weak 5′ end predictions show increased in vivo processing of multiple alternate 5′ ends and have fewer predicted targets. Lastly, we show that several miRNA star sequences score highly and are likely functional. For mir-10 in particular, both arms show abundant processing, and both show highly conserved target sites in Hox genes, suggesting a possible cooperation of the two arms, and their role as a master Hox regulator.
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
Authors: Ruby J. Graham , Stark Alexander , Johnston Wendy K. , Kellis Manolis , Bartel David P. , Lai Eric C.
Published: November 2007

MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing of small RNAs from Drosophila melanogaster to experimentally confirm and complement these predictions. In addition to validating 20 of our top 45 predictions for novel miRNA loci, the large-scale sequencing identified many miRNAs that had not been predicted. In total, 59 novel genes were identified, increasing our tally of confirmed fly miRNAs to 148. The large-scale sequencing also refined the identities of previously known miRNAs and provided insights into their biogenesis and expression. Many miRNAs were expressed in particular developmental contexts, with a large cohort of miRNAs expressed primarily in imaginal discs. Conserved miRNAs typically were expressed more broadly and robustly than were nonconserved miRNAs, and those conserved miRNAs with more restricted expression tended to have fewer predicted targets than those expressed more broadly. Predicted targets for the expanded set of microRNAs substantially increased and revised the miRNA-target relationships that appear conserved among the fly species. Insights were also provided into miRNA gene evolution, including evidence for emergent regulatory function deriving from the opposite arm of the miRNA hairpin, exemplified by mir-10, and even the opposite strand of the DNA, exemplified by mir-iab-4.
Examining protein–protein interactions using endogenously tagged yeast arrays: The Cross-and-Capture system
Authors: Suter Bernhard , Fetchko Michael J. , Imhof Ralph , Graham Christopher I. , Stoffel-Studer Ingrid , Zbinden Caroline , Raghavan Maanasa , Lopez Lianet , Beneti Lucija , Hort Jacqueline , Fillingham Jeffrey , Greenblatt Jack F. , Giaever Guri , Nislow Corey , Stagljar Igor
Published: November 2007

Comprehensive approaches to detect protein–protein interactions (PPIs) have been most successful in the yeast model system. Here we present “Cross-and-Capture,” a novel assay for rapid, sensitive assessment of PPIs via pulldown of differently tagged yeast strain arrays. About 500 yeast genes that function in DNA replication, repair, and recombination and nuclear proteins of unknown function were chromosomally tagged with six histidine residues or triple VSV epitopes. We demonstrate that the assay can interrogate a wide range of previously known protein complexes with increased resolution and sensitivity. Furthermore, we use “Cross-and-Capture” to identify two novel protein complexes: Rtt101p–Mms1p and Sae2p–Mre11p. The Rtt101p–Mms1p interaction was subsequently characterized by genetic and functional analyses. Our studies establish the “Cross-and-Capture” assay as a novel, versatile tool that provides a valuable complement for the next generation of yeast proteomic studies.
Genomic regulatory blocks underlie extensive microsynteny conservation in insects
Authors: Engström Pär G. , Ho Sui Shannan J. , Drivenes Øyvind , Becker Thomas S. , Lenhard Boris
Published: November 2007

Insect genomes contain larger blocks of conserved gene order (microsynteny) than would be expected under a random breakage model of chromosome evolution. We present evidence that microsynteny has been retained to keep large arrays of highly conserved noncoding elements (HCNEs) intact. These arrays span key developmental regulatory genes, forming genomic regulatory blocks (GRBs). We recently described GRBs in vertebrates, where most HCNEs function as enhancers and HCNE arrays specify complex expression programs of their target genes. Here we present a comparison of five Drosophila genomes showing that HCNE density peaks centrally in large synteny blocks containing multiple genes. Besides developmental regulators that are likely targets of HCNE enhancers, HCNE arrays often span unrelated neighboring genes. We describe differences in core promoters between the target genes and the unrelated genes that offer an explanation for the differences in their responsiveness to enhancers. We show examples of a striking correspondence between boundaries of synteny blocks, HCNE arrays, and Polycomb binding regions, confirming that the synteny blocks correspond to regulatory domains. Although few noncoding elements are highly conserved between Drosophila and the malaria mosquito Anopheles gambiae, we find that A. gambiae regions orthologous to Drosophila GRBs contain an equivalent distribution of noncoding elements highly conserved in the yellow fever mosquito Aëdes aegypti and coincide with regions of ancient microsynteny between Drosophila and mosquitoes. The structural and functional equivalence between insect and vertebrate GRBs marks them as an ancient feature of metazoan genomes and as a key to future studies of development and gene regulation.
Revisiting the protein-coding gene catalog ofDrosophila melanogasterusing 12 fly genomes
Authors: Lin Michael F. , Carlson Joseph W. , Crosby Madeline A. , Matthews Beverley B. , Yu Charles , Park Soo , Wan Kenneth H. , Schroeder Andrew J. , Gramates L. Sian , St. Pierre Susan E. , Roark Margaret , Wiley Kenneth L. , Kulathinal Rob J. , Zhang Peili , Myrick Kyl V. , Antone Jerry V. , Celniker Susan E. , Gelbart William M. , Kellis Manolis
Published: November 2007

The availability of sequenced genomes from 12Drosophilaspecies has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have developed quantitative metrics for the evolutionary signatures specific to protein-coding regions and applied them genome-wide, resulting in 1193 candidate new protein-coding exons in theD. melanogastergenome. We have reviewed these predictions by manual curation and validated a subset by directed cDNA screening and sequencing, revealing both new genes and new alternative splice forms of known genes. We also used these evolutionary signatures to evaluate existing gene annotations, resulting in the validation of 87% of genes lacking descriptive names and identifying 414 poorly conserved genes that are likely to be spurious predictions, noncoding, or species-specific genes. Furthermore, our methods suggest a variety of refinements to hundreds of existing gene models, such as modifications to translation start codons and exon splice boundaries. Finally, we performed directed genome-wide searches for unusual protein-coding structures, discovering 149 possible examples of stop codon readthrough, 125 new candidate ORFs of polycistronic mRNAs, and several candidate translational frameshifts. These results affect >10% of annotated fly genes and demonstrate the power of comparative genomics to enhance our understanding of genome organization, even in a model organism as intensively studied asDrosophila melanogaster.
Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
Authors: Andolfatto Peter
Published: November 2007

Several recent studies have estimated that a large fraction of amino acid divergence between species of Drosophila was fixed by positive selection, using statistical approaches based on the McDonald-Kreitman test. However, little is known about associated selection coefficients of beneficial amino acid mutations. Recurrent selective sweeps associated with adaptive substitutions should leave a characteristic signature in genome variability data that contains information about the frequency and strength of selection. Here, I document a significant negative correlation between the level and the frequency of synonymous site polymorphism and the rate of protein evolution in highly recombining regions of the X chromosome of D. melanogaster. This pattern is predicted by recurrent adaptive protein evolution and suggests that adaptation is an important determinant of patterns of neutral variation genome-wide. Using a maximum likelihood approach, I estimate the product of the rate and strength of selection under a recurrent genetic hitchhiking model, λ2Nes ∼ 3 × 10−8. Using an approach based on the McDonald-Kreitman test, I estimate that ∼50% of divergent amino acids were driven to fixation by positive selection, implying that beneficial amino acid substitutions are of weak effect on average, on the order of 10−5 (i.e., 2Nes ∼ 40). Two implications of these results are that most adaptive substitutions will be difficult to detect in genome scans of selection and that population size (and genetic drift) may be an important determinant of the evolutionary dynamics of protein adaptation.
Significant gene content variation characterizes the genomes of inbred mouse strains
Authors: Cutler Gene , Marshall Lisa A. , Chin Ni , Baribault Helene , Kassner Paul D.
Published: November 2007

The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs). While less frequent than SNPs, CNVs have greater potential to affect phenotype. In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains. This microarray comparative genomic hybridization (CGH)-based analysis has identified 2094 putative CNVs, with an average of 10 Mb of DNA in 51 CNVs when individual mouse strains were compared to the reference strain C57BL/6J. This amount of variation results in gene content that can differ by hundreds of genes between strains. These genes include members of large families such as the major histocompatibility and pheromone receptor genes, but there are also many singleton genes including genes with expected phenotypic consequences from their deletion or amplification. Using a whole-genome association analysis, we demonstrate that complex multigenic phenotypes, such as food intake, can be associated with specific copy number changes.
Genome-scale analysis of positionally relocated genes
Authors: Bhutkar Arjun , Russo Susan M. , Smith Temple F. , Gelbart William M.
Published: November 2007

During evolution, genome reorganization includes large-scale events such as inversions, translocations, and segmental or even whole-genome duplications, as well as fine-scale events such as the relocation of individual genes. This latter category, which we will refer to as positionally relocated genes (PRGs), is the subject of this report. Assessment of the magnitude of such PRGs and of possible contributing mechanisms is aided by a comparative analysis of related genomes, where conserved chromosomal organization can aid in identifying genes that have acquired a new location in a lineage of these genomes. Here we utilize two methods to comprehensively identify relocated protein-coding genes in the recently sequenced genomes of 12 species of genusDrosophila. We use exceptions to the general rule of maintenance of chromosome arm (Muller element) association for mostDrosophilagenes to identify one major class of PRGs. We also identify a partially overlapping set of PRGs among “embedded genes,” located within the extents of other surrounding genes. We provide evidence that PRG movements have at least two different origins: Some events occur via retrotransposition of processed RNAs and others via a DNA-based transposition mechanism. Overall, we identify several hundred PRGs that arose within a lineage of the genusDrosophilaphylogeny and provide suggestive evidence that a few thousand such events have occurred within the radiation of the insect order Diptera, thereby illustrating the magnitude of the contribution of PRG movement to chromosomal reorganization during evolution.