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Plant Disease ◽  
2021 ◽  
Author(s):  
Che-Chang Liang ◽  
P. Janet Chen

Poinsettia (Euphorbia pulcherrima Willd. ex Klotzsch.), originated in southern Mexico and northern Guatemala, is the most valuable potted flowering plant in the spurge family (Euphorbiaceae). The European Union and the United States are two biggest poinsettia markets (Taylor et al. 2011), with a wholesale value of $153 million in the United States in 2019. Root knot galls of poinsettia ‘Luv U Pink’ were collected from a production greenhouse located in Nantou County, Taiwan in March 2021. No aboveground symptoms were observed. A nematode population was established from a single female and used for identification and the Koch’s postulate. The perineal patterns of randomly picked 5 females are round or ovoid with moderate to high dorsal arches, but no distinct lateral lines, ventral striae are fine and smooth. The Morphometric characters of second-stage juvenile include: a vermiform body shape, tail narrow and tapering with rounded tail tips, and a distinct hyaline tail end. Measurements of 20 J2 are as follows: body length, 430 (398 - 473) μm; body width, 15.4 (13.4 - 17.8) μm; stylet length,13.4 (13.0 - 14.0) μm; dorsal esophageal gland orifice to basal knob, 3.4 (2.8 - 3.9) μm; tail length, 52.9 (47.6 - 62.2) μm. All morphometric data were consistent with the original description of Meloidogyne enterolobii (Yang and Eisenback 1983). Nematode DNA was extracted using GeneMark Tissue & Cell Genomic DNA Purification Kit (GeneMark, Taiwan) from approximately 1500 J2 and used for amplification of 18S rRNA gene, a D2-D3 region of 28S rRNA gene, and a mtDNA COII region with primer sets 1A/MelR, D2A/D3B, and C2F3/1108, respectively (Power and Harris 1993, Subbotin et al. 2006, Tigano et al. 2005). The sequence of 18S rRNA gene (accession no. MZ948800 haplotype 1 and MZ955998 haplotype 2), haplotype 1 shared 100% identity with that of M. enterolobii from the United States (KP901058) and China (MN832688); haplotype 2 shared 99.8% identity with that of KP901058 and MN832688. The sequence of the D2-D3 region (MZ955995) shared 99% identity with that M. enterolobii from the United States (KP901079). Sequence of the COII region (MZ964625) also shared 99% identity with that of M. enterolobii from the United States (AY446975) and China (MN840970). Phylogenetic trees of the three gene sequences plotted as described by Ye et al. (2021) revealed that the newly described nematode was grouped with M. enterolobii. Sequence analysis of two fragments: 236 bp and 520 bp amplified with gene specific primers Me-F/R and MK7F/R, respectively (Long et al. 2006, Tigano et al. 2010) also confirmed the identity of M. enterolobii. To measure the reproductive factor (Rf), the Poinsettia ‘Luv U Pink’ seedlings with eight true leaves were transplanted into three 12-cm diameter pots each containing 6000 eggs or water (mock control). Forty-five days after inoculation, the average Rf value of three inoculated plants was 6, and no galls were observed on mock control plant roots, confirming that poinsettia is the host of M. enterolobii. M. enterolobii has been reported in several Euphorbia species, including E. heterophylla, E. prostrata, E. punicea and E. tirucalli (Han et al. 2012, Rich et al. 2009). To the best of our knowledge, this is the first report of M. enterolobii infecting E. pulcherrima ‘Luv U Pink’. 


Author(s):  
T W Murphy ◽  
C G Chitko-McKown ◽  
M P Heaton ◽  
B A Freking

Abstract Ovine progressive pneumonia virus (OPPV) is a small ruminant lentivirus that is widespread throughout U.S. sheep flocks. Infections with OPPV are lifelong and effects are multi-systemic with significant implications for animal well-being and productivity. A protein isoform with lysine at position 35 (K35, haplotype “1”) encoded by the ovine transmembrane protein 154 (TMEM154) gene has been associated with reduced susceptibility to infection when two copies are present (i.e., diplotype “1,1”). Conversely, the ancestral protein isoform with glutamate at position 35 (E35, haplotype “3”) is associated with high susceptibility to infection when at least one copy is present. The beneficial effect of TMEM154 K35 alleles on ewe productivity has not been previously measured in controlled challenge experiments and was a major objective of this study. Ewes with TMEM154 diplotypes “1,1”; “1,3”; and “3,3” (n = 31, 47, and 30, respectively) were born and reared by OPPV-infected dams and managed under continual natural exposure to OPPV. Ewes were tested for serological status at 4 mo intervals for up to 5.5 yr. The incidence of infection in ewes with diplotype “1,1” was 6.5 to 9.7% and significantly lower (P < 0.001) than ewes with diplotype “1,3” (60.5 to 97.3%) or “3,3” (64.0 to 91.4%). Furthermore, the incidence among ewes with diplotype “1,1” did not increase from 10 to 67 mo of age (P > 0.99), whereas the incidence among diplotype “1,3” and “3,3” ewes increased steadily until reaching an asymptote at approximately 52 mo of age. Total number and weight of lamb weaned per ewe exposed through 5.5 yr from ewes with diplotype “1,1” far exceeded (P ≤ 0.05) those with diplotypes “1,3” and “3,3” by, on average, 2.1 lambs and 40 kg, respectively. The present study confirmed that TMEM154 diplotype “1,1” animals have reduced incidence of OPPV infection and, correspondingly, improved productivity. In flocks with a high frequency of TMEM154 haplotype “3”, selection for haplotype “1” appears to be a cost-effective approach to mitigate the impact of this economically important disease.


Author(s):  
Syed Ahmad Syarifah-Zulaikha ◽  
Madihah Halim ◽  
Ameyra Zuki Aman ◽  
Salmah Yaakop

The sawtoothed grain beetle, Oryzaephilus surinamensis, is a secondary pest that damages rice products and other stored grains. Analysis based on the cytochrome oxidase subunit I (COI) sequences data, the number of haplotypes (Hap) (n), haplotype diversity (Hd), haplotype network, genetic distance, and phylogeny between O. surinamensis populations from four regions (small-scale), viz. the northern area (Seberang Perai), middle area (Klang), southern area (Pasir Gudang), and east coast (Kuantan) of Peninsular Malaysia, as model sampling locations, were obtained. A total of five haplotypes were detected in all the test populations, two shared (Haplotype 1 and Haplotype 3) and three unique haplotypes (Haplotype 2, Haplotype 4, and Haplotype 5) with haplotype diversity value, Hd = 0.6789 were recorded. Furthermore, the neighbour-joining (NJ), maximum parsimony (MP), and Bayesian inference (BI) trees showed a mixture of individuals from all regions in Peninsular Malaysia (Haplotype 1 to Haplotype 4), except Haplotype 5, which was grouped with foreign populations that inherited similar haplotype with those of the European samples. This study assumed a mixture of populations presumably due to human activities and related explicitly to the exportation and importation of rice products across regions. This information is vital for strategising the control management of this pest species to reduce rice storage losses.


2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Hong-Lei Li ◽  
Lin Wu ◽  
Zhaoming Dong ◽  
Yusong Jiang ◽  
Sanjie Jiang ◽  
...  

AbstractGinger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.


F1000Research ◽  
2021 ◽  
Vol 9 ◽  
pp. 1449
Author(s):  
Aaron M. Dickey ◽  
Timothy P. L. Smith ◽  
Michael L. Clawson ◽  
Michael P. Heaton ◽  
Aspen M. Workman

Background: Small ruminant lentiviruses (SRLVs) cause a multisystemic chronic wasting disease in sheep across much of the world. SRLV subtype A2 is prevalent in North America and further classified into multiple subgroups based on variation in the group antigens gene (gag) and envelope (env) genes. In sheep, the ovine transmembrane protein 154 (TMEM154) gene is associated with SRLV susceptibility. Ewes with at least one copy of TMEM154 encoding a full-length protein with glutamate at position 35 (E35; haplotypes 2 and 3), are highly susceptible to SRLV infection while ewes with any combination of TMEM154 haplotypes which encodes lysine (K35; haplotype 1), or truncated proteins (haplotypes 4 and 6) are several times less so. A2 subgroups 1 and 2 are associated with host TMEM154 genotypes; subgroup 1 with the K35/K35 genotype and subgroup 2 with the E35/E35 genotype. Methods:  Sequence variation within and among full-length assemblies of SRLV subtype A2 subgroups 1 and 2 was analyzed to identify genome-scale recombination patterns and subgroup-specific variants. Results:  Consensus viral genomes were assembled from 23 infected sheep, including animals of assorted TMEM154 genotypes comprised of haplotypes 1, 2, or 3. Viral genome analysis identified viral subgroups 1 and 2 among the samples, and revealed additional sub-structure within subgroup 2 based on models predicting complex patterns of recombination between the two subgroups in several genomes. Animals with evidence of dual subgroup infection also possessed the most diverse quasi-species and the most highly recombined consensus genomes. After accounting for recombination, 413 subgroup diagnostic single nucleotide polymorphisms (SNPs) were identified. Conclusions:  The viral subgroup framework developed to classify SRLV consensus genomes along a continuum of recombination suggests that animals with the TMEM154 E35/K35 genotype may represent a reservoir for producing viral genomes representing recombination between A2 subgroups 1 and 2.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Guilherme G. Verocai ◽  
Caroline Sobotyk ◽  
Allegra Lamison ◽  
Mindy M. Borst ◽  
Erin E. Edwards

Abstract Background Onchocerca lupi is an emerging, zoonotic filarioid nematode associated with ocular disease in companion animals in North America and the Old World. The areas where this parasite is assumed to be endemic in the USA comprise southwestern states. Thus far, all cases reported outside of the southwest are associated with travel or animal movement. Methods An 11-year-old, castrated male Pitbull dog from McAllen, Hidalgo County, southern Texas, with no travel history, was diagnosed with a perforating corneal ulceration of the right eye. Enucleation was performed and tissues submitted for histopathology. Results Histologically, sections of two filarioid nematodes were observed. DNA was extracted from formalin-fixed paraffin-embedded tissue using a commercial kit. We performed PCR targeting the cox1 gene of the mitochondrial DNA, followed by sequencing and phylogenetic analysis. Altogether, these results confirmed the identification of the nematode specimens as O. lupi, phylogenetically belonging to haplotype 1. Conclusion We report the first autochthonous case of O. lupi in a dog from Hidalgo County, southern Texas, USA. Our finding suggests Texas as an additional state where this zoonotic nematode is endemic. Further investigations are required to understand the epidemiology of this parasite along the USA/Mexico border. Graphic abstract


2021 ◽  
Vol 63 (2) ◽  
pp. 55-59
Author(s):  
Thi Mai Pham ◽  
◽  
Thi Nhu Le ◽  
Stefan Jouannic ◽  
Ngan Giang Khong ◽  
...  

QTL9 is a new potential quantitative trait locus related to rice panicle structure, identified through a GWAS analysis of Vietnamese local rice panel. To validate the QTL9, a biparental population was developed using the low branching (G6) and the high branching (G189) accessions from two haplotypes characterised by a contrasting phenotype for the secondary branch number and spikelet number traits. In parallel, using Gene capture technology combined with new generation sequencing identified 1,002 genetic variants in the QTL9 region between two parents, of which 12 SNPs were found in the cleavage site of 5 restriction enzyme. In this study, 12 primer pairs were tested to amplify the CAPS markers, based on the 12 SNPs, in order to be applied to select homozygous F2 lines over the QTL9 region for both haplotypes. 4 CAPS markers were selected distributing over the QTL9 region and displaying polymorphism between two parents. 275 F2plants were genotyped using 3 CAPS markers leading to the selection of 74 homozygotes plants over the QTL9region for haplotype 1, 66 homozygotes plants over the QTL9 region for haplotype 2, and 153 heterozygous plants. Homozygous lines will be used to develop the F3population, phenotyping of two F3 haplotypes will lead to discovering the role of QTL9 related to rice panicle structure.


Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 200
Author(s):  
Patricio Ponce ◽  
Sofía Muñoz-Tobar ◽  
Andrés Carrazco-Montalvo ◽  
Stephany D. Villota ◽  
Josefina Coloma ◽  
...  

Aedes aegypti, also known as the yellow fever mosquito, is the main vector of several arboviruses. In Ecuador, dengue and chikungunya are the most prevalent mosquito-borne diseases. Hence, there is a need to understand the population dynamics and genetic structure of the vector in tropical areas for a better approach towards effective vector control programs. This study aimed to assess the genetic diversity of Ae. aegypti, through the analyses of the mitochondrial gene ND4, using a combination of phylogenetic and population genetic structure from 17 sites in Ecuador. Results showed two haplotypes in the Ecuadorian populations of Ae. aegypti. Haplotype 1 was closely related to Ae. aegypti reported from America, Asia, and West Africa. Haplotype 2 was only related to samples from America. The sampled vectors from the diverse localities showed low nucleotide diversity (π = 0–0.01685) and genetic differentiation (FST = 0.152). AMOVA analyses indicated that most of the variation (85–91%) occurred within populations, suggesting that geographical barriers have little effect on the genetic structure of Ecuadorian populations of Ae. aegypti. These results agree with the one main population (K = 1) detected by Structure. Vector genetic identity may be a key factor in the planning of vector control strategies.


Cassowary ◽  
2021 ◽  
Vol 4 (1) ◽  
pp. 68-86
Author(s):  
Eka Fitri Wulandari ◽  
Nouke Lenda Mawikere ◽  
Barahima Abbas

Sago palm (Metroxylon sago Rottb.) is one of the carbohydrate-producing crops that has great potential in supporting food security programs. This study aims to determine the morphological and genetic diversity based on the mat-K gene marker of 15 accessions of sago pal that have been collected by the Sago Research Consortium. This research was conducted by preparing plant samples, extracting DNA, amplifying DNA with a PCR tools, visualizing the results of DNA amplification, sequencing, editing DNA sequencing, and blasting. The results showed that the sago palm accessions collected by the UNIPA Sago Research Consortium were morphologically different in the Russet stages.  Based on the maturase K (mat-K) gene marker of 15 sago palm accessions were divided into two haplotypes, namely haplotype 1 which experienced deletion at base number 5 (amino acid phenylalanine) and haplotype 2 which did not experience deletion so it had phenylalanine amino acid. Phylogenetic analysis showed that 15 sago palm accessions were divided into 2 groups, namely group 1 and group 2. Sago palm were observed closely related to Metroxylon warburgii with genetic distance of 0.001.


2021 ◽  
Vol 11 ◽  
Author(s):  
Heidi Kaech ◽  
Christoph Vorburger

Secondary endosymbionts of aphids have an important ecological and evolutionary impact on their host, as they provide resistance to natural enemies but also reduce the host’s lifespan and reproduction. While secondary symbionts of aphids are faithfully transmitted from mother to offspring, they also have some capacity to be transmitted horizontally between aphids. Here we explore whether 11 isolates from 3 haplotypes of the secondary endosymbiont Hamiltonella defensa differ in their capacity for horizontal transmission. These isolates vary in the protection they provide against parasitoid wasps as well as the costs they inflict on their host, Aphis fabae. We simulated natural horizontal transmission through parasitoid wasps by stabbing aphids with a thin needle and assessed horizontal transmission success of the isolates from one shared donor clone into three different recipient clones. Specifically, we asked whether potentially costly isolates reaching high cell densities in aphid hosts are more readily transmitted through this route. This hypothesis was only partially supported. While transmissibility increased with titre for isolates from two haplotypes, isolates of the H. defensa haplotype 1 were transmitted with greater frequency than isolates of other haplotypes with comparable titres. Thus, it is not sufficient to be merely frequent—endosymbionts might have to evolve specific adaptations to transmit effectively between hosts.


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