scholarly journals A high-quality functional genome assembly of Delia radicum L. (Diptera: Anthomiidae) annotated from egg to adult

2021 ◽  
Author(s):  
Rebekka Sontowski ◽  
Yvonne Poeschl ◽  
Yu Okamura ◽  
Heiko Vogel ◽  
Cervin Guyomar ◽  
...  
Keyword(s):  
Sequence Data ◽  
Life Stage ◽  
Chemical Defenses ◽  
Delia Radicum ◽  
Economic Losses ◽  
High Quality ◽  
Specific Chemical ◽  
Host Plant Adaptation ◽  
Illumina Sequence ◽  
Genetic Mechanisms

Belowground herbivores are overseen and underestimated, even though they can cause significant economic losses in agriculture. The cabbage root fly Delia radicum (Anthomyiidae) is a common pest in Brassica species, including agriculturally important crops, such as oil seed rape. The damage is caused by the larvae, which feed specifically on the taproots of Brassica plants until they pupate. The adults are aboveground-living generalists feeding on pollen and nectar. Female flies are attracted by chemical cues in Brassica plants for oviposition. An assembled and annotated genome can elucidate which genetic mechanisms underlie the adaptation of D. radicum to its host plants and their specific chemical defenses, in particular isothiocyanates. Therefore, we assembled, annotated and analyzed the D. radicum genome using a combination of different Next Generation Sequencing and bioinformatic approaches. We assembled a chromosome-level D. radicum genome using PacBio and Hi-C Illumina sequence data. Combining Canu and 3D-DNA genome assembler, we constructed a 1.3 Gbp genome with an N50 of 242 Mbp and 6 pseudo-chromosomes. To annotate the assembled D. radicum genome, we combined homology-, transcriptome- and ab initio-prediction approaches. In total, we annotated 13,618 genes that were predicted by at least two approaches. We analyzed egg, larval, pupal and adult transcriptomes in relation to life-stage specific molecular functions. This high-quality annotated genome of D. radicum is a first step to understanding the genetic mechanisms underlying host plant adaptation. As such, it will be an important resource to find novel and sustainable approaches to reduce crop losses to these pests.

scholarly journals A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

2016 ◽  
Vol 1 ◽  
pp. 4 ◽  
Author(s):  
Sarah Auburn ◽  
Ulrike Böhme ◽  
Sascha Steinbiss ◽  
Hidayat Trimarsanto ◽  
Jessica Hostetler ◽  
...  
Keyword(s):  
South America ◽  
Plasmodium Vivax ◽  
Sequence Data ◽  
Ex Vivo ◽  
Vital Role ◽  
Asia Pacific ◽  
Reference Sequence ◽  
Manual Curation ◽  
Illumina Sequence

Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite’s biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.

scholarly journals High quality genome resource of mango bacterial black spot pathogen Xanthomonas citri pv. mangiferaeindicae GXG07 isolated from Guangxi, China

Plant Disease ◽  
2021 ◽  
Author(s):  
Fengzhi Bie ◽  
Yiming Li ◽  
Zhibin Liu ◽  
Meijing Qin ◽  
Shuping Li ◽  
...  
Keyword(s):  
Black Spot ◽  
Economic Losses ◽  
High Fidelity ◽  
Whole Genome ◽  
Sequencing Technology ◽  
Xanthomonas Citri ◽  
High Quality ◽  
Genomic Resources ◽  
High Quality Genome ◽  
Growing Region

Xanthomonas citri pv. mangiferaeindicae (Xcm) is the causal agent of mango bacterial black spot which is present in many mango growing regions and leads to great economic losses to mango industry. Due to the limitation of high-quality genomic resources, little is known about the molecular pathogenesis of Xcm. Here, we used PacBio High Fidelity reads (HiFi) sequencing technology to sequence and analyze the whole genome of an Xcm strain GXG07 isolated from Guangxi, the largest mango growing region in China. PacBio HiFi reads with a mean coverage of 450× had been assembled into three contigs of 5,166,537, 79,634 and 30,169 bp, revealing that the genome of Xcm GXG07 contains one chromosome and two plasmids. This genome provides a resource to better understand the biology and pathogenicity of mango bacterial black spot.

scholarly journals Detecting and Differentiating Phytoplasmas Belonging to Subgroups 16SrIV-A and 16SrIV-D Associated With Lethal Declines of Palms in Florida Using qPCR and High-Resolution Melt Analysis (HRMA)

Plant Disease ◽  
2017 ◽  
Vol 101 (8) ◽  
pp. 1449-1454 ◽  
Author(s):  
Brian W. Bahder ◽  
Ericka E. Helmick ◽  
Nigel A. Harrison
Keyword(s):  
High Resolution ◽  
Sequence Data ◽  
Management Strategies ◽  
Economic Losses ◽  
High Resolution Melt ◽  
High Resolution Melt Analysis ◽  
Melting Temperatures ◽  
Detection And Identification ◽  
Lethal Yellowing ◽  
Sufficient Variation

Lethal yellowing (LY) and Texas Phoenix palm decline (TPPD) are two important phytoplasma diseases of palms in Florida. Both have been responsible for major economic losses historically and remain a constant threat to the sustainability of palm production in the landscaping and nursery industries in Florida. These two diseases cause rapid, lethal decline in afflicted palms, so rapid detection and identification is crucial to implement appropriate management strategies to reduce further spread and losses. In this study, a qPCR assay was developed to detect and identify the causal agents of LY and TPPD. Based on sequence data of the 16S gene for the 16SrIV-A phytoplasma (LY) and the 16SrIV-D phytoplasma (TPPD), two regions were identified in the gene that possessed sufficient variation to yield amplicons with measurable differences in melting temperature based on high resolution melt analysis (HRMA). One region was in the 5′ region and the other was located in the 3′ region of the gene. Products from both regions yielded amplicons with significantly different melting temperatures between the two phytoplasma strains. This research allows for the detection and identification of phytoplasmas in palms rapidly by eliminating many lengthy and post-PCR steps commonly used in phytoplasma identification.

scholarly journals ntEdit: scalable genome sequence polishing

2019 ◽  
Vol 35 (21) ◽  
pp. 4430-4432 ◽  
Author(s):  
René L Warren ◽  
Lauren Coombe ◽  
Hamid Mohamadi ◽  
Jessica Zhang ◽  
Barry Jaquish ◽  
...  
Keyword(s):  
Human Genome ◽  
Genome Sequence ◽  
Sequence Data ◽  
Bloom Filter ◽  
Supplementary Information ◽  
Routine Practice ◽  
High Coverage ◽  
Illumina Sequence ◽  
Genome Assemblies ◽  
Indel Rate

Abstract Motivation In the modern genomics era, genome sequence assemblies are routine practice. However, depending on the methodology, resulting drafts may contain considerable base errors. Although utilities exist for genome base polishing, they work best with high read coverage and do not scale well. We developed ntEdit, a Bloom filter-based genome sequence editing utility that scales to large mammalian and conifer genomes. Results We first tested ntEdit and the state-of-the-art assembly improvement tools GATK, Pilon and Racon on controlled Escherichia coli and Caenorhabditis elegans sequence data. Generally, ntEdit performs well at low sequence depths (<20×), fixing the majority (>97%) of base substitutions and indels, and its performance is largely constant with increased coverage. In all experiments conducted using a single CPU, the ntEdit pipeline executed in <14 s and <3 m, on average, on E.coli and C.elegans, respectively. We performed similar benchmarks on a sub-20× coverage human genome sequence dataset, inspecting accuracy and resource usage in editing chromosomes 1 and 21, and whole genome. ntEdit scaled linearly, executing in 30–40 m on those sequences. We show how ntEdit ran in <2 h 20 m to improve upon long and linked read human genome assemblies of NA12878, using high-coverage (54×) Illumina sequence data from the same individual, fixing frame shifts in coding sequences. We also generated 17-fold coverage spruce sequence data from haploid sequence sources (seed megagametophyte), and used it to edit our pseudo haploid assemblies of the 20 Gb interior and white spruce genomes in <4 and <5 h, respectively, making roughly 50M edits at a (substitution+indel) rate of 0.0024. Availability and implementation https://github.com/bcgsc/ntedit Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Genomics of Avian Viral Infections

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 814 ◽  
Author(s):  
Smith
Keyword(s):  
Viral Infections ◽  
Current Knowledge ◽  
Host Susceptibility ◽  
Host Responses ◽  
Economic Losses ◽  
Poultry Industry ◽  
Special Issue ◽  
Viral Pathogens ◽  
Genetic Mechanisms ◽  
Global Population

The poultry industry currently accounts for the production of around 118 million metric tons of meat and around 74 million metric tons of eggs annually. As the global population continues to increase, so does our reliance on poultry as a food source. It is therefore of vital importance that we safeguard this valuable resource and make the industry as economically competitive as possible. Avian viral infections, however, continue to cost the poultry industry billions of dollars annually. This can be in terms of vaccination costs, loss of birds and decreased production. With a view to improving the health and welfare of commercial birds and to minimizing associated economic losses, it is therefore of great importance that we try to understand the genetic mechanisms underlying host susceptibility and resilience to some of the major viral pathogens that threaten the poultry species. Some avian viruses, through their zoonotic potential, also pose a risk to human health. This Special Issue will present papers that describe our current knowledge on host responses to various viral pathogens, the genetics underlying those responses and how genomics can begin to provide a solution for resolving the threat posed by these infections.

scholarly journals First Report of Stem and Bulb Nematode Ditylenchus dipsaci on Garlic in New Mexico

2017 ◽  
Vol 18 (2) ◽  
pp. 91-92
Author(s):  
Jason M. French ◽  
Jacki Beacham ◽  
Amanda Garcia ◽  
Natalie P. Goldberg ◽  
Stephen H. Thomas ◽  
...  
Keyword(s):  
International Trade ◽  
New Mexico ◽  
Sequence Data ◽  
The State ◽  
Economic Losses ◽  
First Report ◽  
Important Pest ◽  
Ditylenchus Dipsaci ◽  
Production Areas ◽  
Stem And Bulb Nematode

Taken together, symptoms present, microscopic characterization, and ITS-1 sequence data indicate New Mexico garlic samples infested with Ditylenchus dipsaci, making this the first known report of this pest in the state. This discovery is significant because D. dipsaci can be a persistent pest and has the potential to cause significant economic losses on agronomically important hosts including onion, garlic, and alfalfa. Its longevity in the soil and international trade issues will be concerns for producers. Monitoring of production areas in the region will be performed to determine if this was an isolated and contained introduction or if this important pest has become established in New Mexico.

scholarly journals Mutations Associated with Reduced Surotomycin Susceptibility in Clostridium difficile and Enterococcus Species

2015 ◽  
Vol 59 (7) ◽  
pp. 4139-4147 ◽  
Author(s):  
Hannah M. Adams ◽  
Xiang Li ◽  
Carmela Mascio ◽  
Laurent Chesnel ◽  
Kelli L. Palmer
Keyword(s):  
Clostridium Difficile ◽  
Sequence Data ◽  
Acyl Carrier Protein ◽  
Serial Passage ◽  
Restriction Endonuclease Analysis ◽  
Health Concern ◽  
Content Type ◽  
Cyclic Lipopeptide ◽  
Illumina Sequence

ABSTRACTClostridium difficileinfection (CDI) is an urgent public health concern causing considerable clinical and economic burdens. CDI can be treated with antibiotics, but recurrence of the disease following successful treatment of the initial episode often occurs. Surotomycin is a rapidly bactericidal cyclic lipopeptide antibiotic that is in clinical trials for CDI treatment and that has demonstrated superiority over vancomycin in preventing CDI relapse. Surotomycin is a structural analogue of the membrane-active antibiotic daptomycin. Previously, we utilizedin vitroserial passage experiments to deriveC. difficilestrains with reduced surotomycin susceptibilities. The parent strains used included ATCC 700057 and clinical isolates from the restriction endonuclease analysis (REA) groups BI and K. Serial passage experiments were also performed with vancomycin-resistant and vancomycin-susceptibleEnterococcus faeciumandEnterococcus faecalis. The goal of this study is to identify mutations associated with reduced surotomycin susceptibility inC. difficileand enterococci. Illumina sequence data generated for the parent strains and serial passage isolates were compared. We identified nonsynonymous mutations in genes coding for cardiolipin synthase inC. difficileATCC 700057, enoyl-(acyl carrier protein) reductase II (FabK) and cell division protein FtsH2 inC. difficileREA type BI, and a PadR family transcriptional regulator inC. difficileREA type K. Among the 4 enterococcal strain pairs, 20 mutations were identified, and those mutations overlap those associated with daptomycin resistance. These data give insight into the mechanism of action of surotomycin againstC. difficile, possible mechanisms for resistance emergence during clinical use, and the potential impacts of surotomycin therapy on intestinal enterococci.

scholarly journals First Report of Little cherry virus 2 in Flowering and Sweet Cherry Trees in China

Plant Disease ◽  
2011 ◽  
Vol 95 (11) ◽  
pp. 1484-1484 ◽  
Author(s):  
W.-L. Rao ◽  
F. Li ◽  
R.-J. Zuo ◽  
R. Li
Keyword(s):  
Sweet Cherry ◽  
Sequence Data ◽  
Community Gardens ◽  
Economic Losses ◽  
Helicase Domain ◽  
Rt Pcr ◽  
Viral Origin ◽  
First Report ◽  
Flowering Cherry ◽  
Cherry Trees

Many viruses infect Prunus spp. and cause diseases on them. During a survey of stone fruit trees in 2008 and 2009, flowering cherry (Prunus serrulata) and sweet cherry (P. avium) trees with foliar chlorosis and reddening, stem deformity, and tree stunting were observed in private orchards in Anning and Fumin counties of Yunnan Province. Some sweet cherry trees with severe symptoms yielded small and few fruits and had to be removed. Leaf samples were collected from 68 flowering cherry and 30 sweet cherry trees, either symptomatic or asymptomatic, from private orchards and community gardens in Kunming and counties Anning, Chenggong, Fumin, Jinning, Ludian and Yiliang. Total nucleic acids were extracted with a CTAB extraction method and tested by reverse transcription (RT)-PCR assay using virus-specific primers. Little cherry virus 2 (LChV-2), Cherry virus A (CVA), Prunus necrotic ringspot virus (PNRSV), and Prune dwarf virus (PDV) were detected and infection rates were 68.4, 16.3, 9.2, and 7.1%, respectively. Infection of LChV-2 was common in all counties except Ludian where the orchards were healthy. Of 68 infected trees, 29 were found to be infected with LChV-2 and CVA, PDV or PNRSV. LChV-2 was detected in this study by RT-PCR using a pair of novel primers, LCV2-1 (5′-TTCAATATGAGCAGTGTTCCTAAC-3′) and LCV2-4 (5′-ACTCGTCTTGTGACATACCAGTC-3′), in 59 flowering cherry (87%) and 8 sweet cherry (27%) trees, respectively. The primer pair was designed according to alignment of three available LChV-2 sequences (GenBank Nos. NC_005065, AF416335, and AF333237) to amplify the partial RNA-dependent RNA polymerase gene (ORF1b) of 781 bp. The amplicons of selected samples (Anning26 and Yiliang60) were sequenced directly and sequences of 651 bp (GenBank No. HQ412772) were obtained from both samples. Pairwise comparisons and phylogenetic analysis of the sequences show that the two isolates are identical to one another and share 92 to 96% at the amino acid (aa) sequence level to those of other isolates available in the GenBank database. The sequence data confirm that these isolates are a strain of LChV-2 and genetic variation among different strains is relatively high (2). Biological and serological assays are not available for the LChV-2 detection; therefore, the LChV-2 infections of these trees were further confirmed by RT-PCR using primer pair LCV2-5 (5′-TGTTTGTGTCATGTTGTCGGAGAAG-3′) and LCV2-6 (5′-TGAATACCCGAGAACAAGGACTC-3′), which amplified the helicase domain (ORF1a) of ~451 bp. The amplicons from samples Anning26 and Yiliang60 were cloned and sequenced. The 408-bp sequences (excluding primer sequences) were 92 to 98% identical at the aa sequence level to those of other isolates, confirming again their viral origin. LChV-2 (genus Ampelovirus, family Closteroviridae) (4) has been associated with little cherry disease (LChD), a widespread viral disease of sweet and sour cherries (1,3). The virus is transferred between geographic areas mainly by propagated materials. Ornamental and sweet cherries are important crops in China and LChD has the potential to cause significant economic losses. Thus, certified clean stock should be used to establish new orchards. To our knowledge, this is the first report of LChV-2 in cherries in China. References: (1) N. B. Bajet et al. Plant Dis. 92:234, 2008. (2) W. Jelkmann et al. Acta Hortic. 781:321, 2008. (3) B. Komorowska and M. Cieslińska, Plant Dis. 92:1366, 2008. (4) M. E. Rott and W. Jelkmann. Arch. Virol. 150:107, 2005.

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