scholarly journals Transcriptome analysis of the almond moth, Cadra cautella, female abdominal tissues and identification of reproduction control genes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mureed Husain ◽  
Muhammad Tufail ◽  
Khalid Mehmood ◽  
Khawaja Ghulam Rasool ◽  
Abdulrahman Saad Aldawood
Keyword(s):  
Transcriptome Analysis ◽  
Management Strategies ◽  
Economic Losses ◽  
Transcriptome Data ◽  
Illumina Hiseq ◽  
Cadra Cautella ◽  
Farming Community ◽  
Gene Transcripts ◽  
Almond Moth ◽  
Food Commodities

Abstract Background The almond moth, Cadra cautella is a destructive pest of stored food commodities including dates that causes severe economic losses for the farming community worldwide. To date, no genetic information related to the molecular mechanism/strategies of its reproduction is available. Thus, transcriptome analysis of C. cautella female abdominal tissues was performed via next-generation sequencing (NGS) to recognize the genes responsible for reproduction. Results The NGS was performed with an Illumina Hiseq 2000 sequencer (Beijing Genomics Institute: BGI). From the transcriptome data, 9,804,804,120 nucleotides were generated and their assemblage resulted in 62,687 unigenes. The functional annotation analyses done by different databases, annotated, 27,836 unigenes in total. The transcriptome data of C. cautella female abdominal tissue was submitted to the National Center for Biotechnology Information (accession no: PRJNA484692). The transcriptome analysis yielded several genes responsible for C. cautella reproduction including six Vg gene transcripts. Among the six Vg gene transcripts, only one was highly expressed with 3234.95 FPKM value (fragments per kilobase per million mapped reads) that was much higher than that of the other five transcripts. Higher differences in the expression level of the six Vg transcripts were confirmed by running the RT-PCR using gene specific primers, where the expression was observed only in one transcript it was named as the CcVg. Conclusions This is the first study to explore C. cautella reproduction control genes and it might be supportive to explore the reproduction mechanism in this pest at the molecular level. The NGS based transcriptome pool is valuable to study the functional genomics and will support to design biotech-based management strategies for C. cautella.

scholarly journals Comprehensive Transcriptome Analysis of Rare Carpinus putoensis Plants under NO2 stress

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 754
Author(s):  
Qianqian Sheng ◽  
Congzhe Liu ◽  
Min Song ◽  
Jingyuan Xu ◽  
Zunling Zhu
Keyword(s):  
Molecular Mechanism ◽  
Transcriptome Analysis ◽  
Leaf Anatomy ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Sequencing Data ◽  
Illumina Hiseq ◽  
Stimulus Response ◽  
Plant Genes ◽  
Genome Annotations

We evaluated a transcriptome using high-throughput Illumina HiSeq sequencing and related it to the morphology, leaf anatomy, and physiological parameters of Carpinus putoensis putoensis under NO2 stress. The molecular mechanism of the C. putoensis NO2 stress response was evaluated using sequencing data. NO2 stress adversely affected the morphology, leaf anatomy, and total peroxidase (POD) activity. Through RNA-seq analysis, we used NCBI to compare the transcripts with nine databases and obtained their functional annotations. We annotated up to 2255 million clean Illumina paired-end RNA-seq reads, and 250,200 unigene sequences were assembled based on the resulting transcriptome data. More than 89% of the C. putoensis transcripts were functionally annotated. Under NO2 stress, 1119 genes were upregulated and 1240 were downregulated. According to the KEGG pathway and GO analyses, photosynthesis, chloroplasts, plastids, and the stimulus response are related to NO2 stress. Additionally, NO2 stress changed the expression of POD families, and the HPL2, HPL1, and POD genes exhibited high expression. The transcriptome analysis of C. putoensis leaves under NO2 stress supplies a reference for studying the molecular mechanism of C. putoensis resistance to NO2 stress. The given transcriptome data represent a valuable resource for studies on plant genes, which will contribute towards genome annotations during future genome projects.

Aflatoxins biosynthesis, toxicity and intervention strategies: A review

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Developing Countries ◽  
Molecular Basis ◽  
Genetic Regulation ◽  
Intervention Strategies ◽  
Historical Background ◽  
Economic Losses ◽  
Factors Affecting ◽  
Biomarkers Of Exposure ◽  
Food Commodities

Aflatoxins (AFTs) are toxic products of fungal metabolism, associated with serious health consequences and substantial economic losses to agriculture, livestock and poultry sectors, particularly in the developing countries. This review outlines the current information on AFTs in terms of historical background, classification, relative occurrence and co-existence with other mycotoxins in various food commodities. The phenomenon of aflatoxin (AFT) biosynthesis has been elucidated with reference to molecular basis, genetic regulation and factors affecting the AFT production. Moreover, the in vivo disposition kinetics, toxicological action and toxico-pathological consequences of AFTs have also been highlighted. Currently employed strategies for the detection and detoxification of AFTs, biomarkers of exposure assessment, potential economic impact and regulatory considerations regarding the AFTs have been emphasized.

scholarly journals The Effect of Gut Bacteria on the Physiology of Red Palm Weevil, Rhynchophorus ferrugineus Olivier and Their Potential for the Control of This Pest

Insects ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 594
Author(s):  
Qian-Xia Liu ◽  
Zhi-Ping Su ◽  
Hui-Hui Liu ◽  
Sheng-Ping Lu ◽  
Bing Ma ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Management Strategies ◽  
Gut Bacteria ◽  
Economic Losses ◽  
Rhynchophorus Ferrugineus ◽  
Intestinal Immunity ◽  
Red Palm Weevil ◽  
Nutrient Metabolism ◽  
Palm Weevil

Red Palm Weevil (RPW), Rhynchophorus ferrugineus Olivier, is a notorious pest, which infests palm trees and has caused great economic losses worldwide. At present, insecticide applications are still the main way to control this pest. However, pesticide resistance has been detected in the field populations of RPW. Thus, future management strategies based on the novel association biological control need be developed. Recent studies have shown that the intestinal tract of RPW is often colonized by multiple microbial species as mammals and model insects, and gut bacteria have been found to promote the growth, development and immune activity of RPW larvae by modulating nutrient metabolism. Furthermore, two peptidoglycan recognition proteins (PGRPs), PGRP-LB and PGRP-S1, can act as the negative regulators to modulate the intestinal immunity to maintain the homeostasis of gut bacteria in RPW larvae. Here, we summarized the current knowledge on the gut bacterial composition of RPW and their impact on the physiological traits of RPW larvae. In contrast with metazoans, it is much easier to make genetic engineered microbes to produce some active molecules against pests. From this perspective, because of the profound effects of gut bacteria on host phenotypes, it is promising to dissect the molecular mechanisms behind their effect on host physiology and facilitate the development of microbial resource-based management methods for pest control.

scholarly journals Diversity of Colletotrichum Species Associated with Anthracnose Disease in Tropical Fruit Crops—A Review

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 297
Author(s):  
Latiffah Zakaria
Keyword(s):  
Management Strategies ◽  
Economic Losses ◽  
Fruit Crops ◽  
Tropical Fruit ◽  
Colletotrichum Species ◽  
Adequate Knowledge ◽  
Dragon Fruit ◽  
Causative Agents ◽  
Colletotrichum Spp ◽  
Fruit Plantations

In tropical fruit crops, anthracnose is mainly caused by species belonging to the fungal genus, Colletotrichum. These phytopathogens can infect several parts of the fruit crops; however, infection during postharvest or ripening stages is responsible for major economic losses. Due to the formation of black to dark brown sunken lesions on the fruit surface, anthracnose reduces fruit quality and marketability. Among the most common tropical fruit crops susceptible to anthracnose are mango, papaya, banana, avocado, guava, and dragon fruit; these are economically relevant products in many developing countries. It is important to document that the newly recorded Colletotrichum spp. associated with fruit anthracnose can infect multiple hosts, but some species may be host-specific. By using multiple markers, many phylogenetic species of Colletotrichum have been reported as anthracnose-causing pathogens. Taking into account that disease management strategies strongly rely on adequate knowledge of the causative agents, updated information on Colletotrichum species and the hazard posed by the most recently identified species in tropical fruit plantations and harvested fruits becomes vital. Besides, the newly recorded species may be important for biosecurity and should be listed as quarantine pathogens, considering that tropical fruits are traded worldwide.

scholarly journals Community seed network in an era of climate change: dynamics of maize diversity in Yucatán, Mexico

2021 ◽  
Author(s):  
Marianna Fenzi ◽  
Paul Rogé ◽  
Angel Cruz-Estrada ◽  
John Tuxill ◽  
Devra Jarvis
Keyword(s):  
Climate Change ◽  
Crop Production ◽  
Management Strategies ◽  
Farming Systems ◽  
Seed Systems ◽  
Farming Community ◽  
Climate Resilience ◽  
Maize Diversity ◽  
Climatic Period ◽  
Small Holder Farmers

AbstractLocal seed systems remain the fundamental source of seeds for many crops in developing countries. Climate resilience for small holder farmers continues to depend largely on locally available seeds of traditional crop varieties. High rainfall events can have as significant an impact on crop production as increased temperatures and drought. This article analyzes the dynamics of maize diversity over 3 years in a farming community of Yucatán state, Mexico, where elevated levels of precipitation forced farmers in 2012 to reduce maize diversity in their plots. We study how farmers maintained their agroecosystem resilience through seed networks, examining the drivers influencing maize diversity and seed provisioning in the year preceding and following the 2012 climatic disturbance (2011–2013). We found that, under these challenging circumstances, farmers focused their efforts on their most reliable landraces, disregarding hybrids. We show that farmers were able to recover and restore the diversity usually cultivated in the community in the year following the critical climate event. The maize dynamic assessed in this study demonstrates the importance of community level conservation of crop diversity. Understanding farmer management strategies of agrobiodiversity, especially during a challenging climatic period, is necessary to promote a more tailored response to climate change in traditional farming systems.

Efficacy of Cyfluthrin, Cyfluthrin + Piperonyl Butoxide, and Cyfluthrin + Piperonyl Butoxide + Chlorpyrifos-Methyl as Protectants of Stored Peanuts1

1994 ◽  
Vol 21 (1) ◽  
pp. 44-48 ◽  
Author(s):  
Frank H. Arthur
Keyword(s):  
Tribolium Castaneum ◽  
Plodia Interpunctella ◽  
Piperonyl Butoxide ◽  
Red Flour Beetle ◽  
Indianmeal Moth ◽  
Flour Beetle ◽  
Cadra Cautella ◽  
Almond Moth

Abstract Inshell peanuts were treated with 0.5, 1.0, 2.0, and 4.0 ppm cyfluthrin, each rate of cyfluthrin + 8.0 ppm piperonyl butoxide, and each rate of cyfluthrin + piperonyl butoxide + 25 ppm chlorpyrifos-methyl. After 10 months red flour beetle, Tribolium castaneum (Herbst), populations in peanuts treated with 0.5 and 1.0 ppm cyfluthrin averaged 89.5 and 34.2 adults per 12.7 kg peanuts; populations in peanuts treated with 1.0 and 1.5 ppm cyfluthrin + piperonyl butoxide averaged 72.0 amd 41.5 adults per 12.7 kg peanuts. Populations in the remaining 8 treatments ranged from 0.5 to 7.2 adults. Indianmeal moth, Plodia interpunctella (Hübner), and almond moth, Cadra cautella (Walker), populations remained low in all treatments. At 10 months the percentage of insectdamaged kernels from cracked pods ranged from 8.7 to 28.8% in the cyfluthrin and cyfluthrin + piperonyl butoxide treatments, while the percentage of damaged kernels was 4.4 to 6.1% in the 4 treatments with chlorpyrifos-methyl.

scholarly journals De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Inés González-Castellano ◽  
Chiara Manfrin ◽  
Alberto Pallavicini ◽  
Andrés Martínez-Lage
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Specific Expression ◽  
Development Processes ◽  
The Common

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

scholarly journals RNAi of a Putative Grapevine Susceptibility Gene as a Possible Downy Mildew Control Strategy

2021 ◽  
Vol 12 ◽  
Author(s):  
Demetrio Marcianò ◽  
Valentina Ricciardi ◽  
Elena Marone Fassolo ◽  
Alessandro Passera ◽  
Piero Attilio Bianco ◽  
...  
Keyword(s):  
Gene Expression ◽  
Downy Mildew ◽  
Disease Severity ◽  
Fungal Pathogens ◽  
Management Strategies ◽  
Susceptibility Gene ◽  
Plasmopara Viticola ◽  
Pinot Noir ◽  
Economic Losses ◽  
Reproductive Structures

Downy mildew, caused by the oomycete Plasmopara viticola, is one of the diseases causing the most severe economic losses to grapevine (Vitis vinifera) production. To date, the application of fungicides is the most efficient method to control the pathogen and the implementation of novel and sustainable disease control methods is a major challenge. RNA interference (RNAi) represents a novel biotechnological tool with a great potential for controlling fungal pathogens. Recently, a candidate susceptibility gene (VviLBDIf7) to downy mildew has been identified in V. vinifera. In this work, the efficacy of RNAi triggered by exogenous double-stranded RNA (dsRNA) in controlling P. viticola infections has been assessed in a highly susceptible grapevine cultivar (Pinot noir) by knocking down VviLBDIf7 gene. The effects of dsRNA treatment on this target gene were assessed by evaluating gene expression, disease severity, and development of vegetative and reproductive structures of P. viticola in the leaf tissues. Furthermore, the effects of dsRNA treatment on off-target (EF1α, GAPDH, PEPC, and PEPCK) and jasmonic acid metabolism (COI1) genes have been evaluated. Exogenous application of dsRNA led to significant reductions both in VviLBDIf7 gene expression, 5 days after the treatment, and in the disease severity when artificial inoculation was carried out 7 days after dsRNA treatments. The pathogen showed clear alterations to both vegetative (hyphae and haustoria) and reproductive structures (sporangiophores) that resulted in stunted growth and reduced sporulation. Treatment with dsRNA showed signatures of systemic activity and no deleterious off-target effects. These results demonstrated the potential of RNAi for silencing susceptibility factors in grapevine as a sustainable strategy for pathogen control, underlying the possibility to adopt this promising biotechnological tool in disease management strategies.

scholarly journals De novo transcriptome analysis and identification of reproduction control genes from the red palm weevil Rhynchophorus ferrugineus

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251278
Author(s):  
Khawaja Ghulam Rasool ◽  
Khalid Mehmood ◽  
Mureed Husain ◽  
Muhammad Tufail ◽  
Waleed Saleh Alwaneen ◽  
...  
Keyword(s):  
De Novo ◽  
Fat Body ◽  
Polymerase Chain Reaction Analysis ◽  
Rhynchophorus Ferrugineus ◽  
Red Palm Weevil ◽  
Illumina Hiseq ◽  
Severe Problem ◽  
Palm Weevil ◽  
Palm Species ◽  
Gene Transcripts

Recent attacks by the red palm weevil, Rhynchophorus ferrugineus (Olivier), have become a severe problem for palm species. In present work, fat body transcriptome of adult female red palm weevil was analyzed, focusing on the identification of reproduction control genes. Transcriptome study was completed by means of next-generation sequencing (NGS) using Illumina Hiseq 2000 sequencing system. A total of 105,938,182 raw reads, 102,645,544 clean reads, and 9,238,098,960 clean nucleotides with a guanine–cytosine content of 40.31%, were produced. The processed transcriptome data resulted in 43,789 unique transcripts (with mean lengths of 1,172 bp). It was found that 20% of total unique transcripts shared up to 80%–100% sequence identity with homologous species, mainly the mountain pine beetle Dendroctonus ponderosae (59.9%) and red flour beetle Tribolium castaneum (26.9%). Nearly 25 annotated genes were predicted to be involved in red palm weevil reproduction, including five vitellogenin (Vg) transcripts. Among the five Vg gene transcripts, one was highly expressed compared with the other four (FPKM values of 1.963, 1.471, 1.028, and 1.017, respectively), and the five Vg gene transcripts were designated as RfVg, RfVg-equivalent1, RfVg-equivalent2, RfVg-equivalent3, and RfVg-equivalent4, respectively. The high expression level of RfVg verified by RT-polymerase chain reaction analysis suggested that RfVg is the primary functional Vg gene in red palm weevil. A high similarity of RfVg with other Coleopterans was also reflected in a phylogenetic tree, where RfVg was placed within the clade of the order Coleoptera. Awareness of the major genes that play critical roles in reproduction and proliferation of red palm weevil is valuable to understand their reproduction mechanism at a molecular level. In addition, for future molecular studies, the NGS dataset obtained will be useful and will promote the exploration of biotech-based control strategies against red palm weevil, a primary pest of palm trees.

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