Review of Molecular Identification Techniques for Forensically Important Diptera

2019 ◽  
Vol 56 (4) ◽  
pp. 887-902
Author(s):  
M Denise Gemmellaro ◽  
George C Hamilton ◽  
Jessica L Ware

Abstract The medico-legal section of forensic entomology focuses on the analysis of insects associated with a corpse. Such insects are identified, and their life history characteristics are evaluated to provide information related to the corpse, such as postmortem interval and time of colonization. Forensically important insects are commonly identified using dichotomous keys, which rely on morphological characteristics. Morphological identifications can pose a challenge as local keys are not always available and can be difficult to use, especially when identifying juvenile stages. If a specimen is damaged, certain keys cannot be used for identification. In contrast, molecular identification can be a better instrument to identify forensically important insects, regardless of life stage or specimen completeness. Despite more than 20 yr since the first use of molecular data for the identification of forensic insects, there is little overlap in gene selection or phylogenetic methodology among studies, and this inconsistency reduces efficiency. Several methods such as genetic distance, reciprocal monophyly, or character-based methods have been implemented in forensic identification studies. It can be difficult to compare the results of studies that employ these different methods. Here we present a comprehensive review of the published results for the molecular identification of Diptera of forensic interest, with an emphasis on evaluating variation among studies in gene selection and phylogenetic methodology.

2003 ◽  
Vol 69 (1) ◽  
pp. 327-333 ◽  
Author(s):  
Renske Landeweert ◽  
Paula Leeflang ◽  
Thom W. Kuyper ◽  
Ellis Hoffland ◽  
Anna Rosling ◽  
...  

ABSTRACT Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (≥99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had ≥98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.


2012 ◽  
Vol 63 (4) ◽  
pp. 463-470 ◽  
Author(s):  
Zdravka Sever ◽  
Dario Ivić ◽  
Tomislav Kos ◽  
Tihomir Miličević

AbstractSeveral species of the genus Fusarium can cause apple fruit to rot while stored. Since Fusarium taxonomy is very complex and has constantly been revised and updated over the last years, the aim of this study was to identify Fusarium species from rotten apples, based on combined morphological characteristics and molecular data.We identified 32 Fusarium isolates from rotten apple fruit of cultivars Golden Delicious, Jonagold, Idared, and Pink Lady, stored in Ultra Low Oxygen (ULO) conditions. Fusarium rot was detected in 9.4 % to 33.2 % of naturally infected apples, depending on the cultivar. The symptoms were similar in all four cultivars: a soft circular brown necrosis of different extent, with or without visible sporulation. Fusarium species were identified by the morphology of cultures grown on potato-dextrose agar (PDA) and carnation leaf agar (CLA). Twenty one isolates were identified as Fusarium avenaceum and confirmed as such with polymerase chain reaction (PCR) using specific primer pair FA-ITSF and FA-ITSR. F. pseudograminearum,F. semitectum, F. crookwellense, and F. compactum were identified by morphological characteristics. F.avenaceum can produce several mycotoxins and its dominance in Fusarium rot points to the risk of mycotoxin contamination of apple fruit juices and other products for human consumption. Pathogenicity tests showed typical symptoms of Fusarium rot in most of the inoculated wounded apple fruits. In this respect Fusarium avenaceum, as the dominant cause of Fusarium rot in stored apple fruits is a typical wound parasite.


Plant Disease ◽  
2021 ◽  
Author(s):  
Jiahao Lai ◽  
Guihong Xiong ◽  
Bing Liu ◽  
Weigang Kuang ◽  
Shuilin Song

Blueberry (Vaccinium virgatum), an economically important small fruit crop, is characterized by its highly nutritive compounds and high content and wide diversity of bioactive compounds (Miller et al. 2019). In September 2020, an unknown leaf blight disease was observed on Rabbiteye blueberry at the Agricultural Science and Technology Park of Jiangxi Agricultural University in Nanchang, China (28°45'51"N, 115°50'52"E). Disease surveys were conducted at that time, the results showed that disease incidence was 90% from a sampled population of 100 plants in the field, and this disease had not been found at other cultivation fields in Nanchang. Leaf blight disease on blueberry caused the leaves to shrivel and curl, or even fall off, which hindered floral bud development and subsequent yield potential. Symptoms of the disease initially appeared as irregular brown spots (1 to 7 mm in diameter) on the leaves, subsequently coalescing to form large irregular taupe lesions (4 to 15 mm in diameter) which became curly. As the disease progressed, irregular grey-brown and blighted lesion ran throughout the leaf lamina from leaf tip to entire leaf sheath and finally caused dieback and even shoot blight. To identify the causal agent, 15 small pieces (5 mm2) of symptomatic leaves were excised from the junction of diseased and healthy tissue, surface-sterilized in 75% ethanol solution for 30 sec and 0.1% mercuric chloride solution for 2 min, rinsed three times with sterile distilled water, and then incubated on potato dextrose agar (PDA) at 28°C for 5-7 days in darkness. Five fungal isolates showing similar morphological characteristics were obtained as pure cultures by single-spore isolation. All fungal colonies on PDA were white with sparse creeping hyphae. Pycnidia were spherical, light brown, and produced numerous conidia. Conidia were 10.60 to 20.12 × 1.98 to 3.11 µm (average 15.27 × 2.52 µm, n = 100), fusiform, sickle-shaped, light brown, without septa. Based on morphological characteristics, the fungal isolates were suspected to be Coniella castaneicola (Cui 2015). To further confirm the identity of this putative pathogen, two representative isolates LGZ2 and LGZ3 were selected for molecular identification. The internal transcribed spacer region (ITS) and large subunit (LSU) were amplified and sequenced using primers ITS1/ITS4 (Peever et al. 2004) and LROR/LR7 (Castlebury and Rossman 2002). The sequences of ITS region (GenBank accession nos. MW672530 and MW856809) showed 100% identity with accessions numbers KF564280 (576/576 bp), MW208111 (544/544 bp), MW208112 (544/544 bp) of C. castaneicola. LSU gene sequences (GenBank accession nos. MW856810 to 11) was 99.85% (1324/1326 bp, 1329/1331 bp) identical to the sequences of C. castaneicola (KY473971, KR232683 to 84). Pathogenicity was tested on three blueberry varieties (‘Rabbiteye’, ‘Double Peak’ and ‘Pink Lemonade’), and four healthy young leaves of a potted blueberry of each variety with and without injury were inoculated with 20 μl suspension of prepared spores (106 conidia/mL) derived from 7-day-old cultures of LGZ2, respectively. In addition, four leaves of each variety with and without injury were sprayed with sterile distilled water as a control, respectively. The experiment was repeated three times, and all plants were incubated in a growth chamber (a 12h light and 12h dark period, 25°C, RH greater than 80%). After 4 days, all the inoculated leaves started showing disease symptoms (large irregular grey-brown lesions) as those observed in the field and there was no difference in severity recorded between the blueberry varieties, whereas the control leaves showed no symptoms. The fungus was reisolated from the inoculated leaves and confirmed as C. castaneicola by morphological and molecular identification, fulfilling Koch’s postulates. To our knowledge, this is the first report of C. castaneicola causing leaf blight on blueberries in China. The discovery of this new disease and the identification of the pathogen will provide useful information for developing effective control strategies, reducing economic losses in blueberry production, and promoting the development of the blueberry industry.


2020 ◽  
Vol 21 (3) ◽  
Author(s):  
I Gede Swibawa I Gede ◽  
YUYUN FITRIANA ◽  
SOLIKHIN ◽  
RADIX SUHARJO ◽  
F.X. SUSILO ◽  
...  

Abstract. Swibawa IG, Fitriana Y, Solikhin, Suharjo R, Susilo FX, Rani E, Haryani MS, Wardana RA. 2020. Morpho-molecular identification and pathogenicity test on fungal parasites of guava root-knot nematode eggs in Lampung, Indonesia. Biodiversitas 21: 1108-1115. This study aimed to obtain and discover the identity of the species of fungal egg parasites of root-knot nematodes (RKN), which have a high pathogenic ability causing major losses in vegetable crops. The exploration of the fungi was carried out in 2016 and 2018 from Crystal guava plantations in East Lampung, Central Lampung, Tanggamus, and NirAma, a commercial product that has been used for controlling Meloidogyne sp. in Indonesia. Identification was carried out based on morphological characteristics and molecular-based gene sequential analysis of Intergenic Transcribed Spacer (ITS) 1 and ITS 4. A pathogenicity test was carried out in vitro and in a greenhouse using tomato plants as indicator plants. In the in vitro test, observations were made on the percentage of infected RKN eggs. The observations in the greenhouse test were carried out on RKN populations in the soil and roots of tomato plants, root damage (root knots), and damage intensity due to RKN infection. The exploration resulted in five isolates of fungal egg parasites of RKN from the guava plantations in East Lampung (2), Central Lampung (1), Tanggamus (1), and from the isolation results of commercial products (1). The isolates were given codes as B4120X (PT GGP PG1), B3010 (PT GGP PG4), B412G (PT GGP PG 4), B01TG (Tanggamus), and BioP (Commercial products). Based on their morphological characteristics, the isolates were classified into the genus of Paecilomyces. The results of molecular identification showed that the discovered fungi were Purpureocillium lilacinum (Thom.) Luangsa Ard. (Syn. Paecilomyces lilacinus (Thom.) Samson.). Based on the in vitro tests, the five fungal isolates were able to parasitize RKN eggs at 86.4-100%. In the greenhouse test, all isolates significantly suppressed nematode populations in the soil and tomato roots, inhibited the formation of root knots, and produced lower damage intensity compared to controls. Among all the isolates tested, B01TG had the best ability to infect nematode eggs (99.5%), suppressing the formation of root knots, nematode population in the soil and the roots of tomato plants, and the damage intensity compared to other isolates.


Plant Disease ◽  
2021 ◽  
Author(s):  
Jiahao Lai ◽  
Tongke Liu ◽  
Bing Liu ◽  
Weigang Kuang ◽  
Shuilin Song

Sweet potato [Ipomoea batatas (L.) Lam], is an extremely versatile vegetable that possesses high nutritional values. It is also a valuable medicinal plant having anti-cancer, antidiabetic, and anti-inflammatory activities. In July 2020, leaf spot was observed on leaves of sweet potato in Nanchang, China (28°45'51"N, 115°50'52"E), which affected the growth and development of the crop and caused tuberous roots yield losses of 25%. The disease incidence (total number of diseased plants / total number of surveyed plants × 100%) was 57% from a sampled population of 100 plants in the field. Symptomatic plants initially exhibited small, light brown, irregular-shaped spots on the leaves, subsequently coalescing to form large irregular brown lesions and some lesions finally fell off. Fifteen small pieces (each 5 mm2) of symptomatic leaves were excised from the junction of diseased and healthy tissue, surface sterilized in 75% ethanol solution for 30 sec and 0.1% mercuric chloride solution for 2 min, rinsed three times with sterile distilled water and incubated on potato dextrose agar (PDA) plates at 28°C in darkness. A total of seven fungal isolates with similar morphological characteristics were obtained as pure cultures by single-spore isolation. After 5 days of cultivation at 28°C, dark brown or blackish green colonies were observed, which developed brown, thick-walled, simple, or branched, and septate conidiophores. Conidia were 18.28 to 24.91 × 7.46 to 11.69 µm (average 21.27 × 9.48 µm, n = 100) in size, straight or slightly curved, middle cell unequally enlarged, brown to dark brown, apical, and basal cells slightly paler than the middle cells, with three septa. Based on morphological characteristics, the fungal isolates were suspected to be Curvularia plantarum (Raza et al. 2019). To further confirm the identification, three isolates (LGZ1, LGZ4 and LGZ5) were selected for molecular identification. The internal transcribed spacer region (ITS), glyceraldehyde-3-phosphate-dehydrogenase (GAPDH), and translation elongation factor 1-alpha (EF1-α) genes were amplified and sequenced using primers ITS1/ITS4 (Peever et al. 2004), gpd1/gpd2 (Berbee et al. 1999), EF-983F/EF-2218R (Rehner and Buckley 2005), respectively. The sequences of ITS region of the three isolates (accession nos. MW581905, MZ209268, and MZ227555) shared 100% identity with those of C. plantarum (accession nos. MT410571-72, MN044754-55). Their GAPDH gene sequences were identical (accession nos. MZ224017-19) and shared 100% identity with C. plantarum (accession nos. MN264120, MT432926, and MN053037-38). Similarly, EF1-α gene sequences were identical (accession nos. MZ224020-22) and had 100% identity with C. plantarum (accession nos. MT628901, MN263982-83). A maximum likelihood phylogenetic tree was built based on concatenated data from the sequences of ITS, GAPDH, and EF-1α by using MEGA 5. The three isolates LGZ1, LGZ4, and LGZ5 clustered with C. plantarum. The fungus was identified as C. plantarum by combining morphological and molecular characteristics. Pathogenicity tests were conducted by inoculating a conidial suspension (106 conidia/ml) on three healthy potted I. batatas plants (five leaves wounded with sterile needle of each potted plant were inoculated). In addition, fifteen wounded leaves of three potted plants were sprayed with sterile distilled water as a control. All plants were maintained in a climate box (12 h light/dark) at 25°C with 80% relative humidity. All the inoculated leaves started showing light brown flecks after 7 days, whereas the control leaves showed no symptoms. The pathogenicity test was conducted three times. The fungus was reisolated from all infected leaves of potted plants and confirmed as C. plantarum by morphological and molecular identification, fulfilling Koch’s postulates. To our knowledge, this is the first report of C. plantarum causing leaf spot on sweet potato in China. The discovery of this new disease and the identification of the pathogen will contribute to the disease management, provide useful information for reducing economic losses caused by C. plantarum, and lay a foundation for the further research of resistance breeding.


PhytoKeys ◽  
2020 ◽  
Vol 156 ◽  
pp. 125-137
Author(s):  
Thomas Haevermans ◽  
Dulce Mantuano ◽  
Meng-Yuan Zhou ◽  
Vichith Lamxay ◽  
Agathe Haevermans ◽  
...  

Lush jungle flagship species, woody bamboos (Poaceae–Bambusoideae) are famed for their synchronous flowering as well as the extensive “bamboo forests” some species can form in tropical or temperate environments. In portions of their natural distribution, Bambusoideae members developed various adaptations to seasonality in environmental parameters, such as frost or seasonal drought. A new taxon, Laobambos calcareus, described here, is extremely novel in showing the first documented case of succulence in bamboos, with its ability to seasonally vary the volume of its stem depending on the quantity of water stored. Anatomical studies presented in this paper document this specificity at the cellular level. Though no flowers or fruits are known yet, unique morphological characteristics along with an investigation of its phylogenetic affinities using molecular data show that this new taxon should belong to a new genus herein described.


Phytotaxa ◽  
2021 ◽  
Vol 480 (1) ◽  
pp. 1-21
Author(s):  
SOFIA S. SADOGURSKA ◽  
JOÃO NEIVA ◽  
ANNALISA FALACE ◽  
ESTER A. SERRÃO ◽  
ÁLVARO ISRAEL

Brown algae of the genus Cystoseira sensu lato form the most diverse and productive marine ecosystems throughout the Mediterranean Sea and have equal roles also in the Black Sea where they have been decreasing in the recent years. The taxonomy of Cystoseira s.l. taxa from the Black Sea is still not well understood, and questions arise when related taxa have to be delimited. In addition to morphological descriptions, this study provides for the first time molecular data of the Black Sea Cystoseira s.l. distinct morphologies as an additional tool to clarify their identities and phylogenetic affinities. The analysis of two mitochondrial markers (cytochrome oxidase subunit 1—COI, and 23S-tRNAVal intergenic spacer—mt-spacer) showed that Cystoseira s.l. specimens from the Black Sea belong to two recently resurrected genera, namely Gongolaria and Ericaria. Molecular data confirm the morphological identification of G. barbata, which is characterized by high morphological plasticity in the Black Sea. The morphological data presented in this study support the transition of G. barbata to the genus Gongolaria, which was previously proposed based solely on genetic data. For the Black Sea endemic taxon C. bosphorica, sequence divergence suggests conspecificity with Mediterranean Sea species E. crinita and E. barbatula. However, considering original morphological characteristics of the taxon, its geographical isolation, and endemism, the new combination Ericaria crinita f. bosphorica comb. nov. is proposed.


2008 ◽  
Vol 68 (1) ◽  
pp. 221-228 ◽  
Author(s):  
F. Abrunhosa ◽  
M. Melo

The development of the foregut structure and the digestive function of the decapods Litopenaeus vannamei, Sesarma rectum and Callichirus major larvae and post larvae were examined. The protozoeal foregut of L. vannamei is simple, lacking a cardiopyloric valve and bearing a rudimentary filter press. In mysis, the filter press is more developed. In the juvenile stage, grooves and a small lateral tooth arise. In S. rectum, the foregut has a functional cardiopyloric valve and a filter press. The megalopal and juvenile stages of this species have a gastric mill similar to those in adult crabs. In C. major, the foregut of the zoeae is specialized, with the appearance of some rigid structures, but no gastric mill was found. Calcified structures are observed in the megalopae and they become more developed in the juvenile stage. The results support suppositions, previously reported in other studies, that feeding behavior of each larval and postlarval stage is directly related to the morphological characteristics of the foreguts.


Nematology ◽  
2009 ◽  
Vol 11 (5) ◽  
pp. 719-737 ◽  
Author(s):  
Oleksandr Holovachov ◽  
Sven Boström ◽  
Manuel Mundo-Ocampo ◽  
Irma Tandingan De Ley ◽  
Melissa Yoder ◽  
...  

Abstract Hemiplectus muscorum, the type and single representative of its genus, is redescribed on the basis of abundant new material collected in the UK, Canada and the USA using both light and scanning electron microscopy. The phylogenetic relationships of the species are inferred from morphological as well as molecular data. Maximum parsimony, neighbour joining and maximum likelihood analyses of small subunit (SSU) rRNA sequences support a position nested among the Plectidae. This conflicts with our morphological assumptions of character polarity, as it implies that the absence of a valvate bulb in Hemiplectus is a reversal rather than a plesiomorphy. The excretory system of Hemiplectus is described more precisely. Its structure is highly reminiscent of the system in Plectus but differs in the presence of an anterior and posterior pair of pseudocoelomocytes flanking the renette cell. A pair of lateral somatic setae is identified as possible homologues of the 'deirids' in Plectus and Rhabditida. Measurements and descriptions are given of all four juvenile stages.


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