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1. Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

Author:
Srivastava, Avi; Malik, Laraib; Smith, Tom; Sudbery, Ian; Patro, Rob
Source:
Genome biology 2019 v.20 no.1 pp. 65
ISSN:
1474-760X
Subject:
DNA barcoding,   etc   ; computer analysis; computer software; genes;     Show all 4 Subjects
Abstract:
... We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting. Alevin’s approach to UMI deduplication considers transcript-level constraints on the molecules from which UMIs may have arisen and accounts fo ...
DOI:
10.1186/s13059-019-1670-y

2. CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics

Author:
Guo, Chuner; Kong, Wenjun; Kamimoto, Kenji; Rivera-Gonzalez, Guillermo C.; Yang, Xue; Kirita, Yuhei; Morris, Samantha A.
Source:
Genome biology 2019 v.20 no.1 pp. 90
ISSN:
1474-760X
Subject:
DNA barcoding,   etc   ; experimental design; genomics; transcriptome;     Show all 4 Subjects
Abstract:
... High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are heritable, enabling cell populations to be tagged, pooled, and tracked over time in the same exp ...
DOI:
10.1186/s13059-019-1699-y

3. Guide RNAs with embedded barcodes boost CRISPR-pooled screens

Author:
Zhu, Shiyou; Cao, Zhongzheng; Liu, Zhiheng; He, Yuan; Wang, Yinan; Yuan, Pengfei; Li, Wei; Tian, Feng; Bao, Ying; Wei, Wensheng
Source:
Genome biology 2019 v.20 no.1 pp. 20
ISSN:
1474-760X
Subject:
DNA barcoding,   etc   ; RNA; gene editing; screening;     Show all 4 Subjects
Abstract:
... We report a new method using re-designed guide RNAs with internal barcodes (iBARs) embedded in their loop regions. Our iBAR approach outperforms the conventional method by producing screening results with much lower false-positive and false-negative rates especially with a high multiplicity of infection (MOI). Importantly, the iBAR approach reduces the starting cells at high MOI significantly with ...
DOI:
10.1186/s13059-019-1628-0

4. DNA barcode, taxonomic and ecological notes for the identification of the invasive amphipod Monocorophium acherusicum (Costa, 1851)

Author:
Albano, Mariano J.; Rumbold, Carlos; Chiesa, Ignacio L.; Vazquez, Guadalupe; Spivak, Eduardo D.; Obenat, Sandra M.
Source:
New Zealand journal of marine and freshwater research 2019 v.53 no.1 pp. 15-32
ISSN:
1175-8805
Subject:
DNA barcoding,   etc   ; Amphipoda; biofouling; phylogeny; summer; Argentina;     Show all 6 Subjects
Abstract:
... We report the occurrence of the invasive amphipod Monocorophium acherusicum in Mar del Plata port, Argentina, using morphological and molecular analysis and estimated mean abundance to detect monthly variations of this population. We compared M. acherusicum morphology with that of M. insidiosum and Crassicorophium bonelli, the two most similar locally occurring species, to establish the diagnostic ...
DOI:
10.1080/00288330.2018.1469514

5. Skmer: assembly-free and alignment-free sample identification using genome skims

Author:
Sarmashghi, Shahab; Bohmann, Kristine; P. Gilbert, M. Thomas; Bafna, Vineet; Mirarab, Siavash
Source:
Genome biology 2019 v.20 no.1 pp. 34
ISSN:
1474-760X
Subject:
DNA barcoding,   etc   ; data collection; genomics; nuclear genome; species diversity;     Show all 5 Subjects
Abstract:
... The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In co ...
DOI:
10.1186/s13059-019-1632-4

6. Taxonomic review of the predatory genus Cryptalaus Ôhira (Coleoptera: Elateridae) from Korea with a new record of C. yamato (Nakane)

Author:
Choi, Ik-Je; Lee, Seung-Gyu; Suzuki, Wataru; Choi, Subin; Lim, Jongok
Source:
Journal of Asia-Pacific biodiversity(Online) 2019 v.12 no.2 pp. 223-230
ISSN:
2287-884X
Subject:
DNA barcoding,   etc   ; Elateridae; biodiversity; rare species; redescriptions; Japan; South Korea;     Show all 7 Subjects
Abstract:
... We studied the taxonomy of the predatory genus Cryptalaus Ôhira (Coleoptera: Elateridae) in South Korea, including two species, C. berus (Candèze) and C. larvatus pini (Lewis), which have been previously reported from South Korea. In the present study, a rare species, C. yamato (Nakane), which had been regarded as endemic to Japan, is discovered in the central region of South Korea for the first t ...
DOI:
10.1016/j.japb.2019.02.008

7. Distribution of Trichaleurina javanica (Rehm) M. Carbone, Agnello & P. Alvarado (Chorioactidaceae) in India

Author:
Patel, Ravi S.; Vasava, Ajit M.; Rajput, Kishore S.
Source:
Plant biosystems 2019 v.153 no.2 pp. 231-234
ISSN:
1724-5575
Subject:
DNA barcoding,   etc   ; Pezizales; forests; fungi; nucleotide sequences; India;     Show all 6 Subjects
Abstract:
... During the recent field visits to Saurashtra regions of Western India, one of the interesting fungi i.e. Trichaleurina javanica (Rehm) M. Carbone, Agnello & P. Alvarado (Chorioactidaceae, order Pezizales) was collected from Sarkhadiya Hanuman and Sasan (Gir Forest, India). Further confirmation of the identity was carried out by using molecular methods with its DNA barcoding. Review of literature s ...
DOI:
10.1080/11263504.2018.1461704

8. Multiple tests on saffron find new adulterant materials and reveal that Ist grade saffron is rare in the market

Author:
Khilare, Vikram; Tiknaik, Anita; Prakash, Bharathi; Ughade, Balasaheb; Korhale, Ganesh; Nalage, Dinesh; Ahmed, Nadeem; Khedkar, Chandraprakash; Khedkar, Gulab
Source:
Food chemistry 2019 v.272 pp. 635-642
ISSN:
0308-8146
Subject:
DNA barcoding,   etc   ; adulterants; color; compliance; ingredients; markets; microscopy; odors; saffron;     Show all 9 Subjects
Abstract:
... Among spices, Saffron is among the most extensively interrogated for purity and authenticity. Numerous methods have been recommended for authentication of Saffron samples and for detection of adulterants for codex compliance. However, none of these methods can fulfill both of these important quality criteria. This study describes a three step approach to achieving this goal by including the establ ...
DOI:
10.1016/j.foodchem.2018.08.089

9. Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

Author:
Deagle, Bruce E.; Thomas, Austen C.; McInnes, Julie C.; Clarke, Laurence J.; Vesterinen, Eero J.; Clare, Elizabeth L.; Kartzinel, Tyler R.; Eveson, J. Paige
Source:
Molecular ecology 2019 v.28 no.2 pp. 391-406
ISSN:
0962-1083
Subject:
DNA barcoding,   etc   ; DNA; data collection; diet; nucleotide sequences; trophic relationships;     Show all 6 Subjects
Abstract:
... Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or ...
DOI:
10.1111/mec.14734

10. How quantitative is metabarcoding: A meta‐analytical approach

Author:
Lamb, Philip D.; Hunter, Ewan; Pinnegar, John K.; Creer, Simon; Davies, Richard G.; Taylor, Martin I.
Source:
Molecular ecology 2019 v.28 no.2 pp. 420-430
ISSN:
0962-1083
Subject:
DNA barcoding,   etc   ; DNA; biomass; meta-analysis; uncertainty; variance;     Show all 6 Subjects
Abstract:
... Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conduc ...
DOI:
10.1111/mec.14920

11. Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures

Author:
Bell, Karen L.; Burgess, Kevin S.; Botsch, Jamieson C.; Dobbs, Emily K.; Read, Timothy D.; Brosi, Berry J.
Source:
Molecular ecology 2019 v.28 no.2 pp. 431-455
ISSN:
0962-1083
Subject:
DNA barcoding,   etc   ; DNA; bioinformatics; internal transcribed spacers; pollen; species richness;     Show all 6 Subjects
Abstract:
... Pollen DNA metabarcoding—marker‐based genetic identification of potentially mixed‐species pollen samples—has applications across a variety of fields. While basic species‐level pollen identification using standard DNA barcode markers is established, the extent to which metabarcoding (a) correctly assigns species identities to mixes (qualitative matching) and (b) generates sequence reads proportiona ...
DOI:
10.1111/mec.14840

12. The continuously evolving CRISPR barcoding toolbox

Author:
Gaj, Thomas; Perez-Pinera, Pablo
Source:
Genome biology 2018 v.19 no.1 pp. 143
ISSN:
1474-760X
Subject:
DNA barcoding,   etc   ; gene editing; genome; mammals;     Show all 4 Subjects
Abstract:
... Two articles recently described the development of CRISPR technologies that have the potential to fundamentally transform the barcoding and tracing of mammalian cells. ...
DOI:
10.1186/s13059-018-1541-y

13. A small leap toward DNA barcode library creation of ornamental fishes: development of 17 DNA barcodes from Manipur, India

Author:
Khomdram, Bijoya Devi
Source:
Journal of Asia-Pacific biodiversity(Online) 2018 v.11 no.3 pp. 452-458
ISSN:
2287-884X
Subject:
DNA barcoding,   etc   ; biodiversity; ornamental fish; India;     Show all 4 Subjects
Abstract:
... Proper identification is expected to result in proper conservation of a species. Morphology-based identifications are problematic in many cases and often time-consuming. DNA barcoding came out to be the problem solver in these cases. A researcher can easily identify a species by comparing generated barcode sequences with the barcode sequences from a DNA barcode library. We have developed 17 DNA ba ...
DOI:
10.1016/j.japb.2018.06.005

14. Characterization of Simulium (Simulium) hackeri Edwards (Diptera: Simuliidae) from Malaysia: Morphological description of the pupa and larva, and DNA barcoding

Author:
Ya’cob, Zubaidah; Takaoka, Hiroyuki; Low, Van Lun; Sofian-Azirun, Mohd
Source:
Acta tropica 2018 v.185 pp. 110-114
ISSN:
0001-706X
Subject:
DNA barcoding,   etc   ; Simulium; abdomen; females; pupae; Malaysia;     Show all 6 Subjects
Abstract:
... Simulium (Simulium) hackeri Edwards, 1928 of the Simulium variegatum species-group from Malaysia was described initially based on the female specimen from Cameron Highlands, Pahang. In the present study, the pupa and larva of this species are described for the first time. Their morphological characters resemble those of the Simulium variegatum species-group by having six gill filaments per side, a ...
DOI:
10.1016/j.actatropica.2018.04.029

15. How to trace the geographic origin of mushrooms?

Author:
El Sheikha, Aly Farag; Hu, Dian-Ming
Source:
Trends in food science & technology 2018 v.78 pp. 292-303
ISSN:
0924-2244
Subject:
DNA barcoding,   etc   ; fresh produce; mushrooms; provenance; trade;     Show all 5 Subjects
Abstract:
... Mushrooms became one of the most popular food resources worldwide that are very appreciated by consumers. Fresh produce properties including mushrooms are obviously varied based on their geographical origins. In view of the significant increase in the world's production of mushrooms, this will be accompanied by the increasing attention of all actors in the international food trade system (producer ...
DOI:
10.1016/j.tifs.2018.06.008

16. The genus Apsiphortica from China with DNA barcoding information (Diptera: Drosophilidae)

Author:
Gong, Lu; Chen, Hongwei
Source:
Annales de la Société entomologique de France 2018 v.54 no.2 pp. 111-118
ISSN:
2168-6351
Subject:
DNA barcoding,   etc   ; Drosophilidae; new species; China; France;     Show all 5 Subjects
Abstract:
... Two new species of the genus Apsiphortica are described from China: A. orthophallos n. sp. and A. sinuatipenis n. sp. Species delimitations are improved by integrating morphological and DNA barcoding information. The intra- and interspecific pairwise p-distances (proportional distance) are summarized for five Apsiphortica species from China. Furthermore, nucleotide sites with fixed status in the a ...
DOI:
10.1080/00379271.2017.1412809

17. funbarRF: DNA barcode-based fungal species prediction using multiclass Random Forest supervised learning model

Author:
Meher, Prabina Kumar; Sahu, Tanmaya Kumar; Gahoi, Shachi; Tomar, Ruchi; Rao, Atmakuri Ramakrishna
Source:
BMC genetics 2019 v.20 no.1 pp. 2
ISSN:
1471-2156
Subject:
DNA barcoding,   etc   ; computer software; fungi; internal transcribed spacers; models; prediction; ribosomal DNA; species identification;     Show all 8 Subjects
Abstract:
... BACKGROUND: Identification of unknown fungal species aids to the conservation of fungal diversity. As many fungal species cannot be cultured, morphological identification of those species is almost impossible. But, DNA barcoding technique can be employed for identification of such species. For fungal taxonomy prediction, the ITS (internal transcribed spacer) region of rDNA (ribosomal DNA) is used ...
DOI:
10.1186/s12863-018-0710-z

18. Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline

Author:
Pauvert, Charlie; Buée, Marc; Laval, Valérie; Edel-Hermann, Véronique; Fauchery, Laure; Gautier, Angélique; Lesur, Isabelle; Vallance, Jessica; Vacher, Corinne
Source:
Fungal ecology 2019 v.41 pp. 23-33
ISSN:
1754-5048
Subject:
DNA barcoding,   etc   ; Ascomycota; Basidiomycota; algorithms; bioinformatics; computer software; fungal communities; internal transcribed spacers; soil; soil fungi;     Show all 10 Subjects
Abstract:
... Fungal communities associated with plants and soil influence plant fitness and ecosystem functioning. They are frequently studied by metabarcoding approaches targeting the ribosomal internal transcribed spacer (ITS), but there is no consensus concerning the most appropriate bioinformatic approach for the analysis of these data. We sequenced an artificial fungal community composed of 189 strains co ...
DOI:
10.1016/j.funeco.2019.03.005

19. Community of dark-spored myxomycetes in ground litter and soil of taiga forest (Nizhne-Svirskiy Reserve, Russia) revealed by DNA metabarcoding

Author:
Shchepin, Oleg N.; Schnittler, Martin; Erastova, Daria A.; Prikhodko, Ilya S.; Borg Dahl, Mathilde; Azarov, Daniil V.; Chernyaeva, Ekaterina N.; Novozhilov, Yuri K.
Source:
Fungal ecology 2019 v.39 pp. 80-93
ISSN:
1754-5048
Subject:
DNA barcoding,   etc   ; Myxogastrea; boreal forests; chronosequences; conservation areas; fructification; fruiting bodies; niches; soil; soil microorganisms; Russia;     Show all 11 Subjects
Abstract:
... The diversity of dark-spored myxomycetes in forest ground litter and soil from four study plots across a fire chronosequence in Nizhne-Svirskiy Nature Reserve (northwest of Russia) was assessed by a DNA metabarcoding approach. The history of fire disturbances and the season of sampling influenced the composition of myxomycete assemblages. Several species showed substrate preferences different from ...
DOI:
10.1016/j.funeco.2018.11.006

20. Long term persistence of introduced Amblyomma geoemydae tick population under indoor conditions in Austria

Author:
Bilbija, B.; Auer, M.; Široký, P.
Source:
Medical and veterinary entomology 2019 v.33 no.2 pp. 317-321
ISSN:
0269-283X
Subject:
DNA barcoding,   etc   ; Amblyomma; Cuora; control methods; imports; monitoring; pathogens; soil; ticks; turtles; wildlife; Austria;     Show all 12 Subjects
Abstract:
... An indoor terrarium population of Amblyomma geoemydae was established subsequent to the import of a single yellow‐marginated box turtle Cuora flavomarginata. This indoor tick population revealed an unexpected resistance against de‐ticking trials, with persistence between 2010 and 2015, when the ticks were successfully eliminated. Ticks were collected from the bodies and shells of turtles, as well ...
DOI:
10.1111/mve.12361