Created by:
Clarke van Steenderen
Department of Zoology and Entomology
The Centre for Biological Control
Rhodes University, Grahamstown, Eastern Cape, South Africa
2019
e-mail: vsteenderen@gmail.com
OVERVIEW
The R Shiny online application is accessible here:
It can also be accessed by typing
shiny::runGitHub("DactyID", "CJMvS")
into the R console. Ensure that the R shiny package is installed prior to running this line of code.
This program is designed for the quick identification of Dactylopius species (Hemiptera: Dactylopiidae), but can be applied to any taxon if the relevant database of genetic sequences is supplied. The user can either upload a database of their choice, or can select from those provided under the 'Select File' drop down menu (12S, 18S, and two COI markers). The sequences provided were obtained by Clarke van Steenderen as part of his M.Sc. degree. A query nucleotide sequence is entered into the search box, and a phylogenetic tree is created where the query sequence is matched to the database, and highlighted in red. All the sequences in the provided databases will be available on [Genbank] (https://www.ncbi.nlm.nih.gov/genbank/) from July 31 2020.
Disclaimer: The query sequences inputted by the user are not stored by this program, or used in a manner not specified in this document.
UPLOADING YOUR OWN FILE
If you wish to upload your own sequences to serve as a database, a FASTA file is required (.fas extension), containing unaligned nucleotide sequences.
PASTING IN A QUERY SEQUENCE
Insert an optional name into the "Enter sequence name" box. It is set as ">QUERY" by default.
Paste your query nucleotide sequence into the search box, and make sure that it contains only nucleotide bases, and not a name. For example, if the FASTA sequence is:
>sequence1A
AAAAAAGGGGGCCCC
Then only paste in the AAAAAAGGGGGCCCC part.
METHODS
Agglomeration methods to select from are:
- complete
- single
- UPGMA (unweighted pair group method with arithmetic mean)
- WPGMA (weighted pair group method with arithmetic mean)
- NJ (neighbour joining)
- ML (maximum likelihood)
See the [IdClusters] (https://www.rdocumentation.org/packages/DECIPHER/versions/2.0.2/topics/IdClusters) function in the DECIPHER package for more details regarding these methods.
The multiple sequence alignment algorithm uses the R package 'DECIPHER', which can be cited as:
Wright ES (2016). Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R. The R Journal, 8(1), 352-359
EXTRA INFORMATION
Primers used for obtaining gene sequences:
12S:
Forward: 5'-AAGAGTGACGGGCRATTTGTACATA-3'
Reverse: 5'-GTGCCAGCAGTWGCGGTTA-3'
18S:
Forward: 5'-CTGGTTGATCCTGCCAGTAG-3'
Reverse: 5'-CCGCGGCTGCTGGCACCAGA-3'
COI:
Forward (PcoF1): 5'-CCTTCAACTAATCATAAAAATATYAG-3'
Reverse (LepR1): 5'-TAAACTTCTGGATGTCCAAAAAATCA-3'
Forward (DTOMf): 5'-TCCGRATAGAACTWATAAAYACYAA-3'
Reverse (HCO2198): 5'-TAAACTTCAGGGTGACCAAAAAATCA-3'
References for primers:
Campana, M. G., Robles Garcia, N. M., and Tuross, N., 2015. America’s Red Gold: Multiple Lineages of Cultivated Cochineal in Mexico. Ecology and Evolution, 5(3):607–617. doi 10.1002/ece3.1398
[Link] (https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.1398)
Park, D.S., Suh, S.J., Oh, H.W., and Hebert, P. D. N., 2010. Recovery of the Mitochondrial COI Barcode Region in Diverse Hexapoda through tRNA-Based Primers.BMCGenomics, 11:7. doi: 10.1186/1471-2164-11-423
[Link] (https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-423)
Ramirez-Puebla, S.T., Rosenblueth, M., Chavez-Moreno, C. K., Catanho Pereira de Lyra,M. C., Tecante, A., and Martinez-Romero, E., 2010. Molecular Phylogeny of the Genus Dactylopius (Hemiptera: Dactylopiidae) and Identification of the Symbiotic Bacteria. Environmental Entomology, 39(4):1178–1183. doi: 10.1603/EN10037
[Link] (https://academic.oup.com/ee/article/39/4/1178/447419)
Mathenge, C. W., Riegler, M., Beattie, G. A. C., Spooner-Hart, R. N., & Holford, P. (2015). Genetic variation amongst biotypes of Dactylopius tomentosus. Insect Science, 22(3), 360-374. doi: 10.1111/1744-7917.12120
OTHER R PACKAGES USED BY THIS PROGRAM
[shinyhelper] (https://cran.r-project.org/web/packages/shinyhelper/index.html)
GENBANK ACCESSION NUMBERS
12S: MN219994 - MN220135
18S: MN310037 - MN310179
PCOF1 and LepR1: MN372226 - MN372280
DTOMf and HCO2198: MN372281 - MN372299
Note Genbank ID [GQ853358.1] (https://www.ncbi.nlm.nih.gov/nuccore/GQ853358.1) and GQ853350.1 (reported to be D. confusus by Ramirez-Puebla et. al. 2015) and Genbank ID [GQ853357.1] (https://www.ncbi.nlm.nih.gov/nuccore/GQ853357.1) and GQ853349.1 (reported to be D. ceylonicus by Ramirez-Puebla et. al. 2015) both appeared in the D. opuntiae clade according to the databases in this program. Both specimens were recorded to have been collected from Opuntia ficus-indica, and are likely misidentifications.
List of sequences
Abbreviations
aus. = Dactylopius austrinus cey. = Dactylopius ceylonicus
confert. = Dactylopius confertus
confus. = Dactylopius confusus
opunt.f.i. = Dactylopius opuntiae 'ficus' lineage
opunt.str. = Dactylopius opuntiae 'stricta' lineage
toment.big. = Dactylopius tomentosus 'bigelovii' lineage
toment.cal. = Dactylopius tomentosus 'californica' lineage
toment.chol. = Dactylopius tomentosus 'cholla' lineage
toment.cyl. = Dactylopius tomentosus 'cylindropuntia' lineage
toment.ech. = Dactylopius tomentosus 'echinocarpa x acanthocarpa' lineage
toment.i. = Dactylopius tomentosus 'imbricata' lineage
12S
opunt.f.i.MN219994
opunt.f.i.MN219995
opunt.f.i.MN219996
opunt.f.i.MN219997
opunt.f.i.MN219998
opunt.f.i.MN219999
toment.i.MN220000
toment.i.MN220001
toment.i.MN220002
toment.chol.MN220003
toment.chol.MN220004
opunt.MN220005
opunt.f.i.MN220006
opunt.f.i.MN220007
opunt.f.i.MN220008
opunt.MN220009
cey.MN220010
cey.MN220011
aus.MN220012
aus.MN220013
aus.MN220014
confus.MN220015
confus.MN220016
confus.MN220017
confus.MN220018
confus.MN220019
opunt.flag.MN220020
opunt.flag.MN220021
opunt.flag.MN220022
opunt.tuc.MN220023
opunt.tuc.MN220024
opunt.tuc.MN220025
opunt.sed.MN220026
opunt.sed.MN220027
opunt.sed.MN220028
confus.4PM.MN220029
confus.4PM.MN220030
confus.4PM.MN220031
confus.LC.MN220032
confus.LC.MN220033
confus.LC.MN220034
opunt.f.i.MN220035
opunt.f.i.MN220036
cey.MN220037
aus.MN220038
cey.MN220039
toment.chol.MN220040
toment.i.MN220041
toment.i.MN220042
opunt.MN220043
opunt.MN220044
opunt.MN220045
opunt.MN220046
opunt.MN220047
opunt.MN220048
opunt.MN220049
opunt.MN220050
opunt.MN220051
opunt.MN220052
opunt.MN220053
confus.MN220054
confus.MN220055
confus.MN220056
opunt.MN220057
opunt.MN220058
confus.MN220059
confus.MN220060
opunt.MN220061
opunt.MN220062
confus.MN220063
confus.MN220064
opunt.MN220065
opunt.MN220066
opunt.MN220067
toment.chol.MN220068
toment.chol.MN220069
toment.cal.MN220070
toment.cal.MN220071
toment.cal.MN220072
toment.cal.MN220073
opunt.MN220074
opunt.MN220075
opunt.MN220076
opunt.str.MN220077
opunt.str.MN220078
aus.MN220079
opunt.str.MN220080
opunt.str.MN220081
opunt.MN220082
opunt.str.MN220083
opunt.str.MN220084
opunt.str.MN220085
opunt.str.MN220086
opunt.str.MN220087
opunt.str.MN220088
opunt.str.MN220089
opunt.str.MN220090
aus.MN220091
opunt.str.MN220092
opunt.str.MN220093
opunt.str.MN220094
opunt.str.MN220095
opunt.str.MN220096
opunt.str.MN220097
opunt.str.MN220098
opunt.str.MN220099
opunt.str.MN220100
opunt.str.MN220101
toment.i.MN220102
toment.i.MN220103
toment.i.MN220104
toment.i.MN220105
opunt.str.MN220106
opunt.str.MN220107
opunt.MN220108
toment.chol.MN220109
toment.chol.MN220110
opunt.MN220111
toment.chol.MN220112
toment.ech.MN220113
toment.ech.MN220114
toment.ech.MN220115
toment.cyl.MN220116
toment.cyl.MN220117
toment.ech.MN220118
toment.chol.MN220119
toment.chol.MN220120
toment.chol.MN220121
cey.MN220122
cey.MN220123
cey.MN220124
toment.cal.MN220125
toment.cal.MN220126
toment.cal.MN220127
toment.cal.MN220128
toment.big.MN220129
aus.MN220130
aus.MN220131
aus.MN220132
opunt.str.MN220133
opunt.str.MN220134
opunt.str.MN220135
opunt.GQ853353.1
opunt.GQ853352.1
opunt.GQ853351.1
coccus.KJ701988.1
coccus.KJ701987.1
coccus.KJ701986.1
coccus.KJ701968.1
P.nigra.HQ893819.1
C.sinensis.HQ893810.1
C.viridis.HQ893818.1
I.purchasi.HQ893806.1
18S
confert.MN310037
confert.MN310038
opunt.MN310039
opunt.f.i.MN310040
opunt.MN310041
opunt.MN310042
opunt.MN310043
opunt.MN310044
opunt.MN310045
opunt.MN310046
opunt.MN310047
opunt.MN310048
opunt.MN310049
opunt.MN310050
opunt.MN310051
opunt.MN310052
opunt.MN310053
confus.MN310054
confus.MN310055
confus.MN310056
confus.MN310057
opunt.MN310058
opunt.MN310059
confus.MN310060
confus.MN310061
confus.MN310062
confus.MN310063
opunt.MN310064
aus.MN310065
opunt.MN310066
toment.chol.MN310067
toment.chol.MN310068
aus.MN310069
cey.MN310070
opunt.MN310071
toment.chol.MN310072
aus.MN310073
cey.MN310074
opunt.MN310075
toment.i.MN310076
toment.i.MN310077
opunti.f.i.MN310078
opunti.f.i.MN310079
opunti.f.i.MN310080
cey.MN310081
opunt.flag.MN310082
opunt.flag.MN310083
opunt.flag.MN310084
opunt.tuc.MN310085
opunt.tuc.MN310086
opunt.tuc.MN310087
opunt.sed.MN310088
opunt.sed.MN310089
opunt.sed.MN310090
confus.4pm.MN310091
confus.lc.MN310092
confus.lc.MN310093
confus.lc.MN310094
opunt.f.i.MN310095
opunt.f.i.MN310096
opunt.MN310097
opunt.MN310098
confus.MN310099
confus.MN310100
confus.MN310101
confus.MN310102
confus.MN310103
coccus.KJ7019951
coccus.KJ7019941
coccus.KJ7019931
coccus.KJ7019921
coccus.KJ7019911
opunt.MN310104
opunt.MN310105
opunt.MN310106
opunt.MN310107
toment.cal.MN310108
toment.cal.MN310109
toment.cal.MN310110
toment.cal.MN310111
toment.cal.MN310112
toment.chol.MN310113
toment.chol.MN310114
opunt.MN310115
opunt.MN310116
opunt.str.MN310117
opunt.str.MN310118
opunt.str.MN310119
opunt.str.MN310120
opunt.str.MN310121
opunt.str.MN310122
opunt.str.MN310123
opunt.str.MN310124
opunt.str.MN310125
opunt.str.MN310126
opunt.str.MN310127
opunt.str.MN310128
opunt.str.MN310129
aus.MN310130
aus.MN310131
aus.MN310132
cey.MN310133
cey.MN310134
toment.chol.MN310135
toment.i.MN310136
toment.i.MN310137
toment.i.MN310138
opunt.MN310139
opunt.MN310140
opunt.MN310141
opunt.f.i.MN310142
opunt.str.MN310143
opunt.str.MN310144
opunt.str.MN310145
toment.ech.MN310146
opunt.MN310147
toment.i.MN310148
aus.MN310149
toment.big.MN310150
toment.cal.MN310151
cey.MN310152
toment.chol.MN310153
toment.cyl.MN310154
opunt.MN310155
toment.i.MN310156
toment.cyl.MN310157
toment.cal.MN310158
toment.big.MN310159
cey.MN310160
toment.chol.MN310161
opunt.MN310162
opunt.MN310163
toment.i.MN310164
toment.i.MN310165
opunt.MN310166
opunt.MN310167
toment.ech.MN310168
toment.ech.MN310169
toment.cyl.MN310170
toment.cyl.MN310171
toment.chol.MN310172
cey.MN310173
cey.MN310174
toment.cal.MN310175
toment.cal.MN310176
toment.big.MN310177
aus.MN310178
aus.MN310179
opunt.GQ853363.1
toment.GQ853360.1
confus.KT199039.1
aus.AY795538.1
confus.U20402.1
P.nigra.KY9276001
C.sinensis.HQ8937881
I.purchasi.KT199034.1
C.viridis.HQ8937931
COI: PCOF1 and LepR1
confert.MN372226
confert.MN372227
opunt.MN372228
opunt.
opunt.MN372229
opunt.MN372230
opunt.MN372231
opunt.MN372232
opunt.MN372233
opunt.MN372234
opunt.MN372235
opunt.MN372236
opunt.MN372237
confus.MN372238
opunt.
confus.MN372239
confus.MN372240
confus.MN372241
confus.MN372242
confus.MN372243
opunt.MN372244
opunt.MN372245
confus.MN372246
confus.MN372247
confus.MN372248
confus.MN372249
opunt.MN372250
opunt.
toment.chol.MN372251
opunt.MN372252
opunt.f.i.MN372253
toment.i.MN372254
opunt.f.i.
opunt.f.i.MN372255
opunt.f.i.MN372256
opunt.flag.MN372257
opunt.flag.MN372258
opunt.flag.
opunt.tuc.MN372259
opunt.tuc.MN372260
opunt.sed.MN372261
opunt.sed.
opunt.sed.MN372262
confus.4PM.MN372263
confus.4PM.MN372264
confus.4PM.MN372265
confus.lc.MN372266
confus.lc.MN372267
confus.lc.MN372268
opunt.f.i.MN372269
opunt.f.i.MN372270
opunt.f.i.MN372271
opunt.MN372272
opunt.MN372273
confus.MN372274
confus.PCOF1
C.viridis.GU936953.1
I.purchasi.KP692469.1
opunt.str.MN372275
opunt.str.MN372276
opunt.str.MN372277
opunt.str.MN372278
opunt.str.MN372279
opunt.str.MN372280
COI: DTOMf and HCO2198
opunt.eng3
toment.ech.MN372281
toment.ech.MN372282
toment.ech.MN372283
toment.ech.MN372284
toment.cyl.MN372285
toment.cyl.MN372286
toment.chol.MN372287
toment.chol.MN372288
toment.chol.MN372289
toment.chol.MN372290
toment.cal.MN372291
toment.cal.MN372292
toment.cal.MN372293
toment.cal.MN372294
toment.big.MN372295
toment.big.MN372296
toment.big.MN372297
toment.big.
toment.chol.MN372298
toment.i.MN372299
toment.i.GU228788.1
toment.i.GU228787.1
toment.roseaP.GU228786.1
toment.cholDH.GU228781.1
toment.cholE.GU228780.1
toment.cholD.GU228779.1
toment.RoseaY.GU228785.1
toment.fulg.GU228784.1
toment.mamill.GU228783.1
toment.mol.GU228782.1
opunt.GU228789.1