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. 2018 Jun 6;8:8686. doi: 10.1038/s41598-018-26851-1

Table 3.

Description of the sequences on the representative phylogenetic trees generated for four selected viruses analysed using MEGA 6 or 7 software.

Figure and Table Long Name (Format: Sample-virus-protein-length-quality-coverage-year) Short name (Format: Sample-virus-protein-length) Coverage No. of nucleotides Mapping quality threshold NCBI accession number
Avian Paramyxovirus 6 from MAD faecal sample
2 and 4 MAD-Avian-paramyxovirus-6-large-polymerase-protein-459nt-Q32-C-9-192-2016 MAD-APMV6-Pol-459nt 9–192 459 32 MH000419
3 and 5 MAD-Avian-paramyxovirus-6-hemagglutinin-neuraminidase-1839nt-Q32-C-5-103_2016 MAD-APMV6-HN-1839nt 5–103 1839 32 MH000415
4 and 6 MAD-Avian-paramyxovirus-6-fusion-protein-651nt-Q32-C-2-8-2016 MAD-APMV6-FP-651nt 2–8 651 32 MH000412
Long Name Short Name (Format: NCBI accession number-virus-country/state) Country of collection Collection date
NCBI sequences taken for phylogenetic analysis for APMV6
AB759118-Avian-paramyxovirus-6-viral-cRNA-complete-genome-strain:red-necked-stint/Japan/8KS0813/2008 AB759118-APMV6-JP Japan 2008
GQ406232-Avian-paramyxovirus-6-strain-duck/Italy/4524-2/07-complete-genome GQ406232-APMV6-IT Italy 2007
KP762799-Avian-paramyxovirus-6-isolate-red-crested-pochard/Balkhash/5842/2013-complete-genome KP762799-APMV6-KZ Kazakhstan 2013
AY029299-Avian-paramyxovirus-6-complete-genome AY029299-APMV6-TW Taiwan
KT962980-Avian-paramyxovirus-6-isolate-teal/Novosibirsk_region/455/2009-complete-genome KT962980-APMV6-RU Russia 2009
JN571486-Avian-paramyxovirus-6-strain-APMV6/mallard/Belgium/12245/07-nucleoprotein(NP)-phosphoprotein(P)-matrix-protein(M)-fusion-protein(F)-small-hydrophobic-protein(SH)-hemagglutinin-neuramis JN571486-APMV6-BE Belgium 2007
KF267717-Avian-paramyxovirus-6-isolate-mallard/Jilin/127/2011-complete-genome KF267717-APMV6-CN China 2011
Deltacoronavirus from the MAD faecal sample
5 and 8 MAD-Deltacoronavirus-Orf1a-10650nt-Q20-C-6-2326−2016 MAD-DCoV-Orf1a-10650nt 6–2326 10650 20 MH013332
6 and 9 MAD-Deltacoronavirus-Orf1b-polymerase-2076nt-Q20-C-5-475-2016 MAD-DCoV-RPP-2076nt 5–475 2076 20 MH013331
7 and 10 MAD-Deltacoronavirus-spike-glycoprotein-3702nt-Q20-C-36-6274-2016 MAD-DCoV-SP-3702nt 36–6274 3702 20 MH013337
NCBI sequences taken for phylogenetic analysis for DCoV
JQ065049-Common-moorhen coronavirus-HKU21-strain-HKU21-8295-complete-genome JQ065049-MCoV-CN China 2007
JQ065046-Magpie-robin-coronavirus HKU18-strain-HKU18-chu3-complete-genome JQ065046-MrCoV-CN China 2007
FJ376622-Munia-coronavirus-HKU13-3514-complete-genome FJ376622-MuCoV-CN China 2007
FJ376621-Thrush-coronavirus-HKU12-600-complete-genome FJ376621-TCoV-CN China 2007
MF431743-Porcine-deltacoronavirus-strain-SD-complete-genome MF431743-PDCoV-CN China 2014
FJ376620-Bulbul-coronavirus-HKU11-796-complete-genome FJ376620-BCoV-CN China 2007
JQ065047-Night-heron-coronavirus-HKU19-strain-HKU19-6918-complete genome JQ065047-NhCoV-CN China 2007
JQ065048-Wigeon-coronavirus-HKU20-strain-HKU20-9243-complete-genome JQ065048-WCoV-CN China 2008
Figure and Table Long Name (Format: Sample-virus-protein-length-quality-coverage-year) Short name (Format: Sample-virus-protein-length-year) Coverage No. of nucleotides Mapping quality threshold NCBI accession number
Virus related to goose adenovirus 4 (GoA4) and/or duck adenovirus 2 (DuA2) from the MAD faecal sample
GoA4
8 and 11 MAD-Adenovirus-encapsidation-protein-IVa2-279nt-Q20-C-4-69-2016 MAD-AV-IVa2-279nt 4–69 279 20 MH028885
DuA2
9 and 12 MAD-Adenovirus-III-177nt-Q20-C-21-261-2016 MAD-AV-III-177nt 21–261 177 20 MH028886
10 and 13 MAD-Adenovirus-pVIII-114nt-Q32-C-19-67-2016 MAD-AV-pVIII-114nt 19–67 114 32 MH028887
NCBI sequences taken for phylogenetic analysis for AV
KR135164-Duck-adenovirus-2-strain-CH-GD-12-2014-complete-genome KR135164-DAd2-CN China 2014
JF510462-Goose-adenovirus-4-strain-P29-complete-genome JF510462-GAd4-HU Hungary
FN824512-Pigeon-adenovirus-1-complete-genome-strain-IDA4 FN824512-PAd1-NL Netherlands 1995
KC493646-Fowl-adenovirus-5-strain-340-complete-genome KC493646-FAd5-IE Ireland 1970
Hubei chryso-like virus 1 from the MUD faecal sample
11 and 14 MUD-Hubei-chryso-like-virus-1-seg1-RdRp-1496nt-Q20-C-4-58-2016 MUD-HCLV1-s1-Rp-1496nt 4–58 1496 20 MH085092
Long Name Short Name (Format: NCBI accession number-virus-segment-country/state) Country or State of collection Collection date
NCBI sequences taken for phylogenetic analysis for HCLV1
Segment 1
MF176368-Hubei-chryso-like-virus-1-strain-mosWSgb49785-segment1-complete-sequence MF176368-HCLV1-s1-WA Western Australia 2015
MF176309-Hubei-chryso-like-virus-1-strain-mos191gb77171-segment1-complete-sequence MF176309-HCLV1-s1-WA Western Australia 2015
MF176261-Hubei-chryso-like-virus-1-strain-mos172gb42656-segment1-complete-sequence MF176261-HCLV1-s1-WA Western Australia 2015
MF176388-Hubei-chryso-like-virus-1-strain-mosWSX51080-segment-1-complete-sequence MF176388-HCLV1-s1-WA Western Australia 2015
MF176280-Hubei-chryso-like-virus-1-strain-mos172X13576-segment1-complete-sequence MF176280-HCLV1-s1-WA Western Australia 2015
KX882962-Hubei-chryso-like-virus-1-strain-mosHB233224-hypothetical-protein-gene-partial-cds KX882962-HCLV1-CN China 2013

The table gives details of the sequences used for phylogenetic analysis by the Maximum Likelihood method of APMV6, DCoV, AV and HCLV1. The first half of the table for each virus provides details to identify the sample from which the virus was isolated, protein encoded by the consensus sequences that are being analysed, the length of the consensus sequences and gene being analysed, minimum mapping quality threshold used in IGV for the generation of the consensus sequences, the coverage of the consensus sequences from IGV, the year of collection of the sample and the NCBI accession number assigned to the particular consensus sequence. Corresponding short names have been used in the phylogenetic trees which contain the sample, virus, protein and the number of nucleotides. The second half of the table for each virus provides the details of the sequences that were used for the comparative molecular phylogenetic analysis. They were found to be the most closely related sequences to the consensus sequences generated using BLASTN. Corresponding short names have been used in the phylogenetic trees which contain the NCBI accession number, virus and the country of collection. The collection date is given as retrieved from the corresponding NCBI nucleotide reference dataset which together with the country of collection can provide an insight into the possible evolution of the virus through the years.