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The use of 18S ribosomal DNA, ITS and rbcL molecular markers to study the genus Dunaliella (Dunaliellaceae) in Iranian samples: A phylogenetic approach Cover

The use of 18S ribosomal DNA, ITS and rbcL molecular markers to study the genus Dunaliella (Dunaliellaceae) in Iranian samples: A phylogenetic approach

Oceanological and Hydrobiological Studies
Volume 49 (2020): Issue 1 (March 2020)
By: Jaber Dehghani,  Ehsan Atazadeh,  Yadollah Omidi and  Ali Movafeghi  
Open Access
|Mar 2020

Figures & Tables

Figure 1

Morphological characteristics of microalgae. D. salina isolate BAK (from Lake Bakhtegan) at 1M NaCl (a) and at 5M NaCl (b); and D. pseudosalina isolate MAH (from Lake Maharlu) at 1M NaCl (c) and at 5M NaCl (d). f – flagella and s – stigma
Morphological characteristics of microalgae. D. salina isolate BAK (from Lake Bakhtegan) at 1M NaCl (a) and at 5M NaCl (b); and D. pseudosalina isolate MAH (from Lake Maharlu) at 1M NaCl (c) and at 5M NaCl (d). f – flagella and s – stigma

Figure 2

PCR products of 18S rDNA and ITS (~2500 bp) in D. pseudosalina isolate MAH and D. salina isolate BAK (a). RFLP pattern of PCR products presented in gel after digestion by Hhal (restriction enzyme) (b). PCR products of rbcL gene (~900 bp) in D. pseudosalina isolate MAH and D. salina isolate BAK (c). “Lan” 1 indicates the 18S rDNA PCR product of D. salina isolate BAK and “L” indicates Ladder
PCR products of 18S rDNA and ITS (~2500 bp) in D. pseudosalina isolate MAH and D. salina isolate BAK (a). RFLP pattern of PCR products presented in gel after digestion by Hhal (restriction enzyme) (b). PCR products of rbcL gene (~900 bp) in D. pseudosalina isolate MAH and D. salina isolate BAK (c). “Lan” 1 indicates the 18S rDNA PCR product of D. salina isolate BAK and “L” indicates Ladder

Figure 3

The 18S rDNA based phylogenetic tree. The tree was obtained by the ML method (K2 + G model) with 500 bootstrap replications. The capital letters (A–D) show the clades.
The 18S rDNA based phylogenetic tree. The tree was obtained by the ML method (K2 + G model) with 500 bootstrap replications. The capital letters (A–D) show the clades.

Figure 4

The ITS based phylogenetic tree. The tree was obtained by the ML method (K2 + G model) with 500 bootstrap replications. The capital letters (A–D) show the clades.
The ITS based phylogenetic tree. The tree was obtained by the ML method (K2 + G model) with 500 bootstrap replications. The capital letters (A–D) show the clades.

Figure 5

The rbcL based phylogenetic tree. The tree was obtained by the ML method (T92 + G model) with 500 bootstrap replications. The capital letters (A–D) indicate the clades.
The rbcL based phylogenetic tree. The tree was obtained by the ML method (T92 + G model) with 500 bootstrap replications. The capital letters (A–D) indicate the clades.

Figure 6

Combined 18S rDNA, ITS and rbcL based phylogenetic tree. The tree was drawn using the ML method (TN93 + G model) with 500 bootstrap replications. The capital letters (A–D) indicate the clades.
Combined 18S rDNA, ITS and rbcL based phylogenetic tree. The tree was drawn using the ML method (TN93 + G model) with 500 bootstrap replications. The capital letters (A–D) indicate the clades.

The 18S rDNA sequences of Dunaliella spp_ from the NCBI database

Dunaliella spp.Gene size (bp)Accession numberGeographic origin
D. bardawil strain KMMCC 13462054JQ315779.1Republic of Korea
D. bardawil UTEX LB 25382088DQ009777.1USA
D. bioculata UTEX LB 1991687DQ009761.1USA
D. parva2585M62998.1Unknown
D. peircei strain UTEX LB 21922065DQ009778.1USA
D. primolecta UTEX 10001620KJ018734.1USA
D. salina strain KMMCC 14281647JQ315781.1Korea
Dunaliella sp. ABRIINW M1/22120EU678868.1Iran
D. salina UTEX LB 2002065DQ009779.1USA
D. salina strain KU072069KF825551.1Thailand
D. salina strain KU112067KF825550.1Thailand
D. salina strain KU132068KF825552.1Thailand
D. salina isolate BAK1784KU641617Iran
Dunaliella sp. SAS111331722KF054056.1China
D. pseudosalina isolate MAH1735KU641615Iran
D. salina isolate BAK1784KU641617.1Iran
Asteromonas gracilis isolate BA1687KU351659.1Iran
D. viridis strain CONC0022494DQ009776.1USA
D. tertiolecta CCMP 3641620KJ018735.1USA
D. tertiolecta UTEX 9991620KJ018733.1USA
Chlamydomonas reinhardtii1641AB701555Japan
D. lateralis strain Nepal1692DQ009762.1USA
Chlorella vulgaris1770KJ756813UK
D. polymorpha2991KJ756825.1UK

ITS1 and ITS 2 sequences of Dunaliella spp_ from the NCBI database

Dunaliella spp.ITS1 sizeITS2 sizeAccession numberGeographic origin
D. bardawil strain KMMCC 1346214230JQ315779.1Republic of Korea
D. bardawil UTEX 2538210232DQ377085.1USA
D. biocolata strain UTEX 199209328DQ377086.1USA
D. parva213226DQ116746China
D. peircei strain UTEX 2192210226AF313442.1Chile
D. primolecta UTEX 1000210328DQ377092.1USA
D. acidophila strain CCAP 19/35213232HM060646.1

indicates ITS1

Spain
HM060645.1

indicate ITS2 accession number

D. salina strain KMMCC 1428214227JQ315781.1Republic of Korea
Dunaliella sp. ABRIINW M1/2220225EU927373.1Iran
D. Salina UTEX 200209227DQ313197.1Chile
D. salina strain KU07159229KF825555.2Thailand
D. salina strain KU11159229KF825549.1Thailand
D. salina strain KU13159229KF825547.1Thailand
D. salina isolate BAK216233KU641617Iran
Dunaliella sp. SAS11133204230KF054058.1China
D. pseudosalina isolate MAH212225KU641615Iran
Asteromonas gracilis isolate BA214230KU351659.1Iran
D. viridis strain CONC002217228DQ377098.1USA
D. tertiolecta CCMP 364210228DQ377097.1USA
D. tertiolecta UTEX 999210226AF313434.1

indicates ITS1

Chile
AF1313435.1

indicate ITS2 accession number

Chlamydomonas reinhardtii205244U66954Japan
D. lateralis strain Nepal212201DQ377089.1USA
Chlorella vulgaris291404KJ756813UK
D. polymorpha213227KJ756825UK

The rbcL sequences of Dunaliella spp_ from the NCBI database

Dunaliella spp.rbcL sizeAccession numberGeographic origin
Dunaliella bardawil strain KMMCC 1346798JQ315489.1Republic of Korea
Dunaliella bardawil UTEX 25381038DQ313194.1USA
D. biocolata strain UTEX 1991038DQ313195.1USA
D. parva1040DQ173091.1Chila
D. peircei strain UTEX LB 2192869DQ313196.1USA
D. primolecta UTEX 10001038DQ313198.1USA
D. acidophila strain CCAP 19/35667HQ142901.1Spain
D. salina strain KMMCC 1428894JQ315491.1Korea
Dunaliella sp. ABRIINW M1/21320KC149893.1Iran
D. salina UTEX 200869DQ313197.1USA
D. salina strain KU07427KF825555.2Thailand
D. salina strain KU11613KF825554.1Thailand
D. salina strain KU13632KF825553.1Thailand
D. salina isolate BAK789KU682279Iran
Dunaliella sp. SAS11133717KF054057.1China
D. pseudosalina isolate MAH799KU641616Iran
D. viridis strain CONC0021038DQ313206.1USA
D. tertiolecta CCMP 3641038DQ313204.1USA
D. tertiolecta UTEX 9991038DQ313203.1USA
Chlamydomonas reinhardtii1128AB511846Japan
Chlorella vulgaris1428AB260909Japan
Asteromonas gracilis469JN033249.1Chile
DOI: https://doi.org/10.1515/ohs-2020-0009 | Journal eISSN: 1897-3191 | Journal ISSN: 1730-413X
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Language: English
Page range: 88 - 98
Submitted on: Jun 7, 2019
Accepted on: Oct 1, 2019
Published on: Mar 6, 2020
Published by: University of Gdańsk
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Keywords:
ITS,
microalgae,
phylogeny,
18S rDNA,
classification
Related subjects:
Chemistry,
Chemistry, other,
Geosciences,
Geosciences, other,
Life sciences,
Life sciences, other

© 2020 Jaber Dehghani, Ehsan Atazadeh, Yadollah Omidi, Ali Movafeghi, published by University of Gdańsk
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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