Reanalysis and Revision of the Complete Mitochondrial Genome of <i>Artemia urmiana</i> Günther, 1899 (Crustacea: Anostraca)
In the previously published mitochondrial genome sequence of <i>Artemia urmiana</i> (NC_021382 [JQ975176]), the taxonomic status of the examined <i>Artemia</i> had not been determined, due to parthenogenetic populations coexisting with <i>A. urmiana</i> in Urmia L...
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2021-01-01
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| author | Alireza Asem Amin Eimanifar Weidong Li Chun-Yang Shen Farnaz Mahmoudi Shikhsarmast Ya-Ting Dan Hao Lu Yang Zhou You Chen Pei-Zheng Wang Michael Wink |
| author_facet | Alireza Asem Amin Eimanifar Weidong Li Chun-Yang Shen Farnaz Mahmoudi Shikhsarmast Ya-Ting Dan Hao Lu Yang Zhou You Chen Pei-Zheng Wang Michael Wink |
| author_sort | Alireza Asem |
| collection | DOAJ |
| description | In the previously published mitochondrial genome sequence of <i>Artemia urmiana</i> (NC_021382 [JQ975176]), the taxonomic status of the examined <i>Artemia</i> had not been determined, due to parthenogenetic populations coexisting with <i>A. urmiana</i> in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of <i>Artemia</i> (0.25 g cysts consists of 20,000–25,000 cysts), not a single specimen. With regard to coexisting populations in Urmia Lake, and intra- and inter-specific variations in the pooled samples, NC_021382 [JQ975176] cannot be recommended as a valid sequence and any attempt to attribute it to <i>A. urmiana</i> or a parthenogenetic population is unreasonable. With the aid of next-generation sequencing methods, we characterized and assembled a complete mitochondrial genome of <i>A. urmiana</i> with defined taxonomic status. Our results reveal that in the previously published mitogenome (NC_021382 [JQ975176]), tRNA-Phe has been erroneously attributed to the heavy strand but it is encoded in the light strand. There was a major problem in the position of the ND5. It was extended over the tRNA-Phe, which is biologically incorrect. We have also identified a partial nucleotide sequence of 311 bp that was probably erroneously duplicated in the assembly of the control region of NC_021382 [JQ975176], which enlarges the control region length by 16%. This partial sequence could not be recognized in our assembled mitogenome as well as in 48 further examined specimens of <i>A. urmiana</i>. Although, only COX1 and 16S genes have been widely used for phylogenetic studies in <i>Artemia</i>, our findings reveal substantial differences in the nucleotide composition of some other genes (including ATP8, ATP6, ND3, ND6, ND1 and COX3) among <i>Artemia</i> species. It is suggested that these markers should be included in future phylogenetic studies. |
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| issn | 1424-2818 |
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| last_indexed | 2024-03-10T13:30:58Z |
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| spelling | doaj.art-6ac628f525604252888b86dc2feed5d32023-11-21T08:00:17ZengMDPI AGDiversity1424-28182021-01-011311410.3390/d13010014Reanalysis and Revision of the Complete Mitochondrial Genome of <i>Artemia urmiana</i> Günther, 1899 (Crustacea: Anostraca)Alireza Asem0Amin Eimanifar1Weidong Li2Chun-Yang Shen3Farnaz Mahmoudi Shikhsarmast4Ya-Ting Dan5Hao Lu6Yang Zhou7You Chen8Pei-Zheng Wang9Michael Wink10Key Laboratory of Utilization and Protection of Tropical Marine Living Resources, Hainan Tropical Ocean University, Sanya 572000, ChinaIndependent Senior Scientist, Industrial District, Easton, MD 21601, USACollege of Ecology and Environment, Hainan Tropical Ocean University, Haikou 570000, ChinaDepartment of Biology, Chengde Medical University, Chengde 067000, ChinaKey Laboratory of Utilization and Protection of Tropical Marine Living Resources, Hainan Tropical Ocean University, Sanya 572000, ChinaCollege of Marine Science, Shanghai Ocean University, Shanghai 200000, ChinaKey Laboratory of Utilization and Protection of Tropical Marine Living Resources, Hainan Tropical Ocean University, Sanya 572000, ChinaInstitute of Deep Sea Science and Engineering, Chinese Academy of Science, Sanya 572000, ChinaKey Laboratory of Utilization and Protection of Tropical Marine Living Resources, Hainan Tropical Ocean University, Sanya 572000, ChinaKey Laboratory of Utilization and Protection of Tropical Marine Living Resources, Hainan Tropical Ocean University, Sanya 572000, ChinaInstitute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, GermanyIn the previously published mitochondrial genome sequence of <i>Artemia urmiana</i> (NC_021382 [JQ975176]), the taxonomic status of the examined <i>Artemia</i> had not been determined, due to parthenogenetic populations coexisting with <i>A. urmiana</i> in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of <i>Artemia</i> (0.25 g cysts consists of 20,000–25,000 cysts), not a single specimen. With regard to coexisting populations in Urmia Lake, and intra- and inter-specific variations in the pooled samples, NC_021382 [JQ975176] cannot be recommended as a valid sequence and any attempt to attribute it to <i>A. urmiana</i> or a parthenogenetic population is unreasonable. With the aid of next-generation sequencing methods, we characterized and assembled a complete mitochondrial genome of <i>A. urmiana</i> with defined taxonomic status. Our results reveal that in the previously published mitogenome (NC_021382 [JQ975176]), tRNA-Phe has been erroneously attributed to the heavy strand but it is encoded in the light strand. There was a major problem in the position of the ND5. It was extended over the tRNA-Phe, which is biologically incorrect. We have also identified a partial nucleotide sequence of 311 bp that was probably erroneously duplicated in the assembly of the control region of NC_021382 [JQ975176], which enlarges the control region length by 16%. This partial sequence could not be recognized in our assembled mitogenome as well as in 48 further examined specimens of <i>A. urmiana</i>. Although, only COX1 and 16S genes have been widely used for phylogenetic studies in <i>Artemia</i>, our findings reveal substantial differences in the nucleotide composition of some other genes (including ATP8, ATP6, ND3, ND6, ND1 and COX3) among <i>Artemia</i> species. It is suggested that these markers should be included in future phylogenetic studies.https://www.mdpi.com/1424-2818/13/1/14brine shrimp<i>Artemia</i>mitochondrial genomephylogenynucleotide compositionmaternal ancestor |
| spellingShingle | Alireza Asem Amin Eimanifar Weidong Li Chun-Yang Shen Farnaz Mahmoudi Shikhsarmast Ya-Ting Dan Hao Lu Yang Zhou You Chen Pei-Zheng Wang Michael Wink Reanalysis and Revision of the Complete Mitochondrial Genome of <i>Artemia urmiana</i> Günther, 1899 (Crustacea: Anostraca) Diversity brine shrimp <i>Artemia</i> mitochondrial genome phylogeny nucleotide composition maternal ancestor |
| title | Reanalysis and Revision of the Complete Mitochondrial Genome of <i>Artemia urmiana</i> Günther, 1899 (Crustacea: Anostraca) |
| title_full | Reanalysis and Revision of the Complete Mitochondrial Genome of <i>Artemia urmiana</i> Günther, 1899 (Crustacea: Anostraca) |
| title_fullStr | Reanalysis and Revision of the Complete Mitochondrial Genome of <i>Artemia urmiana</i> Günther, 1899 (Crustacea: Anostraca) |
| title_full_unstemmed | Reanalysis and Revision of the Complete Mitochondrial Genome of <i>Artemia urmiana</i> Günther, 1899 (Crustacea: Anostraca) |
| title_short | Reanalysis and Revision of the Complete Mitochondrial Genome of <i>Artemia urmiana</i> Günther, 1899 (Crustacea: Anostraca) |
| title_sort | reanalysis and revision of the complete mitochondrial genome of i artemia urmiana i gunther 1899 crustacea anostraca |
| topic | brine shrimp <i>Artemia</i> mitochondrial genome phylogeny nucleotide composition maternal ancestor |
| url | https://www.mdpi.com/1424-2818/13/1/14 |
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