The Coding Mitogenome of the Freshwater Crayfish Pontastacus leptodactylus (Decapoda:Astacidea:Astacidae) from Lake Vegoritida, Greece and Its Taxonomic Classification
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Genome Composition
3.2. Protein-Coding Genes, tRNAs, and rRNAs
3.3. Phylogenetic Analysis
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Primer Set | Name | Sequence | Tm (°C) | Product Length (bp) | Genes Included |
---|---|---|---|---|---|
1 | MtAst1F MtAst1R | 5′ CAAATCATAAAGATATTGGAAC 3′ 5′ AATGTTGRGGRAAGAATGT 3′ | 49 | 1259 | coxI partial |
2 | MtAst2F MtAst2R | 5′ CAGTKGGRGGTTTAACAGGAG 3′ 5′ GTTATCRRGTGATTATTCTGAAC 3′ | 54 | 1255 | coxI (partial) trnL2 coxII trnK (partial) |
3 | MtAst3F MtAst3R | 5′ CATTCTTGAACTGTACCTTC 3′ 5′ CTACTAAATGATATGCATGGTG 3′ | 52 | 1201 | coxII (partial) trnK trnD atp8 atp6 coxIII (partial) |
4 | MtAst4.2F MtAst4.2R | 5′ GCTGTTGCAATTATTCAGTC 3′ 5′ CCAAAGGTATAAGAAGMGTA 3′ | 50 | 1394 | atp6 (partial) coxIII trnG nad3 (partial) |
5 | MtAst5F MtAst5R | 5′ GGCTTCCAACCAAAAGGTC 3′ 5′ AGTWTAACCGCGACTGCTG 3′ | 49 | ~1500–2000 | D-loop |
6 | MtAst6F MtAst6R | 5′ GAATTTAACCGCTCAAGAAC 3′ 5′ CCTAACTATTTCTCTTCCGAG 3′ | 52 | 1287 | trnN rrnS trnV rrnL (partial) |
7 | MtAst7F MtAst7R | 5′ AGCATCTCATTTACACCGA 3′ 5′ ABTCBAACATGTCTAAGCATC 3′ | 51 | 1424 | rrnL trnL1 nad1 (partial) |
8 | MtAst8F MtAst8R | 5′ TACTTTAGGGATAACAGCGTA 3′ 5′ GGTCAAATTCTTTCACTCCT 3′ | 52 | 1502 | rrnL (partial) trnL1 nad1 trnP trnS2 cytb (partial) |
9 | MtAst9F MtAst9R | 5′ TACCTCGGTTTCGTTATGA 3′ 5′ ATACYCCYAATATTGAATCAG 3′ | 51 | 1243 | nad1 (partial) trnP trnS2 cytb (partial) |
10 | MtAst10F MtAst10R | 5′ GACCTCARGGTAAGACATATC 3′ 5′ TCTCTCCCTAAYTGATTTCC 3′ | 54 | 1463 | cytb (partial) nad6 trnT nad4l |
11 | MtAst11F MtAst11R | 5′ GTCCGCTCRCARGGTAATG 3′ 5′ AAAGGAAGYCAATGAAGAC 3′ | 51 | 1339 | nad4l (partial) nad4 trnH (partial) |
12 | MtAst12F MtAst12R | 5′ GTCATGGTTTATGTTCATCTG 3′ 5′ ACTCAAAATTAGCTCCRAGC 3′ | 52 | 1285 | nad4l (partial) nad4 trnH nad5 (partial) |
13 | MtAst13F MtAst13R | 5′ CGTGTCRGCATTAGTACATTC 3′ 5′ CCCCAAAYCAAGAATTTGAAG 3′ | 54 | 1377 | nad5 (partial) trnF trnI trnM nad2 (partial) |
14 | MtAst14F MtAst14R | 5′ CTACATTGAAGCTGTAGAAGAG 3′ 5′ TTTGACAACTTTGAAGGATG 3′ | 51 | 1213 | trnW (partial) nad2 trnW (partial) |
15 | MtAst15F MtAst15R | 5′ TCAGCAGGCCTATCATTT 3′ 5′ CAAAAGCATGAGCAGTTACTAC 3′ | 51 | 668 | nad2 (partial) trnW trnC trnY coxI (partial) |
Position | Gene | Name | Strand | Start Codon | Stop Codon | Anticodon | Gene Length/bp |
---|---|---|---|---|---|---|---|
1–1537 | Cytochrome c oxidase subunit 1 | cox1 | + | ATT | TTA | 1537 | |
1539–1601 | tRNA | trnL2 | + | TAA | 63 | ||
1602–2288 | Cytochrome c oxidase subunit 2 | cox2 | + | ATG | TAA | 687 | |
2290–2353 | tRNA | trnK | + | TTT | 64 | ||
2355–2420 | tRNA | trnD | + | GTC | 66 | ||
2421–2579 | ATP synthase F0 subunit 8 | atp8 | + | GTG | TAG | 159 | |
2573–3247 | ATP synthase F0 subunit 6 | atp6 | + | ATG | TAA | 675 | |
3247–4035 | Cytochrome c oxidase subunit 3 | cox3 | + | ATG | TAA | 789 | |
4034–4095 | tRNA | trnG | + | TCC | 62 | ||
4096–4449 | NADH dehydrogenase subunit 3 | nad3 | + | ATT | TAA | 354 | |
4451–4512 | tRNA | trnA | + | TGC | 62 | ||
4511–4575 | tRNA | trnR | + | TCG | 65 | ||
4576-4645 | tRNA | trnE | + | TTC | 70 | ||
~1500–2000 base pairs | Gap | dloop | |||||
4858–4926 | tRNA | trnQ | − | TTG | 69 | ||
4935–5001 | tRNA | trnS1 | − | TCT | 67 | ||
5002–5065 | tRNA | trnN | − | GTT | 64 | ||
5143–5956 | rRNA | rrnS | + | 814 | |||
5959–6027 | tRNA | trnV | + | TAC | 69 | ||
5993–7371 | rRNA (partial) | rrnL | + | 1379 | |||
7318–7380 | tRNA | trnL1 | + | TAG | 63 | ||
7405–8343 | NADH dehydrogenase subunit 1 | nad1 | + | ATA | TAA | 939 | |
8363–8424 | tRNA | trnP | + | TGG | 62 | ||
8429–8495 | tRNA | trnS2 | − | TGA | 67 | ||
8496–9630 | Cytochrome b | cytb | − | ATG | ATT | 1135 | |
9630–10,139 | NADH dehydrogenase subunit 6 | nad6 | − | ATT | TAA | 510 | |
10,167–10,232 | tRNA | trnT | − | TGT | 66 | ||
10,235–10,528 | NADH dehydrogenase subunit 4 | nad4L | + | ATG | TAA | 294 | |
10,525–11,871 | NADH dehydrogenase subunit 4 | nad4 | + | ATA | TAA | 1347 | |
11,871–11,932 | tRNA | trnH | + | GTG | 62 | ||
11,933–13,666 | NADH dehydrogenase subunit 5 | nad5 | + | ATG | TAA | 1734 | |
13,666–13,727 | tRNA | trnF | + | GAA | 62 | ||
13,735–13,798 | tRNA | trnI | + | GAT | 64 | ||
13,798–13,862 | tRNA | trnM | + | CAT | 65 | ||
13,863–14,855 | NADH dehydrogenase subunit 2 | nad2 | + | GTG | TAA | 993 | |
14,855–14,921 | tRNA | trnW | + | TCA | 67 | ||
14,923–14,986 | tRNA | trnC | − | GCA | 64 | ||
14,987–15,050 | tRNA | trnY | − | GTA | 64 |
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Alvanou, M.V.; Apostolidis, A.P.; Lattos, A.; Michaelidis, B.; Giantsis, I.A. The Coding Mitogenome of the Freshwater Crayfish Pontastacus leptodactylus (Decapoda:Astacidea:Astacidae) from Lake Vegoritida, Greece and Its Taxonomic Classification. Genes 2023, 14, 494. https://doi.org/10.3390/genes14020494
Alvanou MV, Apostolidis AP, Lattos A, Michaelidis B, Giantsis IA. The Coding Mitogenome of the Freshwater Crayfish Pontastacus leptodactylus (Decapoda:Astacidea:Astacidae) from Lake Vegoritida, Greece and Its Taxonomic Classification. Genes. 2023; 14(2):494. https://doi.org/10.3390/genes14020494
Chicago/Turabian StyleAlvanou, Maria V., Apostolos P. Apostolidis, Athanasios Lattos, Basile Michaelidis, and Ioannis A. Giantsis. 2023. "The Coding Mitogenome of the Freshwater Crayfish Pontastacus leptodactylus (Decapoda:Astacidea:Astacidae) from Lake Vegoritida, Greece and Its Taxonomic Classification" Genes 14, no. 2: 494. https://doi.org/10.3390/genes14020494