Integrative Taxonomy Reveals New Insights into the Species Validity of the Neocaridina davidi-N. denticulata-N. heteropoda Complex and Mitogenomic Phylogeny of Caridean Shrimps
Abstract
:1. Introduction
2. Materials and Methods
2.1. Specimen Collection and Morphological Examination
2.2. Mitogenome Assembly and Annotation
2.3. Phylogenetic Analysis
2.4. Gene Order Analysis
3. Results
3.1. Morphological Classification
3.2. Organization and Characterization of Mitogenomes
3.3. Genetic Distances
3.4. Phylogenetic Analysis
3.5. Mitochondrial Gene Order and Rearrangements
4. Discussion
4.1. Morphological Differences
4.2. Genetic Distances and Species Validity
4.3. Mitogenomic Phylogeny
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Strand | Position | Size | Codon | Intergenic Nucleotides | |||
---|---|---|---|---|---|---|---|---|
From | To | Start | Stop | Anticodon | ||||
cox1 | H | 1/1/1 | 1536/1536/1536 | 1536/1536/1536 | ATG/ATG/ATG | TAA/TAA/TAA | 0/0/0 | |
trnL2 | H | 1539/1539/1539 | 1602/1602/1602 | 64/64/64 | TAA/TAA/TAA | 2/2/2 | ||
cox2 | H | 1604/1604/1604 | 2291/2291/2291 | 688/688/688 | ATG/ATG/ATG | T--/T--/T-- | 1/1/1 | |
trnK | H | 2292/2292/2292 | 2359/2359/2359 | 68/68/68 | TTT/TTT/TTT | 0/0/0 | ||
trnD | H | 2365/2368/2368 | 2431/2435/2435 | 67/68/68 | GTC/GTC/GTC | 5/8/8 | ||
atp8 | H | 2432/2436/2436 | 2590/2594/2594 | 159/159/159 | ATC/ATT/ATT | TAA/TAA/TAA | 0/0/0 | |
atp6 | H | 2584/2588/2588 | 3258/3262/3262 | 675/675/675 | ATG/ATG/ATG | TAA/TAA/TAA | −7/−7/−7 | |
cox3 | H | 3258/3262/3262 | 4043/4047/4047 | 786/786/786 | ATG/ATG/ATG | TAG/TAG/TAG | −1/−1/−1 | |
trnG | H | 4047/4051/4051 | 4110/4115/4115 | 64/65/65 | TCC/TCC/TCC | 3/3/3 | ||
nad3 | H | 4111/4116/4116 | 4464/4469/4469 | 354/354/354 | ATC/ATC/ATC | TAA/TAA/TAA | 0/0/0 | |
trnA | H | 4463/4468/4468 | 4526/4531/4531 | 64/64/64 | TGC/TGC/TGC | −2/−2/−2 | ||
trnR | H | 4527/4532/4532 | 4589/4594/4594 | 63/63/63 | TCG/TCG/TCG | 0/0/0 | ||
trnN | H | 4594/4599/4599 | 4660/4665/4665 | 67/67/67 | GTT/GTT/GTT | 4/4/4 | ||
trnS1 | H | 4661/4666/4666 | 4727/4732/4732 | 67/67/67 | TCT/TCT/TCT | 0/0/0 | ||
trnE | H | 4728/4733/4733 | 4795/4800/4800 | 68/68/68 | TTC/TTC/TTC | 0/0/0 | ||
trnF | L | 4794/4799/4799 | 4859/4864/4864 | 66/66/66 | GAA/GAA/GAA | −2/−2/−2 | ||
nad5 | L | 4860/4865/4865 | 6587/6592/6592 | 1728/1728/1728 | ATG/ATG/ATG | TAA/TAA/TAA | 0/0/0 | |
trnH | L | 6588/6593/6593 | 6653/6658/6658 | 66/66/66 | GTG/GTG/GTG | 0/0/0 | ||
nad4 | L | 6654/6659/6659 | 7992/7997/7997 | 1339/1339/1339 | ATG/ATG/ATG | T--/T--/T-- | 0/0/0 | |
nad4l | L | 7986/7991/7991 | 8288/8293/8293 | 303/303/303 | ATG/ATG/ATG | TAA/TAA/TAA | −7/−7/−7 | |
trnT | H | 8291/8296/8296 | 8356/8361/8361 | 66/66/66 | TGT/TGT/TGT | 2/2/2 | ||
trnP | L | 8357/8362/8362 | 8422/8427/8426 | 66/66/65 | TGG/TGG/TGG | 0/0/0 | ||
nad6 | H | 8425/8430/8429 | 8940/8945/8944 | 516/516/516 | ATT/ATT/ATT | TAA/TAA/TAA | 2/2/2 | |
cob | H | 8940/8945/8944 | 10076/10081/10080 | 1137/1137/1137 | ATG/ATG/ATG | TAG/TAG/TAG | −1/−1/−1 | |
trnS2 | H | 10075/10080/10079 | 10144/10149/10148 | 70/70/70 | TGA/TGA/TGA | −2/−2/−2 | ||
nad1 | L | 10163/10168/10167 | 11104/11109/11108 | 942/942/942 | ATT/ATT/ATT | TAA/TAA/TAA | 18/18/18 | |
trnL1 | L | 11129/11134/11133 | 11196/11200/11199 | 68/67/67 | TAG/TAG/TAG | 24/24/24 | ||
rrnL | L | 11197/11201/11200 | 12530/12534/12530 | 1334/1334/1331 | 0/0/0 | |||
trnV | L | 12531/12535/12531 | 12597/12601/12597 | 67/67/67 | TAC/TAC/TAC | 0/0/0 | ||
rrnS | L | 12598/12602/12598 | 13458/13463/13459 | 861/862/862 | 0/0/0 | |||
CR | H | 13459/13464/13460 | 14137/14142/14137 | 679/679/678 | 0/0/0 | |||
trnI | H | 14138/14143/14138 | 14202/14207/14202 | 65/65/65 | GAT/GAT/GAT | 0/0/0 | ||
trnQ | L | 14211/14216/14211 | 14278/14283/14278 | 68/68/68 | TTG/TTG/TTG | 8/8/8 | ||
trnM | H | 14284/14289/14284 | 14349/14354/14349 | 66/66/66 | CAT/CAT/CAT | 5/5/5 | ||
nad2 | H | 14350/14355/14350 | 15354/15359/15354 | 1005/1005/1005 | ATT/ATT/ATT | TAA/TAA/TAA | 0/0/0 | |
trnW | H | 15353/15358/15353 | 15422/15427/15423 | 70/70/71 | TCA/TCA/TCA | −2/−2/−2 | ||
trnC | L | 15422/15427/15423 | 15486/15491/15487 | 65/65/65 | GCA/GCA/GCA | −1/−1/−1 | ||
trnY | L | 15487/15492/15488 | 15553/15558/15554 | 67/67/67 | GTA/GTA/GTA | 0/0/0 |
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Yang, M.; Cui, X.; Li, X.; Dong, D.; Kang, X.; Gan, Z. Integrative Taxonomy Reveals New Insights into the Species Validity of the Neocaridina davidi-N. denticulata-N. heteropoda Complex and Mitogenomic Phylogeny of Caridean Shrimps. Curr. Issues Mol. Biol. 2024, 46, 12279-12298. https://doi.org/10.3390/cimb46110729
Yang M, Cui X, Li X, Dong D, Kang X, Gan Z. Integrative Taxonomy Reveals New Insights into the Species Validity of the Neocaridina davidi-N. denticulata-N. heteropoda Complex and Mitogenomic Phylogeny of Caridean Shrimps. Current Issues in Molecular Biology. 2024; 46(11):12279-12298. https://doi.org/10.3390/cimb46110729
Chicago/Turabian StyleYang, Mei, Xiaodong Cui, Xinzheng Li, Dong Dong, Xianjiang Kang, and Zhibin Gan. 2024. "Integrative Taxonomy Reveals New Insights into the Species Validity of the Neocaridina davidi-N. denticulata-N. heteropoda Complex and Mitogenomic Phylogeny of Caridean Shrimps" Current Issues in Molecular Biology 46, no. 11: 12279-12298. https://doi.org/10.3390/cimb46110729