Leishmania Mitochondrial Genomes: Maxicircle Structure and Heterogeneity of Minicircles
Abstract
:1. Introduction
2. Materials and Methods
2.1. Parasites, DNA Isolation and Illumina Sequencing
2.2. Assembly of Leishmania Maxicircle and Minicircle Sequences From Total DNA NGS Short Reads
2.3. Validation of Assemblies by PCR Amplification
2.4. Phylogenetic Analysis
2.5. Analysis of Conserved Motifs in Leishmania Minicircles by LOGOS Software
2.6. Data Availability
3. Results
3.1. Assembly and Annotation of the L. major Maxicircle
3.2. Assembly and Annotation of the Maxicircles in L. infantum, L. braziliensis and Other Leishmania Species
3.3. Assembly of Minicircle Sequences and Analysis of the Minicircle Populations Existing in L. major, L. infantum and L. braziliensis
3.4. Experimental Validation of In-Silico Assembled Minicircles
3.5. Usefulness of Minicircle and Maxicircles Sequences for Species Identification and Phylogenetic Analysis
4. Discussion
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Coordinates (strand: Plus (+) or minus (−)) | |||
---|---|---|---|
Gene a | L. major | L. infantum | L. braziliensis |
12S rRNA | 1302-2462 (+) | 993-2156 (+) | 815-1974 (+) |
9S rRNA | 2498-3107 (+) | 2181-2790 (+) | 2005-2615 (+) |
ND8 | 3200-3450 (+) | 2885-3198 (+) | 2688-2878 (+) |
ND9 | 3511-3802 (−) | 3185-3524 (−) | 3086-3313 (−) |
MURF5 | 3777-4082 (−) | 3496-3792 (−) | 3333-3632 (−) |
ND7 | 4095-5271 (+) | 3806-4979 (+) | 3650-4802 (+) |
CO3 | 5275-6155 (+) | 4999-5879 (+) | 4884-5719 (+) |
CYb | 6166-7270 (+) | 5889-6998 (+) | 5743-6830 (+) |
ATPase 6 | 7336-7934 (+) | 7061-7660 (+) | 6878-7467 (+) |
ND2 | 7939-9272 (−) | 7665-8996 (−) | 7482-8807 (−) |
G3 | 9232-9397 (+) | 8958-9120 (+) | 8775-8941 (+) |
ND1 | 9361-10302 (−) | 9085-10026 (−) | 8930-9855 (−) |
CO2 | 10311-10939 (+) | 10029-10657 (+) | 9862-10490 (+) |
MURF2 | 10931-12009 (+) | 10649-11728 (+) | 10482-11573 (+) |
CO1 | 12000-13649 (−) | 11719-13368 (−) | 11564-13196 (−) |
G4 | 13698-13861 (−) | 13372-13493 (−) | 13292-13459 (−) |
ND4 | 13987-15299 (+) | 13705-15017 (+) | 13512-14823 (+) |
G5 (ND3) | 15282-15524 (−) | 15000-15218 (−) | 14806-15004 (−) |
RPS12 | 15474-15670 (+) | 15258-15425 (+) | 15036-15191 (+) |
ND5 | 15751-17522 (+) | 15493-17265 (+) | 15253-17024 (+) |
Minicircle Type | Circular | Linear/Partial | Uncertain | Total | ||
---|---|---|---|---|---|---|
Species | Number | Size Range | Mean Size | |||
L. major (Friedlin) | 97 | 660–876 | 691 | 7 | - | 104 |
L. infantum (JPCM5) | 49 | 775–832 | 797 | 28 | 15 | 92 |
L. braziliensis (M2904) | 3 | 741–749 | 744 | 3 | 22 | 28 |
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Camacho, E.; Rastrojo, A.; Sanchiz, Á.; González-de la Fuente, S.; Aguado, B.; Requena, J.M. Leishmania Mitochondrial Genomes: Maxicircle Structure and Heterogeneity of Minicircles. Genes 2019, 10, 758. https://doi.org/10.3390/genes10100758
Camacho E, Rastrojo A, Sanchiz Á, González-de la Fuente S, Aguado B, Requena JM. Leishmania Mitochondrial Genomes: Maxicircle Structure and Heterogeneity of Minicircles. Genes. 2019; 10(10):758. https://doi.org/10.3390/genes10100758
Chicago/Turabian StyleCamacho, Esther, Alberto Rastrojo, África Sanchiz, Sandra González-de la Fuente, Begoña Aguado, and Jose M. Requena. 2019. "Leishmania Mitochondrial Genomes: Maxicircle Structure and Heterogeneity of Minicircles" Genes 10, no. 10: 758. https://doi.org/10.3390/genes10100758