Distribution and Polymorphisms of Group I Introns in Mitochondrial Genes from Cryptococcus neoformans and Cryptococcus gattii
Abstract
:1. Introduction
2. Materials and Methods
2.1. Fungal Isolates and Genotyping
2.2. PCR and Sequencing of the Group I Introns Present in the cob and cox1 Genes of Cryptococcus
2.3. Characterization of the Amplified Group I Introns and Search for Endonuclease Genes
2.4. Phylogenetic Analyses
2.5. Statistical Analyses
3. Results
3.1. Size and Sequence Polymorphism of the Group I Introns from Mitochondrial Genes cob and cox1 among Cryptococcus neoformans and Cryptococcus gattii Genotypes
3.2. Distribution of Group I Introns in the Mitogenome of Cryptococcus neoformans and Cryptococcus gattii
3.3. Phylogenetic Analyses
3.4. Proposal of PCR Reactions for Differentiation of Cryptococcus Species Based on Mitochondrial Group I Introns
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Intron | Forward Primer (5′-3′) | Reverse Primer (5′-3′) |
---|---|---|---|
cob | 1 | COBE1F ATGTTAACTACGGATGGATG | COB1E2R GTACCAATCCAAGGAATAGC |
2 | COB1E2F GCTATTCCTTGGATTGGTAC | COB1E3R CAGAAGGCAAATCGTGTTAG | |
cox1 | 1 | COX1E1F CCAACTATACAATGTAATCGC | COX1E2R TGAAATCATACCRAAACCTGG |
2 | COX1E2F CAGGTTTYGGTATGATTTCAC | COX1E3R GCTGCTGTAAAGTAAGCTCG | |
3 | COX1E3F CGAGCTTACTTTACAGCAGC | COX1E4R ATTGTAAATAGAGCTACAAATCC | |
4 and 5 | COX1E4F GGATTTGTAGCTCTATTTACAAT | COX1E6R GAGGCATTCCAGCTAGTCC |
Sequenced Introns | Classification (RNAweasel) | Homing Endonuclease (Conserved Domain Database) | |||
---|---|---|---|---|---|
Gene | Strain/Genotype | Family | e-Value | Family | HEG Accession/e-Value |
cob | BT8/VG2 (1) | ID | 8.02 × 10−36 | – | – |
CFP61/VGIII (1) | ID | 9.18 × 10−38 | LAGLIDADG | Accession cl03916/E-value 4.32 × 10−14 | |
CFP56/VNII (1) | ID | 4.29 × 10−36 | LAGLIDADG | Accession pfam03161/E-value 6.51 × 10−58 | |
CFP58/VNIV (1) | ID | 4.29 × 10−36 | LAGLIDADG | Accession pfam03161/E-value 7.64 × 10−56 | |
FC4/VNIII (1) | ID | 3.16 × 10−36 | LAGLIDADG | Accession cl03916/E-value 5.31 × 10−12 | |
BT8/VG2 (2) | IA | 1.49 × 10−22 | LAGLIDADG | Accession cl24136/E-value 4.06 × 10−3 | |
CFP58/VNIV (2) | IA | 2.06 × 10−22 | LAGLIDADG | Accession cl24136/E-value 4.09 × 10−3 | |
BT26/VNI (2) | IA | 3.10 × 10−22 | LAGLIDADG | Accession cl24136/E-value 5.12 × 10−3 | |
CFP59/VGI (2) | IA | 3.68 × 10−20 | – | – | |
HGT17/VNI (2) | IA | 1.38 × 10−18 | LAGLIDADG | Accession cl24136/E-value 5.13 × 10−3 | |
cox1 | FC4/VNIII (1) | IB | 2.70 × 10−25 | LAGLIDADG | Accession pfam00961/E-value 2.92 × 10−6 |
BT28/VNIV (1) | IB | 2.70 × 10−25 | LAGLIDADG | Accession pfam00961/E-value 2.92 × 10−6 | |
BT27/VGII (1) | IB | 1.41 × 10−24 | LAGLIDADG | Accession cl08299/E-value 3.83 × 10−7 | |
FC3/VGIII (1) | IB | 2.54 × 10−25 | LAGLIDADG | Accession cl08299/E-value 2.92 × 10−6 | |
CFP56/VNII (2) | IB | 1.48 × 10−22 | LAGLIDADG | Accession pfam14528/E-value 4.26 × 10−4 | |
Fc4/VNIII (2) | IB | 1.48 × 10−22 | LAGLIDADG | Accession pfam14528/E-value 3.20 × 10−4 | |
BT28/VNIV (2) | IB | 9.30 × 10−23 | LAGLIDADG | Accession pfam14528/E-value 1.56 × 10−4 | |
BT27/VGII (2) | IB | 8.97 × 10−20 | LAGLIDADG | Accession pfam14528/E-value 2.75 × 10−4 | |
FC3/VGIII (2) | IB | 8.65 × 10−23 | LAGLIDADG | Accession pfam14528/E-value 1.55 × 10−4 | |
FC9/VGIV (2) | IB | 3.61 × 10−29 | LAGLIDADG LAGLIDADG | Accession pfam00961/E-value 1.67 × 10−12 Accession cl24136/E-value 9.98 × 10−3 | |
LCR2002368/VNI (3) | Similar to IB | 1.52 × 10−29 | LAGLIDADG | Accession cl03916/E-value 1.25 × 10−28 | |
FC4/VNIII (3) | Similar to IB | 5.06 × 10−29 | LAGLIDADG | Accession pfam03161/E-value 1.31 × 10−49 | |
BT28/VNIV (3) | Similar to IB | 5.80 × 10−30 | LAGLIDADG | Accession pfam03161/E-value 5.30 × 10−53 | |
CFP59/VGI (3) | Similar to IB | 5.80 × 10−30 | LAGLIDADG | Accession pfam03161/E-value 2.42 × 10−51 | |
CFP61/VGIII (3) | Similar to IB | 5.68 × 10−31 | – | – | |
FC4/VNIII (4) | Similar to IB | 1.12 × 10−9 | LAGLIDADG | Accession pfam00961/E-value 4.68 × 10−12 | |
BT28/VNIV (4) | Similar to IB | 1.30 × 10−9 | LAGLIDADG | Accession pfam00961/E-value 4.68 × 10−12 | |
CFP59/VGI (4) | Similar to IB | 1.30 × 10−9 | LAGLIDADG LAGLIDADG | Accession pfam00961/E-value 5.67 × 10−13 Accession cl24136/E-value 8.57 × 10−3 | |
BT27/VGII (4) | Similar to IB | 1.98 × 10−7 | LAGLIDADG | Accession pfam00961/E-value 1.07 × 10−11 | |
CN894/VGII (4) | NI | NI | LAGLIDADG | Accession pfam00961/E-value 7.76 × 10−12 | |
FC3/VGIII (4) | NI | NI | LAGLIDADG | Accession pfam00961/E-value 4.80 × 10−12 | |
FC9/VGIV (4) | Similar to IB | 1.37 × 10−9 | LAGLIDADG LAGLIDADG | Accession pfam00961/E-value 5.59 × 10−13 Accession cl24136/E-value 8.49 × 10−3 | |
Fc4/VNIII (5) | IA | 7.78 × 10−17 | – | – | |
BT28/VNIV (5) | IA | 8.84 × 10−17 | – | – | |
CN894/VGII (5) | IA | 2.98 × 10−19 | – | – | |
FC3/VGIII (5) | IA | 9.06 × 10−17 | – | – |
PCR Target | Primer’s Pair | C. neoformans Complex Expected Product Sizes (bp) | |||
C. neoformans | Hybrid | C. deneoformans | |||
VNI | VNII | VNIII | VNIV | ||
mtLSU * | CryLSUF/CryLSUR | 300 or 1300 | 1300 | 2000 or 2500 | 300 or 1900 |
introns 4 and 5 of cox1 | COX1E4F/COX1E6R | 300 | 300 | 1600 | 1600 |
PCR Target | Primer’s Pair | C. gattii Complex Expected Product Sizes (bp) | |||
C. gattii | C. deuterogattii | C. bacillosporus | C. tetragattii | ||
VGI | VGII | VGIII | VGIV | ||
mtLSU * | CryLSUF/CryLSUR | 300 or 1100 | 300 | 1800 | 1300 |
intron 1 of cob | COBE1F/COB1E2R | 1200 | 250 or 600 | 250 or 1200 | 250 |
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Gomes, R.M.O.d.S.; da Silva, K.J.G.; Ferreira, L.C.; Arantes, T.D.; Theodoro, R.C. Distribution and Polymorphisms of Group I Introns in Mitochondrial Genes from Cryptococcus neoformans and Cryptococcus gattii. J. Fungi 2023, 9, 629. https://doi.org/10.3390/jof9060629
Gomes RMOdS, da Silva KJG, Ferreira LC, Arantes TD, Theodoro RC. Distribution and Polymorphisms of Group I Introns in Mitochondrial Genes from Cryptococcus neoformans and Cryptococcus gattii. Journal of Fungi. 2023; 9(6):629. https://doi.org/10.3390/jof9060629
Chicago/Turabian StyleGomes, Ronald Muryellison Oliveira da Silva, Kássia Jéssica Galdino da Silva, Leonardo Capistrano Ferreira, Thales Domingos Arantes, and Raquel Cordeiro Theodoro. 2023. "Distribution and Polymorphisms of Group I Introns in Mitochondrial Genes from Cryptococcus neoformans and Cryptococcus gattii" Journal of Fungi 9, no. 6: 629. https://doi.org/10.3390/jof9060629