Comparative Evolution of S7 Intron 1 and Ribosomal Internal Transcribed Spacer in Coilia nasus (Clupeiformes: Engraulidae)
Abstract
:1. Introduction
2. Results and Discussion
2.1. Results
2.1.1. Composition and Variation of rpS7 Intron 1
2.1.2. Compositional Information of ITS1
2.1.3. Phylogenetic Analysis of rpS7 Gene
2.1.4. Mitochondrial COI Molecular Variety
2.2. Discussion
3. Experimental Section
3.1. Sample Collection
3.2. DNA Extraction, PCR Amplification, Cloning, and Sequencing
3.3. Molecular Data Analysis
4. Conclusions
Acknowledgments
References
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Sequence | Frequency | Haplotype | |
---|---|---|---|
Code | 0000000001111111112222222233333344444444444555555555555566666666677777 | ||
5555577880015568990113459934566912233668899000011233456900113344812234 | |||
2567856171930927561485444627616220556057938346907548233347461801121943 | |||
JJ1a | tgtggattttacttcgacttgttaatttacccaagatatacattaggattgctctatactaaacacttga | 2 | H1 |
JJ1b | a a . . . . c . . . . a . . t . . . . . . . . . . c . . . g . . . . . c . g . . . . . g . a . . . . . . a . c . . . . . . . . . g . . . c . | 3 | H2 |
JJ2a | . . . . . c . . . . . . . . . . . . . . . c . . g . . . . . . . . . . . . . . . . . . . . . . . c . . . . . . . . . . . . . . . g . . c c . | 1 | H3 |
JJ2b | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . g . . . . . . . . . . . . c . . . g . . g t . . c . | 2 | H4 |
JJ3 | . . . . . . . . . . . . . c . . . . . . . . a . . . . . . . t . . . . c c . . . . . . . . . . . . . . . . . . . . c t . . . . . g . . . c . | 3 | H5 |
JJ4 | a a . . . . c . . . . a . . t . . . . . . . . . . c . . . . . . . . . c . g . . . . . g . a - - . . . . . t . . . . . . . . . t g . . . c . | 2 | H6 |
JJ5a | a . . . t . . . . . . a . . . . . . . . . . . . . c . . . . . - . . . c . g . . . g . g . a . . . . . . . . . . . . . . . . . . g . . . c g | 2 | H7 |
JJ5b | a a . . . . c . . . . a . . t . . . . . . . . . . c . . . . . . . . . c . g . . . . . g . a - - . c . . . t . . . . . . . . . t g . . . c . | 2 | H8 |
PY1 | a . . . t . . . . . . a . . . . . . . . . . . . . c . . . . . - . . . c . g . . . . . g . a . . . . . . . . . . a . . . . . . . g . . . c . | 3 | H9 |
PY2 | a a . . . . c . . a . a a . t . . . c c . . . . . c . c . g . . . . . c . g . . . . . g . a . . . . . . . . c g . . . . . . . . g . . . c . | 2 | H10 |
PY3a | a . . . t . . c . . . a . . . . . . . . . . . . . c . . . . . - . . . c . g . . . . c g . a . . . . . . . . . . . . . . . . - . g . . . c . | 2 | H11 |
PY3b | a . . . t . . . . . . a . . . . . . . . . . . . . c . . . . . - . . . c . g . . . . . g . a . . . . . . . . . . . . . . . . . . g . . . c . | 5 | H12 |
PY4 | a . . . t . . . . . . a . . . . . . . . . . c . . c . . . . . - . . . c . g . . . . . g . a . . . . . . . . . . a . . c . . . . g . . . c . | 6 | H13 |
TH1a | . . - - . . . . . . . . . . . . . . . . a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . c . . . . . . g . . . c . | 2 | H14 |
TH1b | . . . . . . . . . . g . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . t . . . . . c . . g . . . g . . . c . | 1 | H15 |
TH2 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . c . . . . . . g . c . c . | 3 | H16 |
TH3 | . . . . . . . . . . . . . . . . . . . . . . . . . . . . g . . . . . . . . . . . . . . . . . . g . . . . . . . . . c . . . . . . g . . . c . | 3 | H17 |
TH4 | . . - - . . . . . . . . . . . . . . . . . . . . . . c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . c . . . . . . g . . . c . | 5 | H18 |
TH5b | . . . . . . . . c . g . . . . . . . . . . . . t . . . . . . . . . . . . . . . g t . . . . . . . . . . . . . . . . c . . . . . . g . . . c . | 2 | H19 |
TH6a | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . c . . . . . . . . . . . . . . . . . . . . . c t . . . . . g . . . c . | 3 | H20 |
TH6b | . . . . . . . . . . . . . . . - . . . . . . . . . c . . . . . . . . . c . . c . . . . . . . . . . . a . . . . . . c t . . . . . g . . . c . | 2 | H21 |
YE1 | a a . . . . c . . . . a . . t . . . . . . . . . . c . . . g . . . . . c . g . . . . . g . a . . . . . . . . c . . . . . . . . . g . . . c . | 3 | H22 |
YE2 | a a . . . . c . . . . a a . t . . . . . . . . . . c . . . g . . . . . c . g . . . . . g . a . . . . . . . . c . . . . . . . . . g . . . c . | 3 | H23 |
XS1b | a . . . . . . . . . . a . . . . - - . . . . . . . c . . . . . . g . . c . . . . . . . . . . . . . . . . . . . . . c . . . . . . . . . . c . | 2 | H24 |
XS2b | a a . . . . c . . . . a . . t . . . . . . . . . . c . . . . . . . . . c . g . . . . . g . a - - . . . . . t . . . . . . . . . t g . c . c . | 2 | H25 |
WH1 | a a . . . . c . . . . a . . t . . . . . . . . . . a . . . . . . . g . c . g . . . . . g . a . . . . . . . . . . . . . . . . . . g . . . c . | 3 | H26 |
WH2 | a a . . . . c . . . . a . . t . . . . . . . . . . c . . . g . . . . t c . g . . . . . g . a . . . . . . . . . . . . . . . . . . g . . . c . | 3 | H27 |
WH4 | a . . . . . . . . . . a . . . . - - . . . . . . . c . . . . . . g . . c . . . . . . . . . . . . . . . . . . . . . c . . . . . . g . . . . . | 6 | H28 |
AS | . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . c . . . . . . g . . . c . | 15 | H29 |
Position | 52 | 113 | 296 | 435 | ||
---|---|---|---|---|---|---|
Parent | AS(5) * | T | C | T | A | |
TH(5) * | T | C | T | A | ||
Hybrid | JJ1 | a | T | C | T | A |
b | A | A | C | C | ||
JJ6 | a | T | C | T | A | |
b | A | A | C | C | ||
Hybrid | XS1 | a | T | C | T | A |
b | A | A | C | C | ||
XS2 | a | T | C | T | A | |
b | A | A | C | C | ||
Parent | PY(6) * | A | A | C | C |
Nucleotide Composition (%) | Variable Sites | Haplotypes | AMOVA (%) | ||||||
---|---|---|---|---|---|---|---|---|---|
A + T | G + C | single | parsi | indel | H | Hd | among | within | |
rpS7 | 56.5 | 43.5 | 35 | 26 | 9 | 29 | 0.76 | 29.9 | 70.1 |
ITS1 | 31.8 | 68.2 | 21 | 2 | 18 | 29 | 0.69 | 10.3 | 89.7 |
COI | 55.5 | 45.5 | 4 | 6 | 0 | 9 | 0.68 | 1.9 | 98.1 |
Nucleotide Diversity | Trans/Transv | Neutrality Tests | |||||||
among | within | s | v | s/v | Taj D | P * | Fu | P * | |
rpS7 | 0.013–0.017 | 0.013 | 45 | 16 | 2.8 | −1.328 | N | −2.377 | N |
ITS1 | 0.003–0.009 | 0.006 | 16 | 9 | 1.8 | −2.263 | Y | −2.377 | N |
COI | 0.001–0.005 | 0.003 | 8 | 2 | 4.0 | −1.070 | N | −1.018 | N |
Repeats | Sequence Position | Region of Secondary Structure |
---|---|---|
(CT)5–8CC(CT)3 | 96–121 | 4th internal loop |
(CT)8 | 96–111 | 4th internal loop |
(CCAAA)1–2 | 281–297 | 2th internal loop |
Primer | Gene | Sequence (5′-3′) | Source |
---|---|---|---|
S7RPEX2R | rpS7-1 | TGGCCTCTTCCTTGGCCGTC | Reference [6] |
S7RPEX2R | rpS7-1 | AACTCGTCTGGCTTTTCGCC | Reference [6] |
ITS1F | ITS1 | AGGTGAACCTGCGGAAGG | Present study |
ITS2R | ITS1 | TGATCCACCGCTAAGAGTTGTA | Present study |
COIBF | COI | TGGCAATYACACGTTGATTYT | Present study |
COIBR | COI | TTHCCBGCRTRRTARGCTACRA | Present study |
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Liu, D.; Guo, H.-Y.; Tang, W.-Q.; Yang, J.-Q. Comparative Evolution of S7 Intron 1 and Ribosomal Internal Transcribed Spacer in Coilia nasus (Clupeiformes: Engraulidae). Int. J. Mol. Sci. 2012, 13, 3085-3100. https://doi.org/10.3390/ijms13033085
Liu D, Guo H-Y, Tang W-Q, Yang J-Q. Comparative Evolution of S7 Intron 1 and Ribosomal Internal Transcribed Spacer in Coilia nasus (Clupeiformes: Engraulidae). International Journal of Molecular Sciences. 2012; 13(3):3085-3100. https://doi.org/10.3390/ijms13033085
Chicago/Turabian StyleLiu, Dong, Hong-Yi Guo, Wen-Qiao Tang, and Jin-Quan Yang. 2012. "Comparative Evolution of S7 Intron 1 and Ribosomal Internal Transcribed Spacer in Coilia nasus (Clupeiformes: Engraulidae)" International Journal of Molecular Sciences 13, no. 3: 3085-3100. https://doi.org/10.3390/ijms13033085