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Phylogenetic Relationship among the Wild Rice [Oryza rufipogon Griff.] of NBU Campus and Cultivated Rice as Revealed by Chloroplast matK Gene
- Subhas Chandra Roy
- Genetic variation and phylogenetic relationship was carried out in Asian common wild rice and cultivated rice using chloroplast matK gene sequence information. The matK gene was PCR amplified from Asian common wild rice (Oryza rufipogon Griff.) of NBU campus using specific primer and sequenced based on Sanger method. The matK gene sequence of 1420 bp was deposited in the NCBI GenBank with Accession No-KM516199. Fifteen others matK sequences were retrieved from NCBI Genbank and analysed for phylogenetic relationship using bioinformatics algorithm. All the matK sequences are aligned in ClustalX2 and aligned sequence fragments were 1201 with 7.09% variable and 4.79% phylogenetically informative sites and the estimated transition/transversion bias (R) was 1.65. Substitution pattern and rates were estimated under the Kimura (1980) 2-parameter model in MEGA6. Sites with alignment gaps or missing data was 20, invariable (monomorphic) sites 1034, variable (polymorphic) sites 147, total number of mutations was 154, singleton variable sites 112, and parsimony informative sites 35 analyzed in DNAsp v.5 program. Number of haplotypes h- 14, haplotype (gene) diversity, Hd: 0.983, variance of haplotype diversity: 0.00077, standard Deviation of Haplotype diversity: 0.028, Nucleotide diversity, Pi: 0.02352. Haplotypes of cultivated rice and crop wild relatives (AA genome) were more similar than those of distantly related species (BB, CC/DD, EE and GG genomes). It observed that the EE genome species is most closely related to the CC genome and CCDD genomes but BBCC genome species had different origins. Their maternal parents had either the BB or CC genome. The CpG rich matK sequences were rich in AA genome followed in BB, BBCC and EE, FF genotypes, whereas CpA rich sequences belonged to AA genome and in out group E. longifolia (unknown genome). The nucleotide frequencies are 30.12% (A), 35.72% (T/U), 17.60% (C), and 16.57% (G). The transition/transversion rate ratios are k1 = 3.379 (purines) and k2 = 3.465 (pyrimidines). The overall transition/transversion bias is R = 1.65, where R = [A*G*k1 + T*C*k2]/[(A+G)*(T+C)]. Maximum likelihood estimate of transition/transversion bias was estimated in MEGA6. The estimated Transition/ Transversion bias (R) is 1.65. Substitution pattern and rates were estimated under the Kimura (1980) 2-parameter model (Kimura 1980). For estimating ML values, a tree topology was automatically computed. The maximum Log likelihood for this computation was -3109.393 (MEGA6).
- Select Volume / Issue:
- Year:
- 2015
- Type of Publication:
- Article
- Keywords:
- Rice; Oryza Species; Oryza rufipogon; matK Gene; Phylogeny; Variation
- Journal:
- IJAIR
- Volume:
- 3
- Number:
- 6
- Pages:
- 1768-1774
- Month:
- May
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