Chloroplast DNA

Chloroplast DNA

Genetic Diversity in Natural Resources Management

Published in Yeqiao Wang, Landscape and Land Capacity, 2020

Thomas Joseph McGreevy, Jeffrey A. Markert

DeYoung and Honeycutt[38] provided an overview of the different types of molecular genetic tools or molecular markers that can be used to generate genetic data. These molecular markers include 1) expressed proteins; 2) Restriction Fragment Length Polymorphisms (RFLPs); 3) Random Amplified Polymorphic DNA (RAPDs); 4) Amplified Fragment Length Polymorphisms (AFLPs[40]); 5) nucleotide sequence data from nuclear, mitochondrial, or chloroplast DNA; 6) Simple Sequence Repeats (SSRs); and 7) Single-Nucleotide Polymorphisms (SNPs).

Indel-K2P: a modified Kimura 2 Parameters (K2P) model to incorporate insertion and deletion (Indel) information in phylogenetic analysis

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Journal Information

Published in Cyber-Physical Systems, 2022

Asim Kumar Mahadani, Shashank Awasthi, Goutam Sanyal, Partha Bhattacharjee, Sanjeev Pippal

Core plant DNA barcode loci of Chloroplast DNA sequence, trnL-trnF within the group taxa of Phalaenopsis were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/genbank/). Additionally, the unique accession numbers of each DNA sequence were recorded (table 1). The sequences from different Phalaenopsis species were aligned using the ClustalX [30] T-COFFEE [18] and MUSCLE [34,31].Few obvious misalignments were corrected manually using the similarity criterion. Implementations of K2P, Indel-K2P model and other experiments were conducted in MATLAB with Bioinformatics toolbox on a computer with OS Windows 7 professional running on 3.10 GHz Intel Core i5 processor and 8 GB 1600 MHz DDR3 memory.

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Genetic Diversity in Natural Resources Management

Indel-K2P: a modified Kimura 2 Parameters (K2P) model to incorporate insertion and deletion (Indel) information in phylogenetic analysis