Literature DB >> 34773616

Primer Design for the Analysis of Closely Related Species: Application of Noncoding mtDNA and cpDNA Sequences.

Lidia Skuza1,2.   

Abstract

Noncoding regions of the chloroplast (cpDNA) and mitochondrial (mtDNA) genomes are commonly used in plant phylogenetic and population studies. Consensus primers, which are homologous to most coding regions, but amplify variable noncoding regions, are very useful for this purpose. However, high genetic diversity of plants poses a problem in developing molecular methods that require conserved DNA sequences between species.This chapter describes the protocol for designing PCR primers suitable for analysis of closely related plant species. As an example, we used PCR primer design for cpDNA noncoding regions of the rye (Secale).
© 2022. Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Noncoding sequences; Primer design; Related species; Species identification; cpDNA1; mtDNA

Mesh：

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Year:  2022        PMID： 34773616     DOI： 10.1007/978-1-0716-1799-1_6

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  7 in total

1.  Plant conserved non-coding sequences and paralogue evolution.

Authors:  Steven Lockton; Brandon S Gaut
Journal:  Trends Genet       Date:  2005-01       Impact factor: 11.639

2.  Revealing genetic diversity of tree peonies at micro-evolution level with hyper-variable chloroplast markers and floral traits.

Authors:  Zhili Suo; Chuanhong Zhang; Yongqi Zheng; Lixia He; Xiaobai Jin; Boxin Hou; Jiajue Li
Journal:  Plant Cell Rep       Date:  2012-09-09       Impact factor: 4.570

3.  Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, MATK, RPL20-RPS18 spacer, and TRNV intron sequences.

Authors:  X R Wang; Y Tsumura; H Yoshimaru; K Nagasaka; A E Szmidt
Journal:  Am J Bot       Date:  1999-12       Impact factor: 3.844

4.  A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants.

Authors:  Jan Van de Velde; Michiel Van Bel; Dries Vaneechoutte; Klaas Vandepoele
Journal:  Plant Physiol       Date:  2016-06-03       Impact factor: 8.340

5.  Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae).

Authors:  Wenpan Dong; Chao Xu; Delu Li; Xiaobai Jin; Ruili Li; Qi Lu; Zhili Suo
Journal:  PeerJ       Date:  2016-11-10       Impact factor: 2.984

6.  Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes.

Authors:  Chao Xu; Wenpan Dong; Wenqing Li; Yizeng Lu; Xiaoman Xie; Xiaobai Jin; Jipu Shi; Kaihong He; Zhili Suo
Journal:  Front Plant Sci       Date:  2017-01-19       Impact factor: 5.753

7.  Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis.

Authors:  Lidia Skuza; Izabela Szućko; Ewa Filip; Tomasz Strzała
Journal:  PLoS One       Date:  2019-02-27       Impact factor: 3.240
  7 in total

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