scholarly journals Comparative Analysis of Complete Chloroplast Genome Sequences and Insertion-Deletion (Indel) Polymorphisms to Distinguish Five Vaccinium Species

Forests ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 927
Author(s):  
Yonguk Kim ◽  
Jawon Shin ◽  
Dool-Ri Oh ◽  
Ah-Young Kim ◽  
Chulyung Choi
Keyword(s):  
Comparative Analysis ◽  
Nucleotide Diversity ◽  
Complete Chloroplast Genome ◽  
Sliding Windows ◽  
Noncoding Regions ◽  
Comprehensive Information ◽  
Indel Polymorphisms ◽  
Species Groups ◽  
Interspecific Distance ◽  
Discriminatory Capacity

We report the identification of interspecific barcoding InDel regions in Vaccinium species. We compared five complete Vaccinium chloroplast (cp) genomes (V. bracteatum, V. vitis-idaea, V. uliginosum, V. macrocarpon, and V. oldhamii) to identify regions that can be used to distinguish them. Comparative analysis of nucleotide diversity from five cp genomes revealed 25 hotspot coding and noncoding regions, occurring in 65 of a total of 505 sliding windows, that exhibited nucleotide diversity (Pi) > 0.02. PCR validation of 12 hypervariable InDel regions identified seven candidate barcodes with high discriminatory powers: accD-trnT-GGU, rpoB-rpoA, ycf2-trnL-GAA, rps12-ycf15, trnV-GAC, and ndhE-ndhF. Among them, the rpoB-rpoA(2) and ycf2-trnL-CAA sequences clearly showed the intraspecific and interspecific distance among five Vaccinium species by using a K2P technique. In phylogenetic analysis, included five Vaccinium species (n = 19) in the Bayesian and Neighbor-Joining (NJ) analysis revered all species in two major clades and resolved taxonomic position within species groups. These two locus provide comprehensive information that aids the phylogenetics of this genus and increased discriminatory capacity during species authentication.

scholarly journals The complete chloroplast genome of Saxifraga sinomontana (Saxifragaceae) and comparative analysis with other Saxifragaceae species

2019 ◽  
Vol 42 (4) ◽  
pp. 601-611 ◽  
Author(s):  
Yan Li ◽  
Liukun Jia ◽  
Zhihua Wang ◽  
Rui Xing ◽  
Xiaofeng Chi ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
De Novo ◽  
Single Copy ◽  
Bootstrap Support ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Abstract Saxifraga sinomontana J.-T. Pan & Gornall belongs to Saxifraga sect. Ciliatae subsect. Hirculoideae, a lineage containing ca. 110 species whose phylogenetic relationships are largely unresolved due to recent rapid radiations. Analyses of complete chloroplast genomes have the potential to significantly improve the resolution of phylogenetic relationships in this young plant lineage. The complete chloroplast genome of S. sinomontana was de novo sequenced, assembled and then compared with that of other six Saxifragaceae species. The S. sinomontana chloroplast genome is 147,240 bp in length with a typical quadripartite structure, including a large single-copy region of 79,310 bp and a small single-copy region of 16,874 bp separated by a pair of inverted repeats (IRs) of 25,528 bp each. The chloroplast genome contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs, with 18 duplicates in the IRs. The gene content and organization are similar to other Saxifragaceae chloroplast genomes. Sixty-one simple sequence repeats were identified in the S. sinomontana chloroplast genome, mostly represented by mononucleotide repeats of polyadenine or polythymine. Comparative analysis revealed 12 highly divergent regions in the intergenic spacers, as well as coding genes of matK, ndhK, accD, cemA, rpoA, rps19, ndhF, ccsA, ndhD and ycf1. Phylogenetic reconstruction of seven Saxifragaceae species based on 66 protein-coding genes received high bootstrap support values for nearly all identified nodes, suggesting a promising opportunity to resolve infrasectional relationships of the most species-rich section Ciliatae of Saxifraga.

scholarly journals Comparative analysis of complete chloroplast genome sequences of four major Amorphophallus species

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Erxi Liu ◽  
Chaozhu Yang ◽  
Jiangdong Liu ◽  
Surong Jin ◽  
Nunung Harijati ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Genome Sequences ◽  
Complete Chloroplast Genome

scholarly journals Comparative Analysis of the Complete Chloroplast Genome of the Alloplasmic Sunflower (Helianthus L.) Lines with Various CMS Types

2018 ◽  
Vol 14 (1) ◽  
pp. 39-47
Author(s):  
Kirill Azarin ◽  
Maxim Makarenko ◽  
Alexander Usatov ◽  
Vladimir Khachumov ◽  
Alexey Kovalevich ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Complete Chloroplast Genome
Sign in / Sign up

Export Citation Format

Share Document