Abstract
The whole chloroplast genome has been increasingly used over the past three decades for systematic and ordered analysis of evolutionary relationships, variation within species, and developmental studies.There were several other studies on the Asteraceae family, but the studies were on the family level.This study investigates the plastomes of an important Asteraceae tribe, Cichorieae, that are widely distributed, morphologically complex, include several species reproduce apomictically.Plastomes belonging to 36 different species in 12 different genera have been studied in detail and compared.The comparisons were based on plastome structure, number of coding and noncoding genes, and number of rRNA and tRNA genes.Further, the repetitive DNA types, frequency, and their position in the chloroplast genomes have been analyzed.Moreover, SSRs types and frequency were compared and analyzed.In addition, a number of coding and noncoding regions were studied and used to construct a phylogenetic tree.The investigation of this study indicated the distinctiveness of sequence divergence among the plastomes of Cichorieae tribe species in various aspects.The results provided excellent phylogenetic linkages that can be used for advanced comparative studies at both generic and species levels.Most noncoding and coding regions showed the least variation; however, major variations were shown by those regions that have rarely been used in chloroplast phylogenetics.Regions of coding (clpP, matK, ndhA, rpoC1, rpoC2, and ycf1) and non-coding (ndhF-rpl32, petN-psbM, psbE-petL, rps4-ndhJ, rps15-ycf1, trnL-trnF, trnT-psbD, and ycf3-trnS) are recommended to use in studying Cichorieae tribe members to achieve better phylogenetic construction, population genetic analysis, and use as a marker for accurate and automated species identification.The tandem repeat of 21-30 period size is the most variable among the Cichorieae tribe plastomes.Ttra-, penta-, and hexanucleotide SSR types were found in Cichorium intybus, Crepidiastrum, Sonchus, and Taraxacum plastomes, while, they were not found in other plastomes under study.These SSRs may be useful for identifying species, detecting hybridization, determining phylogeny, and differentiating populations.
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Claims 8
Claim · model-written summary
Most noncoding and coding plastome regions showed the least variation among Cichorieae species.
Verbatim
t0“Cichorieae Tribe (Asteraceae)”
e1“Most noncoding and coding regions showed the least variation”
Claim · model-written summary
Regions rarely used in chloroplast phylogenetics showed major variation among Cichorieae plastomes.
Verbatim
t0“Cichorieae Tribe (Asteraceae)”
e2“major variations were shown by those regions that have rarely been used in chloroplast phylogenetics”
Claim · model-written summary
The 21-30 period tandem repeat is the most variable repeat type among Cichorieae plastomes.
Verbatim
e3“The tandem repeat of 21-30 period size is the most variable among the Cichorieae tribe plastomes”
Claim · model-written summary
Tetra-, penta- and hexanucleotide SSRs were found in Cichorium intybus, Crepidiastrum, Sonchus and Taraxacum plastomes only.
- Taxon
- Cichorium intybus
Cichorium intybuse4 - Outcome
- penta-, and hexanucleotide SSR typese4
- Qualifier
- Crepidiastrum, Sonchus, and Taraxacume4
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e4“Ttra-, penta-, and hexanucleotide SSR types were found in Cichorium intybus, Crepidiastrum, Sonchus, and Taraxacum plastomes, while, they were not found in other plastomes under study”
Claim · model-written summary
The SSRs may be useful for identifying species, detecting hybridization, determining phylogeny and differentiating populations.
Verbatim
t0“Cichorieae Tribe (Asteraceae)”
e5“These SSRs may be useful for identifying species, detecting hybridization, determining phylogeny, and differentiating populations”
Claim · model-written summary
The listed coding and noncoding regions are recommended for Cichorieae phylogenetic construction and species identification.
Verbatim
e6“Regions of coding (clpP, matK, ndhA, rpoC1, rpoC2, and ycf1) and non-coding (ndhF-rpl32, petN-psbM, psbE-petL, rps4-ndhJ, rps15-ycf1, trnL-trnF, trnT-psbD, and ycf3-trnS) are recommended to use in studying Cichorieae tribe members to achieve better phylogenetic construction”
Claim · model-written summary
The study indicated distinct sequence divergence among Cichorieae plastomes.
Not reportedDirection
Verbatim
t0“Cichorieae Tribe (Asteraceae)”
e7“The investigation of this study indicated the distinctiveness of sequence divergence among the plastomes of Cichorieae tribe species”
Claim · model-written summary
Plastome data gave excellent phylogenetic linkages at generic and species levels.
Not reportedDirection
Verbatim
t0“Cichorieae Tribe (Asteraceae)”
e6“The results provided excellent phylogenetic linkages that can be used for advanced comparative studies at both generic and species levels”