Comparative analysis of the complete chloroplast genome sequences in psammophytic<i>Haloxylon</i>species (Amaranthaceae)

Dong, Wenpan; Xu, Chao; Li, Delu; Jin, Xianglin; Li, Ruili; Lu, Qi; Suo, Zhili

doi:10.7717/peerj.2699

Cited by 72 publications

(59 citation statements)

References 42 publications

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“…Fifty-four SSRs (19.64%) were located in intron regions. The distribution of SSRs is variable significantly among the four regions in each of the six Lagerstroemia cp genomes, which is identical with previous reports (Dong et al, 2016; Yang et al, 2016). …”

Section: Resultssupporting

confidence: 91%

“…Although cp genomes are highly conserved in terms of genomic structure and size, the IR/SC junction position change caused by expansion and contraction of the IR/SC boundary regions was usually considered as a primary mechanism in creating the length variation of the higher plant cp genomes (Kim and Lee, 2005; Asaf et al, 2016; Dong et al, 2016; Yang et al, 2016; Zhang et al, 2016). In this study, however, the IR/SC junction position change was not observed among the six cp genomes.…”

Section: Resultsmentioning

confidence: 99%

“…Simple sequence repeats (SSRs) in the cp genome can be highly variable at the intra-specific level, and are therefore often used as genetic markers in population genetics and evolutionary studies (Dong et al, 2013, 2016; Kaur et al, 2015; Suo et al, 2016; Yang et al, 2016). We analyzed the simple sequence repeats (SSRs) in the cp genomes (Tables 2, 3, Tables S2, S3).…”

Section: Resultsmentioning

confidence: 99%

“…Chloroplasts are key organelles in plants for photosynthesis and other biochemical pathways such as the biosynthesis of starch, fatty acids, pigments, and amino acids (Dong et al, 2013, 2016; Raman and Park, 2016). Chloroplast (cp) genome, as one of the three DNA genomes (the other two are nuclear and mitochondrial genomes) in plant body, with uniparental inheritance, has a highly conserved circular DNA arrangement ranging from 115 to 165 kb.…”

Section: Introductionmentioning

confidence: 99%

“…Chloroplast (cp) genome, as one of the three DNA genomes (the other two are nuclear and mitochondrial genomes) in plant body, with uniparental inheritance, has a highly conserved circular DNA arrangement ranging from 115 to 165 kb. Complete cp genome sequences have been widely accepted as an informative and valuable data source for understanding evolutionary biology because of their relatively stable genome structure, gene content, and gene order (Dong et al, 2012, 2013, 2014, 2016; Suo et al, 2012, 2015, 2016; Curci et al, 2015; Downie and Jansen, 2015; Song et al, 2015). Along with the accumulation of complete cp genome sequences, comparative study of chloroplast genomes from Lagerstroemia plants is helpful for upgrading our evaluation on the application value of the cp genomes.…”

Section: Introductionmentioning

confidence: 99%

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Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

Dong

Li³

et al. 2017

Front. Plant Sci.

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Crape myrtles are economically important ornamental trees of the genus Lagerstroemia L. (Lythraceae), with a distribution from tropical to northern temperate zones. They are positioned phylogenetically to a large subclade of rosids (in the eudicots) which contain more than 25% of all the angiosperms. They commonly bloom from summer till fall and are of significant value in city landscape and environmental protection. Morphological traits are shared inter-specifically among plants of Lagerstroemia to certain extent and are also influenced by environmental conditions and different developmental stages. Thus, classification of plants in Lagerstroemia at species and cultivar levels is still a challenging task. Chloroplast (cp) genome sequences have been proven to be an informative and valuable source of cp DNA markers for genetic diversity evaluation. In this study, the complete cp genomes of three Lagerstroemia species were newly sequenced, and three other published cp genome sequences of Lagerstroemia were retrieved for comparative analyses in order to obtain an upgraded understanding of the application value of genetic information from the cp genomes. The six cp genomes ranged from 152,049 bp (L. subcostata) to 152,526 bp (L. speciosa) in length. We analyzed nucleotide substitutions, insertions/deletions, and simple sequence repeats in the cp genomes, and discovered 12 relatively highly variable regions that will potentially provide plastid markers for further taxonomic, phylogenetic, and population genetics studies in Lagerstroemia. The phylogenetic relationships of the Lagerstroemia taxa inferred from the datasets from the cp genomes obtained high support, indicating that cp genome data may be useful in resolving relationships in this genus.

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Section: Resultssupporting

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

Dong

Li³

et al. 2017

Front. Plant Sci.

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124

101

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

Skuza

2021

Methods in Molecular Biology

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First reported chloroplast genome sequence of Punica granatum (cultivar Helow) from Jabal Al-Akhdar, Oman: phylogenetic comparative assortment with Lagerstroemia

et al. 2018

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Pomegranate (Punica granatum L.) is one of the oldest known edible fruits. It has grown in popularity and is a profitable fruit crop due to its attractive features including a bright red appearance and its biological activities. Scientific exploration of the genetics and evolution of these beneficial traits has been hampered by limited genomic information. In this study, we sequenced the complete chloroplast (cp) genome of the native P. granatum (cultivar Helow) cultivated in the mountains of Jabal Al-Akhdar, Oman. The results revealed a P. granatum cp genome length of 158,630 bp, characterized by a relatively conserved structure containing 2 inverted repeat regions of 25,466 bp, an 18,686 bp small single copy regions, and an 89,015 bp large single copy region. The 86 protein-coding genes included 37 transfer RNA genes and 8 ribosomal RNA genes. Comparison of the P. granatum whole cp genome with seven Lagerstroemia species revealed an overall high degree of sequence similarity with divergence among intergenic spacers. The location, distribution, and divergence of repeat sequences and shared genes of the Punica and Lagerstroemia species were highly similar. Analyses of nucleotide substitution, insertion/deletions, and highly variable regions in these cp genomes identified potential plastid markers for taxonomic and phylogenetic studies in Myrtales. A phylogenetic study of the cp genomes and 76 shared coding regions generated similar cladograms. The complete cp genome of P. granatum will aid in taxonomical studies of the family Lythraceae.

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Comparative analysis of the complete chloroplast genome sequences in psammophyticHaloxylonspecies (Amaranthaceae)

Cited by 72 publications

References 42 publications

Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

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

First reported chloroplast genome sequence of Punica granatum (cultivar Helow) from Jabal Al-Akhdar, Oman: phylogenetic comparative assortment with Lagerstroemia

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