Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii

Guo, Shuai; Guo, Lili; Zhao, Wei; Xu, Jiang; Li, Yuying; Zhang, Xiaoyan; Shen, Xiaofeng; Wu, Mingli; Hou, Xiaogai

doi:10.3390/molecules23020246

Cited by 64 publications

(65 citation statements)

References 74 publications

(75 reference statements)

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“…The observed GC content is generally consistent with the results of previous intensive studies [3,[84][85][86][87], which confirms that the cp genome of Fagaceae species is rich in adenine and thymine (AT). GC skewness is considered an indicator of replication terminals, replication origin, lag chains and DNA lead chains [88][89][90] as well as a dominant factor in codon bias.…”

Section: Discussionsupporting

confidence: 90%

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

Chang

Liu

et al. 2019

Forests

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Quercus bawanglingensis Huang, Li et Xing, an endemic evergreen oak of the genus Quercus (Fagaceae) in China, is currently listed in the Red List of Chinese Plants as a vulnerable (VU) plant.No chloroplast (cp) genome information is currently available for Q. bawanglingensis, which would be essential for the establishment of guidelines for its conservation and breeding. In the present study, the cp genome of Q. bawanglingensis was sequenced and assembled into double-stranded circular DNA with a length of 161,394 bp. Two inverted repeats (IRs) with a total of 51,730 bp were identified, and the rest of the sequence was separated into two single-copy regions, namely, a large single-copy (LSC) region (90,628 bp) and a small single-copy (SSC) region (19,036 bp). The genome of Q. bawanglingensis contains 134 genes (86 protein-coding genes, 40 tRNAs and eight rRNAs). More forward (29) than inverted long repeats (21) are distributed in the cp genome. A simple sequence repeat (SSR) analysis showed that the genome contains 82 SSR loci, involving 84.15% A/T mononucleotides. Sequence comparisons among the nine complete cp genomes, including the genomes of Q. bawanglingensis, Q. tarokoensis Hayata (NC036370), Q. aliena var. acutiserrata Maxim. ex , Lithocarpus balansae (Drake) A. Camus (KP299291) and Castanea mollissima Bl. (HQ336406), demonstrated that the diversity of SC regions was higher than that of IR regions, which might facilitate identification of the relationships within this extremely complex family. A phylogenetic analysis showed that Fagus engleriana and Trigonobalanus doichangensis form the basis of the produced evolutionary tree. Q. bawanglingensis and Q. tarokoensis, which belong to the group Ilex, share the closest relationship. The analysis of the cp genome of Q. bawanglingensis provides crucial genetic information for further studies of this vulnerable species and the taxonomy, phylogenetics and evolution of Quercus. single-copy regions (LSC and SSC) [4,5]. Due to its uniparental inheritance, highly conserved structure, general lack of recombination and small effective population size, the analysis of cp DNA has been deemed a useful method for evolution research and the exploration of plant systematics [6][7][8][9]. In fact, the availability of sufficient data on cp genomes is crucial for phylogenetic relationship reconstruction, i.e., the assessment of relationships within angiosperms [10][11][12], the identification of members of Pinaceae [13] and Pinus [14], and adequate comparisons, i.e., cp genomes from sister species [15] and possibly multiple individuals [16]. At present, approximately 3000 plastid genomes of Eukaryota are shareable in the National Center for Biotechnology Information database (NCBI; Available online: https: //www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?opt=plastid&taxid=2759&sort=Genome) due to improvements in sequencing technologies. In addition, molecular genetic methodologies based on nuclear and organellar genomes are crucial for conservation studies [17], particularly the con...

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Section: Discussionsupporting

confidence: 90%

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

Chang

Liu

et al. 2019

Forests

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“…It is obvious that the DNA G + C content of the IR region is higher than that of other regions (LSC, SSC). This phenomenon is very common in other plants [23,24]. GC skewness has been shown to be an indicator of DNA lead chains, lag chains, replication origin, and replication terminals [25,26,27].…”

Section: Resultsmentioning

confidence: 99%

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima

Zang

et al. 2018

IJMS

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Quercus acutissima, an important endemic and ecological plant of the Quercus genus, is widely distributed throughout China. However, there have been few studies on its chloroplast genome. In this study, the complete chloroplast (cp) genome of Q. acutissima was sequenced, analyzed, and compared to four species in the Fagaceae family. The size of the Q. acutissima chloroplast genome is 161,124 bp, including one large single copy (LSC) region of 90,423 bp and one small single copy (SSC) region of 19,068 bp, separated by two inverted repeat (IR) regions of 51,632 bp. The GC content of the whole genome is 36.08%, while those of LSC, SSC, and IR are 34.62%, 30.84%, and 42.78%, respectively. The Q. acutissima chloroplast genome encodes 136 genes, including 88 protein-coding genes, four ribosomal RNA genes, and 40 transfer RNA genes. In the repeat structure analysis, 31 forward and 22 inverted long repeats and 65 simple-sequence repeat loci were detected in the Q. acutissima cp genome. The existence of abundant simple-sequence repeat loci in the genome suggests the potential for future population genetic work. The genome comparison revealed that the LSC region is more divergent than the SSC and IR regions, and there is higher divergence in noncoding regions than in coding regions. The phylogenetic relationships of 25 species inferred that members of the Quercus genus do not form a clade and that Q. acutissima is closely related to Q. variabilis. This study identified the unique characteristics of the Q. acutissima cp genome, which will provide a theoretical basis for species identification and biological research.

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“…Pan is stored in the Paeonia Specimen Museum of Henan University of Science and Technology under accession number PL2018041502. Total genomic DNA was extracted using the CTAB method (Guo et al 2018). Genomic DNA purity was tested by Qubit 2.0 and NanoDrop.…”

Section: Paeonia Lactiflora; Wild Species; Chloroplast Genome; Phylogmentioning

confidence: 99%

Phylogeny analysis of a wild species of Paeonia lactiflora from Henan province based on the complete chloroplast genome

Wang

Guo

Fan

et al. 2020

Mitochondrial DNA Part B

Self Cite

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The complete chloroplast genome sequence of a wild Paeonia lactiflora species from Henan province, Paeonia obovata subsp. Willmottiae (Stapf) D. Y. Hong et K. Y. Pan, was applied to support the difference of Paeonia lactiflora by next-generation sequencing. The length of complete chloroplast genome is 152,660 bp, including a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of identical inverted repeat (IR) regions (IRa and IRb) with length of 84,363 bp, 16,983 bp and 25,657 bp, respectively. Altogether, 115 genes in chloroplast genome were annotated including 81 protein-encoding genes, 30 tRNA genes, and 4 rRNA genes. Paeonia obovata subsp. Willmottiae (Stapf) D. Y. Hong et K. Y. Pan clustered in the clade of Paeonia lactiflora showed a closer relationship with Paeonia sect. Mudan rather than Paeonia Brownii. ARTICLE HISTORY

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Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii

Cited by 64 publications

References 74 publications

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima

Phylogeny analysis of a wild species of Paeonia lactiflora from Henan province based on the complete chloroplast genome

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