Characterization of the complete chloroplast genome of Koelreuteria paniculata (Sapindaceae)

Kim, Sang-Chul; Baek, Seung-Hoon; Hong, Kyung-Nak; Lee, Jei-Wan

doi:10.1007/s12686-017-0767-4

Cited by 7 publications

(6 citation statements)

References 8 publications

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“…However, the 3' end was found in the IRa and IRb region. These results are similar to other species in the nettle family [22].…”

Section: Genome Annotationsupporting

confidence: 89%

Comparative Chloroplast Genomics of Four Pilea Species (Urticaceae): High Levels of Sequences Divergence Provides New Insight into Interspecific Diversity in Pilea

Li¹,

Tang²,

Zeng³

et al. 2020

Preprint

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Background Pilea is a genus of perennial herbs from the family Urticaceae, which are used for courtyard ornamental. For some species, they are used as medicinal plants in traditional Chinese medicine as well. The morphological characteristics of medicinal species from Pilea are similar, and it is difficult to accurately distinguish them based only on morphological characteristics. Besides, the species classification of Pilea are still controversial. The classification of many species are still in an unresolved state. At present, there is no information about the chloroplast genomes of Pilea, which limits our further understanding of this genus. Here, we first reported 4 chloroplast genomes of Pilea taxa (P. mollis, P. glauca, P. peperomioides and P. serpyllacea), and performed comprehensive comparative analysis. Results The four chloroplast genomes have similar structural characteristics and gene order with other angiosperms. These genomes all have a typical quartile structure, which contains 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Besides, we detected SSRs and repeat sequences, and analyzed the expansion/contraction of IR regions. In particular, the comparative analysis showed a rather level of sequence divergence in the non-coding regions, even in the protein-coding regions of the four genome sequences, suggesting a high level of genetic diversity in Pilea. Moreover, we identified eight hypervariable regions, including petN-psbM; psbZ-trnG-GCC; trnT-UGU-trnL-UAA; accD-psbI; ndhF-rpl32; rpl32-trnL-UAG; ndhA-intron and ycf1, are proposed for use as DNA barcode regions. Phylogenetic analysis showed that four Pilea species form a monophyletic cluster with a 100% bootstrap value. Conclusion The results obtained here could provide abundant information for the phylogenetic position of Pilea and further species identification. High levels of sequences divergence promote our understanding of the interspecific diversity of this genus, also provide reference for the rational classification of unsolved species in the future.

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“…However, the 3' end was found in the IRa and IRb region. These results are similar to other species in the nettle family [22].…”

Section: Genome Annotationsupporting

confidence: 89%

Comparative Chloroplast Genomics of Four Pilea Species (Urticaceae): High Levels of Sequences Divergence Provides New Insight into Interspecific Diversity in Pilea

Li¹,

Tang²,

Zeng³

et al. 2020

Preprint

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“…Within the H. bodinieri and E. cavaleriei cp genomes, the clpP, rps12, and ycf3 genes possess one intron, and 15 genes contain two introns. Pseudogenization of the gene infA was has been detected in H. bodinieri and E. cavaleriei cp genomes, the same results were observed in those of other Sapindaceae species [77][78][79]. Besides, we detected the pseudogenization of rpl22 and rpl2 genes in H. bodinieri cp genome and the latter was also annotated as pseudogene in that of Acer takesimense [80].…”

Section: Features Of Complete Chloroplast Genome and Comparative Analysessupporting

confidence: 75%

Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

Yang

2021

Preprint

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Background Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. Results The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisted of Aesculus chinensis and A. wangii, strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. Conclusion This study revealed that the cp genome size of the Hippocastanoideae was generally smaller across Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.

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“…We downloaded four whole chloroplast genome sequences of Sapindaceae family from the National Center for Biotechnology Information (NCBI) Organelle Genome and Nucleotide Resources database, including D. longan [ 46 ], L. chinensis , P. tomentosa [ 59 ], S. mukorossi [ 60 ], D. viscosa [ 61 , 62 ], E. cavaleriei [ 62 ], K. paniculata [ 63 ] and X. sorbifolium [ 64 ]. The mVISTA online program (Shuffle-LAGAN mode) [ 65 , 66 ] was used to compare chloroplast genome sequence of rambutan with the other species from Sapindaceae, in which the annotation of D. longan was the reference.…”

Section: Methodsmentioning

confidence: 99%

Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae

Dong

Lin

et al. 2021

Plants

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Rambutan (Nephelium lappaceum L.) is an important fruit tree that belongs to the family Sapindaceae and is widely cultivated in Southeast Asia. We sequenced its chloroplast genome for the first time and assembled 161,321 bp circular DNA. It is characterized by a typical quadripartite structure composed of a large (86,068 bp) and small (18,153 bp) single-copy region interspersed by two identical inverted repeats (IRs) (28,550 bp). We identified 132 genes including 78 protein-coding genes, 29 tRNA and 4 rRNA genes, with 21 genes duplicated in the IRs. Sixty-three simple sequence repeats (SSRs) and 98 repetitive sequences were detected. Twenty-nine codons showed biased usage and 49 potential RNA editing sites were predicted across 18 protein-coding genes in the rambutan chloroplast genome. In addition, coding gene sequence divergence analysis suggested that ccsA, clpP, rpoA, rps12, psbJ and rps19 were under positive selection, which might reflect specific adaptations of N. lappaceum to its particular living environment. Comparative chloroplast genome analyses from nine species in Sapindaceae revealed that a higher similarity was conserved in the IR regions than in the large single-copy (LSC) and small single-copy (SSC) regions. The phylogenetic analysis showed that N. lappaceum chloroplast genome has the closest relationship with that of Pometia tomentosa. The understanding of the chloroplast genomics of rambutan and comparative analysis of Sapindaceae species would provide insight into future research on the breeding of rambutan and Sapindaceae evolutionary studies.

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Characterization of the complete chloroplast genome of Koelreuteria paniculata (Sapindaceae)

Cited by 7 publications

References 8 publications

Comparative Chloroplast Genomics of Four Pilea Species (Urticaceae): High Levels of Sequences Divergence Provides New Insight into Interspecific Diversity in Pilea

Comparative Chloroplast Genomics of Four Pilea Species (Urticaceae): High Levels of Sequences Divergence Provides New Insight into Interspecific Diversity in Pilea

Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae

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