Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera)

Huang, Ya‐Yi; Matzke, A. J. M.; Matzke, Marjori

doi:10.1371/journal.pone.0074736

Cited by 100 publications

(86 citation statements)

References 60 publications

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“…Both F. ussuriensis and F. cirrhosa chloroplast genomes had a quadripartite structure similar to most land plants consisting of a pair of IRs (52,678 and 52,156 bp, respectively) separated by LSC (81,732 and 81,390 bp) and SSC (17,114 and 17,537 bp) regions ( Figure 1, Table 1). The Fritillaria chloroplast genomes were AT-rich (63% in both species), and LSC (65.3% and 64.2% in F. ussuriensis and F. cirrhosa) and SSC (69.4% and 69.6% in F. ussuriensis and F. cirrhosa) regions were more AT-rich than the IR regions (57.6% and 57.4% in F. ussuriensis and F. cirrhosa), which is similar to other chloroplast genomes [6,7,[14][15][16].…”

Section: Chloroplast Genome Organization Of Two Fritillaria Speciessupporting

confidence: 61%

The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species

Park¹,

Kim²,

Yeo³

et al. 2017

Preprint

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Abstract:The genus Fritillaria belongs to the widely distributed family Liliaceae. The bulbs of Fritillaria ussuriensis and Fritillaria cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species is therefore required. Here, we report the complete chloroplast (cp) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria cp genomes were 151,524 and 151,083 bp in length, respectively, including a pair of inverted repeat regions (52,678 and 52,156 bp) separated by a large single copy region (81,732 and 81,390 bp) and small single copy region (17,114 and 17,537 bp). A total of 111 genes in F. ussuriensis and 112 in F. cirrhosa comprised 77 proteincoding genes in F. ussuriensis and 78 in F. cirrhosa, 30 tRNA genes, and four rRNA genes. The gene order, content, and orientation of the two Fritillaria cp genomes exhibited the general structure of flowering plants, and were similar to those of other Fritillaria species. Comparison of the six Fritillaria species' cp genomes indicated seven highly divergent regions in intergenic spacers and in the matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF coding regions. We established the position of the six species through phylogenic analysis. The complete chloroplast genome sequences of two Fritillaria species will be useful genomics resources for identification of Fritillaria species and for studying the phylogenetic relationship among Fritillaria species within the Liliaceae family.

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Section: Chloroplast Genome Organization Of Two Fritillaria Speciessupporting

confidence: 61%

The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species

Park¹,

Kim²,

Yeo³

et al. 2017

Preprint

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“…In addition, 8 editing sites in C. scarabaeoides and C. cajan were identified, which were not predicted by PREPcp. Among all the genes analyzed, ndh gene displays the maximum number of editing sites (Supplementary Tables S6, S7), ndh genes have been reported to contain maximum number of editing sites (Corneille et al, 2000; Huang et al, 2013), since they are considered to be dispensable (Burrows et al, 1998; Shikanai et al, 1998), therefore accumulation of editing sites may have been permitted in ndh transcript due to dearth of stringent requirement of ndh function.…”

Section: Resultsmentioning

confidence: 99%

Chloroplast Genome Sequence of Pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes

et al. 2016

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Pigeonpea (Cajanus cajan (L.) Millspaugh), a diploid (2n = 22) legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides (L.) Thouars were generated. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harboring the C. scarabaeoides cytoplasm was used for sequencing the plastid genome. The cp genome of C. cajan is 152,242bp long, having a quadripartite structure with LSC of 83,455 bp and SSC of 17,871 bp separated by IRs of 25,398 bp. Similarly, the cp genome of C. scarabaeoides is 152,201bp long, having a quadripartite structure in which IRs of 25,402 bp length separates 83,423 bp of LSC and 17,854 bp of SSC. The pigeonpea cp genome contains 116 unique genes, including 30 tRNA, 4 rRNA, 78 predicted protein coding genes and 5 pseudogenes. A 50 kb inversion was observed in the LSC region of pigeonpea cp genome, consistent with other legumes. Comparison of cp genome with other legumes revealed the contraction of IR boundaries due to the absence of rps19 gene in the IR region. Chloroplast SSRs were mined and a total of 280 and 292 cpSSRs were identified in C. scarabaeoides and C. cajan respectively. RNA editing was observed at 37 sites in both C. scarabaeoides and C. cajan, with maximum occurrence in the ndh genes. The pigeonpea cp genome sequence would be beneficial in providing informative molecular markers which can be utilized for genetic diversity analysis and aid in understanding the plant systematics studies among major grain legumes.

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“…Recent studies, using advanced genome sequencing techniques, have improved the prospects for resolving phylogenetic homogeneity at taxonomic levels and have enhanced the current understanding of the structural and functional evolution of economically important plants and their traits [12–15]. In the last decade, numerous studies have reported the results of chloroplast genome sequencing for economically and ecologically important tree species, such as Eucommia ulmoides [16], Poplus cathayana [17], Quercus spinosa [18], Acacia ligulata [19], Pinus armandii [20], Cocos nucifera [21], Citrus aurantiifolia [22], Musa acuminata [23], Norway spruce [24], etc. The elucidation of the chloroplast genomes of important tree species has facilitated to understand the evaluation of gene structure and has targeted conservation and propagation strategies [12–13].…”

Section: Introductionmentioning

confidence: 99%

The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman

et al. 2017

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Boswellia sacra (Burseraceae), a keystone endemic species, is famous for the production of fragrant oleo-gum resin. However, the genetic make-up especially the genomic information about chloroplast is still unknown. Here, we described for the first time the chloroplast (cp) genome of B. sacra. The complete cp sequence revealed a circular genome of 160,543 bp size with 37.61% GC content. The cp genome is a typical quadripartite chloroplast structure with inverted repeats (IRs 26,763 bp) separated by small single copy (SSC; 18,962 bp) and large single copy (LSC; 88,055 bp) regions. De novo assembly and annotation showed the presence of 114 unique genes with 83 protein-coding regions. The phylogenetic analysis revealed that the B. sacra cp genome is closely related to the cp genome of Azadirachta indica and Citrus sinensis, while most of the syntenic differences were found in the non-coding regions. The pairwise distance among 76 shared genes of B. sacra and A. indica was highest for atpA, rpl2, rps12 and ycf1. The cp genome of B. sacra reveals a novel genome, which could be used for further studied to understand its diversity, taxonomy and phylogeny.

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Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera)

Cited by 100 publications

References 60 publications

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

Chloroplast Genome Sequence of Pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes

The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman

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