The complete chloroplast genome of a commercially exploited ornamental plant, <i>Bougainvillea glabra</i> (Caryophyllales: Nyctaginaceae)

Ni, Jing; Lee, Shiou Yih; Xing, Hu; Wang, Wei; Zhang, Jifang; Ruan, Linhui; Dai, Seping; Li, Guofeng

doi:10.1080/23802359.2019.1674721

Cited by 3 publications

(9 citation statements)

References 5 publications

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“…In addition to SSRs, tandem repeats (TRs) were also determined in the six cp genomes using Tandem Repeats Finder v4.04. Bougainvillea glabra (26) has the highest number of identified tandem repeats, whereas Bougainvillea peruviana (17) and Bougainvillea pachyphylla (19) have the lowest. The remaining three (B. praecox, B. spectabilis, B. cultivar) have the same number of tandem repeats.…”

Section: Simple Sequence Repeats and Tandem Repeat Analysesmentioning

confidence: 99%

“…Several of the phylogenetic reconstructions focusing on the Nyctaginaceae family were based on a single gene or a few gene regions from plastid or nuclear DNA [15,46], but none of them explicitly discussed the relationships among species of Bougainvillea. With the advent of next-generation sequencing, several cultivated Bougainvillea spectabilis and Bougainvillea glabra genomes have been published, but due to the lack of other available sequences, phylogenetic analyses have focused only on Bougainvillea's placement within the Nyctaginaceae family [17,18]. Thus, in this study, the phylogeny of Bougainvillea was reconstructed using eight complete chloroplast genomes of Bougainvillea (including the sequences from GenBank) and six other species from the Nyctaginaceae family.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

“…Hence, the majority of the available sequences in the GenBank are from the commercially cultivated Bougainvillea. Short-genome announcement papers have presented the gene content and structure of B. glabra and B. spectabilis [17,18]. It was also shown that Bougainvillea is clustered together with Acleisanthes, Mirabilis, and Nyctaginia; however, specific relationships cannot be inferred due to the lack of available sequences [17].…”

Section: Introductionmentioning

confidence: 99%

“…Short-genome announcement papers have presented the gene content and structure of B. glabra and B. spectabilis [17,18]. It was also shown that Bougainvillea is clustered together with Acleisanthes, Mirabilis, and Nyctaginia; however, specific relationships cannot be inferred due to the lack of available sequences [17]. Currently, there is very little information available on the genetic structures of Bougainvillea, particularly on their plastome features and specific phylogenetic placements.…”

Section: Introductionmentioning

confidence: 99%

“…repeats, whereas Bougainvillea peruviana (17) and Bougainvillea pachyphylla (19) have the lowest. The remaining three (B. praecox, B. spectabilis, B. cultivar) have the same number of tandem repeats.…”

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confidence: 97%

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Comparative Analysis of Complete Chloroplast Genome Sequences of Wild and Cultivated Bougainvillea (Nyctaginaceae)

Bautista

Zheng

et al. 2020

Plants

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Bougainvillea (Nyctaginaceae) is a popular ornamental plant group primarily grown for its striking colorful bracts. However, despite its established horticultural value, limited genomic resources and molecular studies have been reported for this genus. Thus, to address this existing gap, complete chloroplast genomes of four species (Bougainvillea glabra, Bougainvillea peruviana, Bougainvillea pachyphylla, Bougainvillea praecox) and one Bougainvillea cultivar were sequenced and characterized. The Bougainvillea cp genomes range from 153,966 bp to 154,541 bp in length, comprising a large single-copy region (85,159 bp–85,708 bp) and a small single-copy region (18,014 bp–18,078 bp) separated by a pair of inverted repeats (25,377–25,427 bp). All sequenced plastomes have 131 annotated genes, including 86 protein-coding, eight rRNA, and 37 tRNA genes. These five newly sequenced Bougainvillea cp genomes were compared to the Bougainvillea spectabilis cp genome deposited in GeBank. The results showed that all cp genomes have highly similar structures, contents, and organization. They all exhibit quadripartite structures and all have the same numbers of genes and introns. Codon usage, RNA editing sites, and repeat analyses also revealed highly similar results for the six cp genomes. The amino acid leucine has the highest proportion and almost all favored synonymous codons have either an A or U ending. Likewise, out of the 42 predicted RNA sites, most conversions were from serine (S) to leucine (L). The majority of the simple sequence repeats detected were A/T mononucleotides, making the cp genomes A/T-rich. The contractions and expansions of the IR boundaries were very minimal as well, hence contributing very little to the differences in genome size. In addition, sequence variation analyses showed that Bougainvillea cp genomes share nearly identical genomic profiles though several potential barcodes, such as ycf1, ndhF, and rpoA were identified. Higher variation was observed in both B. peruviana and B. pachyphylla cp sequences based on SNPs and indels analysis. Phylogenetic reconstructions further showed that these two species appear to be the basal taxa of Bougainvillea. The rarely cultivated and wild species of Bougainvillea (B. pachyphylla, B. peruviana, B. praecox) diverged earlier than the commonly cultivated species and cultivar (B. spectabilis, B. glabra, B. cv.). Overall, the results of this study provide additional genetic resources that can aid in further phylogenetic and evolutionary studies in Bougainvillea. Moreover, genetic information from this study is potentially useful in identifying Bougainvillea species and cultivars, which is essential for both taxonomic and plant breeding studies.

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Section: Simple Sequence Repeats and Tandem Repeat Analysesmentioning

confidence: 99%

Section: Phylogenetic Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 97%

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Comparative Analysis of Complete Chloroplast Genome Sequences of Wild and Cultivated Bougainvillea (Nyctaginaceae)

Bautista

Zheng

et al. 2020

Plants

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Complete Chloroplast Genomes and Phylogenetic Relationships of Bougainvillea spectabilis and Bougainvillea glabra (Nyctaginaceae)

Zhang,

Huang,

Zhou

et al. 2023

IJMS

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Bougainvillea L. (Nyctaginaceae) is a South American native woody flowering shrub of high ornamental, economic, and medicinal value which is susceptible to cold damage. We sequenced the complete chloroplast (cp) genome of B. glabra and B. spectabilis, two morphologically similar Bougainvillea species differing in cold resistance. Both genomes showed a typical quadripartite structure consisting of one large single-copy region, one small single-copy region, and two inverted repeat regions. The cp genome size of B. glabra and B. spectabilis was 154,520 and 154,542 bp, respectively, with 131 genes, including 86 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes. In addition, the genomes contained 270 and 271 simple sequence repeats, respectively, with mononucleotide repeats being the most abundant. Eight highly variable sites (psbN, psbJ, rpoA, rpl22, psaI, trnG-UCC, ndhF, and ycf1) with high nucleotide diversity were identified as potential molecular markers. Phylogenetic analysis revealed a close relationship between B. glabra and B. spectabilis. These findings not only contribute to understanding the mechanism by which the cp genome responds to low-temperature stress in Bougainvillea and elucidating the evolutionary characteristics and phylogenetic relationships among Bougainvillea species, but also provide important evidence for the accurate identification and breeding of superior cold-tolerant Bougainvillea cultivars.

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Comparative Analyses of Chloroplast Genome Provide Effective Molecular Markers for Species and Cultivar Identification in Bougainvillea

Lin,

Lee,

et al. 2023

IJMS

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Bougainvillea is popular in ornamental horticulture for its colorful bracts and excellent adaptability, but the complex genetic relationship among this genus is fuzzy due to limited genomic data. To reveal more genomic resources of Bougainvillea, we sequenced and assembled the complete chloroplast (cp) genome sequences of Bougainvillea spectabilis ‘Splendens’. The cp genome size was 154,869 bp in length, containing 86 protein-coding genes, 38 tRNAs, and eight rRNAs. Cp genome comparison across 12 Bougainvillea species (B. spectabilis, B. glabra, B. peruviana, B. arborea, B. praecox, B. stipitata, B. campanulata, B. berberidifolia, B. infesta, B. modesta, B. spinosa, and B. pachyphylla) revealed five mutational hotspots. Phylogenetic analysis suggested that B. spectabilis published previously and B. glabra clustered into one subclade as two distinct groups, sister to the subclade of B. spectabilis ‘Splendens’. We considered the phylogeny relationships between B. spectabilis and B. glabra to be controversial. Based on two hypervariable regions and three common plastid regions, we developed five molecular markers for species identification in Bougainvillea and applied them to classify 53 ornamental Bougainvillea cultivars. This study provides a valuable genetic resource for Bougainvillea breeding and offers effective molecular markers to distinguish the representative ornamental species of Bougainvillea.

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The complete chloroplast genome of a commercially exploited ornamental plant, Bougainvillea glabra (Caryophyllales: Nyctaginaceae)

Cited by 3 publications

References 5 publications

Comparative Analysis of Complete Chloroplast Genome Sequences of Wild and Cultivated Bougainvillea (Nyctaginaceae)

Comparative Analysis of Complete Chloroplast Genome Sequences of Wild and Cultivated Bougainvillea (Nyctaginaceae)

Complete Chloroplast Genomes and Phylogenetic Relationships of Bougainvillea spectabilis and Bougainvillea glabra (Nyctaginaceae)

Comparative Analyses of Chloroplast Genome Provide Effective Molecular Markers for Species and Cultivar Identification in Bougainvillea

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