Complete chloroplast genome sequences of three aroideae species (Araceae): lights into selective pressure, marker development and phylogenetic relationships

Li, Bicong; Liu, Tao; Ali, Asjad; Xiao, Yao; Shan, Nan; Sun, Jingyu; Huang, Yongji; Zhou, Qinghong; Zhu, Qianglong

doi:10.1186/s12864-022-08400-3

Cited by 15 publications

(15 citation statements)

References 58 publications

(78 reference statements)

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“…Chloroplast genomes are rich in SSRs, long repeats, highly divergent regions, SNPs and indels [39][40][41]. They have been extensively used to identify species and cultivars [36] and for phylogenetic analyses [37,41]. In the present study, SSR detection results were the same as most other Araceae plants; for example, most SSRs were mononucleotide repeats and usually comprised short repeats of A/T [31,41,42].…”

Section: Plos Onementioning

confidence: 50%

“…Additionally, our findings showed that trnN-GUU was duplicated in IR/SSC borders in two chloroplast genomes of 'Lady Valentine' and 'Red Vein', respectively, and ycf1 was duplicated in IR/SSC borders in the other five Aglaonema genomes (Fig 6). The same phenomenon exists in some species of the family Araceae [39][40][41].…”

Section: Plos Onementioning

confidence: 74%

Section: Plos Onementioning

confidence: 99%

“…They have been extensively used to identify species and cultivars [36] and for phylogenetic analyses [37,41]. In the present study, SSR detection results were the same as most other Araceae plants; for example, most SSRs were mononucleotide repeats and usually comprised short repeats of A/T [31,41,42]. Additionally, divergent analyses implemented by mVISTA and nucleotide diversity revealed 9 highly divergent regions among 7 Aglaonema chloroplast genomes, including rnH-GUG-CDS1_psbA, trnS-GCU_trnS-CGA-CDS1, rps4-trnT-UGU, trnF-GAA-ndhJ, petD-CDS2-rpoA, ycf1-ndhF, rps15-ycf1-D2, ccsA-ndhD, and trnY-GUA-trnE-UUC (Figs 7 and 8).…”

Section: Plos Onementioning

confidence: 99%

“…Additionally, divergent analyses implemented by mVISTA and nucleotide diversity revealed 9 highly divergent regions among 7 Aglaonema chloroplast genomes, including rnH-GUG-CDS1_psbA, trnS-GCU_trnS-CGA-CDS1, rps4-trnT-UGU, trnF-GAA-ndhJ, petD-CDS2-rpoA, ycf1-ndhF, rps15-ycf1-D2, ccsA-ndhD, and trnY-GUA-trnE-UUC (Figs 7 and 8). In contrast to previous studies, six highly divergent regions (trnH-GUG_psbA, rps4-trnT-UGU, trnF-GAA-ndhJ, rps15-ycf1, ccsA-ndhD, and petD-rpoA) were used as DNA barcodes in Araceae plants or were in the marker development of DNA barcodes [9,41]. We suggest that the remaining three highly divergent regions of trnS-GCU_trnS-CGA-CDS1, ycf1-ndhF, and trnY-GUA-trnE-UUC can be used as special DNA barcodes for Aglaonema species and cultivar identification and phylogenetic analyses in the future.…”

Section: Plos Onementioning

confidence: 99%

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Comparative chloroplast genomes and phylogenetic relationships of Aglaonema modestum and five variegated cultivars of Aglaonema

Zhu

et al. 2022

PLoS ONE

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Aglaonema, commonly called Chinese evergreens, are widely used for ornamental purposes. However, attempts to identify Aglaonema species and cultivars based on leaf morphology have been challenging. In the present study, chloroplast sequences were used to elucidate the phylogenetic relationships of cultivated Aglaonema in South China. The chloroplast genomes of one green species and five variegated cultivars of Aglaonema, Aglaonema modestum, ‘Red Valentine’, ‘Lady Valentine’, ‘Hong Yan’, ‘Hong Jian’, and ‘Red Vein’, were sequenced for comparative and phylogenetic analyses. The six chloroplast genomes of Aglaonema had typical quadripartite structures, comprising a large single copy (LSC) region (91,092–91,769 bp), a small single copy (SSC) region (20,816–26,501 bp), and a pair of inverted repeat (IR) regions (21,703–26,732 bp). The genomes contained 112 different genes, including 79–80 protein coding genes, 28–29 tRNAs and 4 rRNAs. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) were generally conserved among the six sequenced genomes, but the IR-SSC boundary regions were significantly different, and ‘Red Vein’ had a distinct long repeat number and type frequency. For comparative and phylogenetic analyses, Aglaonema costatum was included; it was obtained from the GenBank database. Single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were determined among the seven Aglaonema genomes studied. Nine divergent hotspots were identified: trnH-GUG-CDS1_psbA, trnS-GCU_trnS-CGA-CDS1, rps4-trnT-UGU, trnF-GAA-ndhJ, petD-CDS2-rpoA, ycf1-ndhF, rps15-ycf1-D2, ccsA-ndhD, and trnY-GUA-trnE-UUC. Additionally, positive selection was found for rpl2, rps2, rps3, ycf1 and ycf2 based on the analyses of Ka/Ks ratios among 16 Araceae chloroplast genomes. The phylogenetic tree based on whole chloroplast genomes strongly supported monophyletic Aglaonema and clear relationships among Aroideae, Lasioideae, Lemnoideae, Monsteroideae, Orontioideae, Pothoideae and Zamioculcadoideae in the family Araceae. By contrast, protein coding gene phylogenies were poorly to strongly supported and incongruent with the whole chloroplast genome phylogenetic tree. This study provided valuable genome resources and helped identify Aglaonema species and cultivars.

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Section: Plos Onementioning

confidence: 50%

Section: Plos Onementioning

confidence: 74%

Section: Plos Onementioning

confidence: 99%

Section: Plos Onementioning

confidence: 99%

Section: Plos Onementioning

confidence: 99%

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Comparative chloroplast genomes and phylogenetic relationships of Aglaonema modestum and five variegated cultivars of Aglaonema

Zhu

et al. 2022

PLoS ONE

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Chloroplast Genomics and Their Uses in Crop Improvement

Mathuria,

Chaudhary,

Mehak

et al. 2024

Advances in Genomics

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Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes

Feng,

Zheng,

Jiang

et al. 2024

Sci Rep

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The subfamily Polygonoideae encompasses a diverse array of medicinal and horticultural plants that hold significant economic value. However, due to the lack of a robust taxonomy based on phylogenetic relationships, the classification within this family is perplexing, and there is also a scarcity of reports on the chloroplast genomes of many plants falling under this classification. In this study, we conducted a comprehensive analysis by sequencing and characterizing the complete chloroplast genomes of six Polygonoideae plants, namely Pteroxygonum denticulatum, Pleuropterus multiflorus, Pleuropterus ciliinervis, Fallopia aubertii, Fallopia dentatoalata, and Fallopia convolvulus. Our findings revealed that these six plants possess chloroplast genomes with a typical quadripartite structure, averaging 162,931 bp in length. Comparative chloroplast analysis, codon usage analysis, and repetitive sequence analysis demonstrated a high level of conservation within the chloroplast genomes of these plants. Furthermore, phylogenetic analysis unveiled a distinct clade occupied by P. denticulatum, while P. ciliinrvis displayed a closer relationship to the three plants belonging to the Fallopia genus. Selective pressure analysis based on maximum likelihood trees showed that a total of 14 protein-coding genes exhibited positive selection, with psbB and ycf1 having the highest number of positive amino acid sites. Additionally, we identified four molecular markers, namely petN-psbM, psal-ycf4, ycf3-trnS-GGA, and trnL-UAG-ccsA, which exhibit high variability and can be utilized for the identification of these six plants.

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Complete chloroplast genome sequences of three aroideae species (Araceae): lights into selective pressure, marker development and phylogenetic relationships

Cited by 15 publications

References 58 publications

Comparative chloroplast genomes and phylogenetic relationships of Aglaonema modestum and five variegated cultivars of Aglaonema

Comparative chloroplast genomes and phylogenetic relationships of Aglaonema modestum and five variegated cultivars of Aglaonema

Chloroplast Genomics and Their Uses in Crop Improvement

Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes

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