Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

Liang, Daqu; Wang, Haoyun; Zhang, Jun; Zhao, Yuanxiang; Wang, Feng

doi:10.3390/life12010092

Cited by 18 publications

(25 citation statements)

References 75 publications

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“…The boundary regions between the SSC and the two IR regions were relatively highly conserved, and the distribution and location of genes in these regions were consistent. However, the boundary regions between the LSC and the two IR regions varied greatly, which were similar with the finding in many angiosperm plants [ 64 , 65 ]. The contraction and expansion of IR borders can reflect the genetic relationship of plant species [ 66 , 67 ].…”

Section: Discussionsupporting

confidence: 83%

Complete Plastome of Physalis angulata var. villosa, Gene Organization, Comparative Genomics and Phylogenetic Relationships among Solanaceae

Zhan

Zhang

Zhang³

et al. 2022

Genes

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Physalis angulata var. villosa, rich in withanolides, has been used as a traditional Chinese medicine for many years. To date, few extensive molecular studies of this plant have been conducted. In the present study, the plastome of P. angulata var. villosa was sequenced, characterized and compared with that of other Physalis species, and a phylogenetic analysis was conducted in the family Solanaceae. The plastome of P. angulata var. villosa was 156,898 bp in length with a GC content of 37.52%, and exhibited a quadripartite structure typical of land plants, consisting of a large single-copy (LSC, 87,108 bp) region, a small single-copy (SSC, 18,462 bp) region and a pair of inverted repeats (IR: IRA and IRB, 25,664 bp each). The plastome contained 131 genes, of which 114 were unique and 17 were duplicated in IR regions. The genome consisted of 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. A total of 38 long, repeat sequences of three types were identified in the plastome, of which forward repeats had the highest frequency. Simple sequence repeats (SSRs) analysis revealed a total of 57 SSRs, of which the T mononucleotide constituted the majority, with most of SSRs being located in the intergenic spacer regions. Comparative genomic analysis among nine Physalis species revealed that the single-copy regions were less conserved than the pair of inverted repeats, with most of the variation being found in the intergenic spacer regions rather than in the coding regions. Phylogenetic analysis indicated a close relationship between Physalis and Withania. In addition, Iochroma, Dunalia, Saracha and Eriolarynx were paraphyletic, and clustered together in the phylogenetic tree. Our study published the first sequence and assembly of the plastome of P. angulata var. villosa, reported its basic resources for evolutionary studies and provided an important tool for evaluating the phylogenetic relationship within the family Solanaceae.

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Section: Discussionsupporting

confidence: 83%

Complete Plastome of Physalis angulata var. villosa, Gene Organization, Comparative Genomics and Phylogenetic Relationships among Solanaceae

Zhan

Zhang

Zhang³

et al. 2022

Genes

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“…is a sister to C. kweichowensis Kuang & A.M.Lu and C. illinoinensis (Wangenh.) K.Koch [66]; and Fagus longipetiolata Seemen and F. engleriana Seemen ex Diels form a close relationship [41]. Here, we performed phylogenetic analyses for Ferula and other genera of Apiaceae using complete plastomes, and we recognized Ferula as a monophyletic group with the integration of Soranthus, Schumannia, Talassia (PP = 1, BS = 100%).…”

Section: Plastomes Might Provide New Insight On Phylogenetic Relation...mentioning

confidence: 88%

“…Plastomes are considered an effective means used in taxonomic and evolutionary studies to assess evolutionary relationships and compare genome structure at different taxonomic levels [34][35][36][37][38][39][40][41][42]. Generally, the plastomes are highly conserved in genome structure, gene order, and gene content [32].…”

Section: Comparison Of Ferula Plastid Genomementioning

confidence: 99%

“…At present, chloroplast genome sequences and nuclear genome sequences can be obtained using shallow whole genome sequencing technology. This is considered an effective means of improving the rate of species identification and has been developed as a tool for plant phylogenetic studies at different taxonomic levels [34][35][36][37][38][39][40][41][42]. For example, the complete plastomes and nrDNA sequences obtained based on shallow genome sequencing have greatly improved the species identification rate of Rhododendron, which is also difficult to classify [43].…”

Section: Introductionmentioning

confidence: 99%

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Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.

et al. 2022

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Background Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species. Results The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species. Conclusion Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus.

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“…(de Longevialle et al, 2008). The previous studies show that the ClpP gene contains two introns make the low selection effect ratio (ka/ks = 0) of the ClpP gene (Liang and Chen, 2021;Liang et al, 2022). The evolution rate of the ClpP gene is related with species that is clearly evident.…”

Section: Frontiers Inmentioning

confidence: 94%

The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements

et al. 2022

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Salix floderusii is a rare alpine tree species in the Salix genus. Unfortunately, no extensive germplasm identification, molecular phylogeny, and chloroplast genomics of this plant have been conducted. We sequenced the chloroplast (cp) genome of S. floderusii for the first time using second-generation sequencing technology. The cp genome was 155,540 bp long, including a large single-copy region (LSC, 84,401 bp), a small single-copy region (SSC, 16,221 bp), and inverted repeat regions (IR, 54,918 bp). A total of 131 genes were identified, including 86 protein genes, 37 tRNA genes, and 8 rRNA genes. The S. floderusii cp genome contains 1 complement repeat, 24 forward repeats, 17 palindromic repeats, and 7 reverse repeats. Analysis of the IR borders showed that the IRa and IRb regions of S. floderusii and Salix caprea were shorter than those of Salix cinerea, which may affect plastome evolution. Furthermore, four highly variable regions were found, including the rpl22 coding region, psbM/trnD-GUC non-coding region, petA/psbJ non-coding region, and ycf1 coding region. These high variable regions can be used as candidate molecular markers and as a reference for identifying future Salix species. In addition, phylogenetic analysis indicated that the cp genome of S. floderusii is sister to Salix cupularis and belongs to the Subgenus Vetrix. Genes (Sf-trnI, Sf-PpsbA, aadA, Sf-TpsbA, Sf-trnA) obtained via cloning were inserted into the pBluescript II SK (+) to yield the cp expression vectors, which harbored the selectable marker gene aadA. The results of a spectinomycin resistance test indicated that the cp expression vector had been successfully constructed. Moreover, the aadA gene was efficiently expressed under the regulation of predicted regulatory elements. The present study provides a solid foundation for establishing subsequent S. floderusii cp transformation systems and developing strategies for the genetic improvement of S. floderusii.

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Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

Cited by 18 publications

References 75 publications

Complete Plastome of Physalis angulata var. villosa, Gene Organization, Comparative Genomics and Phylogenetic Relationships among Solanaceae

Complete Plastome of Physalis angulata var. villosa, Gene Organization, Comparative Genomics and Phylogenetic Relationships among Solanaceae

Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.

The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements

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