Plastid Phylogenomic Analyses Reveal a Cryptic Species of Ligusticopsis (Apiaceae, Angiosperms)
Abstract
:1. Introduction
2. Results
2.1. Morphological Analysis
2.2. Comparative Plastome Analyses
2.3. Codon Usage Analyses
2.4. Simple Sequence Repeats Analyses (SSRs)
2.5. Phylogenetic Analysis
3. Discussion
3.1. Plastome Characteristic
3.2. Comparison of Ligusticopsis Plastomes
3.3. Phylogenetic Analysis
3.4. Taxonomic Treatment
1 | Plants densely villous or strigose | 2 |
Plants nearly smooth | 4 | |
2 | Rays of umbel almost draw from the base, extremely elongated | L. hispida |
Plants compound umbels with long pedicels, umbrella not elongated | 3 | |
3 | Bracts well developed, 2-pinnately divided | L. involucratum |
Bracts caducous, 1-pinnately divided | L. capillaceum | |
4 | Umbels predominantly simple, rays drawn from base very unequal | L. litangensis |
Compound umbels, rays subequal | 5 | |
5 | Basal leaves and lower stem leaves are 1-pinnately compound | L. integrifolia |
Basal leaves and lower stem leaves are 2–4-pinnately compound | 6 | |
6 | Calyx teeth inconspicuous | 7 |
Calyx teeth prominent | 8 | |
7 | Bracteoles margin not membranous | L. modesta |
Bracteoles with white membranous margin | L. oliverianum | |
8 | Stems unbranched, scapiform, cauline leaves usually absent | L. scapiforme |
Stems simple or branched, cauline leaves present | 9 | |
9 | Calyx teeth linear | 10 |
Calyx teeth subulate | 11 | |
10 | Bracteoles with broad white membranous margins | L. wallichiana |
Bracteoles without white membranous margins | L. brachyloba | |
11 | Leaf blade 1-2-pinnate, ultimate segments ovate to oblong-ovate | L. rechingeriana |
Leaf blade 3-4-pinnate, ultimate segments linear | L. dielsiana |
4. Materials and Methods
4.1. Plant Sample, Morphological Observation and Anatomy
4.2. DNA Extraction, Sequencing, Assembly and Annotation
4.3. Phylogenetic Analyses
4.4. Comparative Plastome Analyses
4.5. Codon Usage and SSRs Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | LSC Length (bp) | SSC Length (bp) | IR Length (bp) | Total Genome | Number of Genes | ||||
---|---|---|---|---|---|---|---|---|---|
Length (bp) | GC (%) | Total | CDS | rRNA | tRNA | ||||
L. litangensis | 91,559 | 17,669 | 19,127 | 147,482 | 37.4 | 129 | 85 | 8 | 36 |
L. dielsiana | 91,666 | 17,582 | 19,415 | 148,078 | 37.4 | 129 | 85 | 8 | 36 |
L. capillacea | 91,907 | 17,503 | 19,199 | 147,808 | 37.5 | 129 | 85 | 8 | 36 |
L. scapiformis | 92,214 | 17,581 | 19,156 | 148,107 | 37.5 | 129 | 85 | 8 | 36 |
L. rechingerana | 91,813 | 17,654 | 19,529 | 148,525 | 37.3 | 129 | 85 | 8 | 36 |
L. brachyloba | 92,265 | 17,588 | 19,390 | 148,633 | 37.4 | 129 | 85 | 8 | 36 |
L. hispida | 91,846 | 17,627 | 19,162 | 147,797 | 37.4 | 129 | 85 | 8 | 36 |
L. integrifolia | 92,305 | 17,575 | 19,158 | 148,196 | 37.5 | 129 | 85 | 8 | 36 |
L. involucrata | 91,782 | 17,560 | 19,205 | 147,752 | 37.4 | 129 | 85 | 8 | 36 |
L. modesta | 92,247 | 17,568 | 19,159 | 148,133 | 37.5 | 129 | 85 | 8 | 36 |
L. wallichiana | 92,281 | 17,567 | 19,373 | 148,594 | 37.4 | 129 | 85 | 8 | 36 |
L. oliveriana | 92,262 | 17,558 | 19,279 | 148,378 | 37.5 | 129 | 85 | 8 | 36 |
L. litangensis | 91,559 | 17,669 | 19,127 | 147,482 | 37.4 | 129 | 85 | 8 | 36 |
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Tian, R.; Aou, X.; Song, B.; Li, Z.; He, X.; Zhou, S. Plastid Phylogenomic Analyses Reveal a Cryptic Species of Ligusticopsis (Apiaceae, Angiosperms). Int. J. Mol. Sci. 2023, 24, 7419. https://doi.org/10.3390/ijms24087419
Tian R, Aou X, Song B, Li Z, He X, Zhou S. Plastid Phylogenomic Analyses Reveal a Cryptic Species of Ligusticopsis (Apiaceae, Angiosperms). International Journal of Molecular Sciences. 2023; 24(8):7419. https://doi.org/10.3390/ijms24087419
Chicago/Turabian StyleTian, Rongming, Xueyimu Aou, Boni Song, Zixuan Li, Xingjin He, and Songdong Zhou. 2023. "Plastid Phylogenomic Analyses Reveal a Cryptic Species of Ligusticopsis (Apiaceae, Angiosperms)" International Journal of Molecular Sciences 24, no. 8: 7419. https://doi.org/10.3390/ijms24087419