Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, DNA Extraction and Sequencing
2.2. Genome Assembly and Annotation
2.3. Characterization, Comparative Analyses and Phylogenetic Inference
3. Results
3.1. Comparative Genomics among De Novo Assembled Chloroplast Genomes
3.2. Contraction and Expansion of Inverted Repeats
3.3. Analyses of Codon Usage, Amino Acid Frequency and RNA Editing
3.4. Repeats Analyses
3.5. Analyses of Substitution Types
3.6. Phylogenetic Inference of Araceae
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Species | Data in GB | Whole Genome Reads (millions) | Phred Score | Chloroplast Reads (millions) | Average Coverage | Maximum Coverage | NCBI Accession |
---|---|---|---|---|---|---|---|
Orontium aquaticum | 5.43 | 20.86 | 37.2 | 0.20 | 124.8 | 1347 | MT226773 |
Lasia spinosa | 8.35 | 32.00 | 37.6 | 1.74 | 1021 | 1929 | MT226772 |
Zamioculcas zamiifolia | 11.3 | 43.29 | 35.69 | 1.29 | 774.4 | 1293 | MT226775 |
Stylochaeton bogneri | 3.31 | 12.71 | 37.39 | 0.15 | 92.7 | 749 | MT226774 |
Characteristic | O. aquaticum | L. spinosa | Z. zamiifolia | S. bogneri | |
---|---|---|---|---|---|
Size (base pair; bp) | 164,016 | 169,980 | 167,405 | 163,770 | |
LSC length (bp) | 87,269 | 91,150 | 91,357 | 89,869 | |
SSC length (bp) | 13,967 | 18,551 | 19,326 | 20,497 | |
IR length (bp) | 31,390 | 32,053 | 28,361 | 26,702 | |
Number of genes* | 131 (113) | 131 (113) | 130 (113) | 130 (113) | |
Protein-coding genes* | 85 (79) | 85 (79) | 84 (79) | 84 (79) | |
tRNA genes* | 37 (30) | 37 (30) | 37 (30) | 37 (30) | |
rRNA genes* | 8 (4) | 8 (4) | 8 (4) | 8 (4) | |
Duplicate genes | 18 | 18 | 17 | 17 | |
GC content | Total (%) | 37.3 | 36.1 | 35.9 | 35.7 |
LSC (%) | 35.7 | 33.9 | 34.2 | 34.0 | |
SSC (%) | 31.9 | 31.0 | 30.4 | 29.5 | |
IR (%) | 40.6 | 41.8 | 39.7 | 40.5 | |
CDS (%) | 37.7 | 37.8 | 37.5 | 37.9 | |
rRNA (%) | 55.2 | 54.6 | 55.0 | 55.0 | |
tRNA (%) | 53.1 | 52.9 | 53.2 | 53.1 | |
All gene % | 39.2 | 39.3 | 39.0 | 39.2 |
Substitution Type | Lasia spinosa | Zamioculcas zamiifolia | Stylochaeton bogneri |
---|---|---|---|
A/C | 479 | 467 | 562 |
C/T | 1376 | 1269 | 1459 |
A/G | 1432 | 1316 | 1543 |
A/T | 275 | 254 | 316 |
C/G | 160 | 156 | 195 |
G/T | 305 | 322 | 407 |
Ts/Tv | 2.3 | 2.15 | 2.03 |
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Abdullah; Henriquez, C.L.; Mehmood, F.; Shahzadi, I.; Ali, Z.; Waheed, M.T.; Croat, T.B.; Poczai, P.; Ahmed, I. Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae. Plants 2020, 9, 737. https://doi.org/10.3390/plants9060737
Abdullah, Henriquez CL, Mehmood F, Shahzadi I, Ali Z, Waheed MT, Croat TB, Poczai P, Ahmed I. Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae. Plants. 2020; 9(6):737. https://doi.org/10.3390/plants9060737
Chicago/Turabian StyleAbdullah, Claudia L. Henriquez, Furrukh Mehmood, Iram Shahzadi, Zain Ali, Mohammad Tahir Waheed, Thomas B. Croat, Peter Poczai, and Ibrar Ahmed. 2020. "Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae" Plants 9, no. 6: 737. https://doi.org/10.3390/plants9060737