New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material and DNA Extraction
2.2. Chloroplast Genome Sequencing, Assembly, Annotation, and Visualization
2.3. Analysis of Microsatellites and Repeat Sequences
2.4. Variation Hotspots Detection and Sequence Divergence Analysis
2.5. Comparative Genome Analysis
2.6. Phylogenomic Analysis
3. Results
3.1. Genome Organization and Features
3.2. IR Expansion and Shrinkage
3.3. Divergence Analysis of Sequence and High Variation Region
3.4. Repeat Structure and SSR Analysis
3.5. Phylogenetic Analysis
4. Discussion
4.1. Genome Features and Sequence Divergence among Crataegus Species
4.2. Repeat Structure and SSR Analysis of the Plastomes of Crataegus Species
4.3. Potential Highly Variable Chloroplast Barcodes
4.4. Phylogenetic Relationships
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Taxon | Identification Code | Biogeographic Region | Collection Site |
---|---|---|---|
C. bretschneideri | ZF1H | Northeast, China | Shenyang |
C. pinnatifida | CZSLH | Northeast, China | Shenyang |
C. pinnatifida var. major | JD1H | North, China | Shenyang |
C. maximowiczii | MSZ1H | Northeast, China | Shenyang |
Characteristics | C. bretschneideri | C. pinnatifida | C. pinnatifida var. Major | C. maximowiczii |
---|---|---|---|---|
Total size(bp) | 159,607 | 159,656 | 159,676 | 159,875 |
LSC length (bp) | 87,601 | 87,749 | 87,744 | 87,874 |
SSC length (bp) | 19,312 | 19,139 | 19,164 | 19,233 |
IR length (bp) | 26,347 | 26,384 | 26,384 | 26,384 |
Overall GC content(%) | 36.6% | 36.7% | 36.6% | 36.6% |
GC in LSC (%) | 34.4% | 34.4% | 34.4% | 34.3% |
GC in IR (%) | 42.7% | 42.6% | 42.6% | 42.6% |
GC in SSC (%) | 30.3% | 30.6% | 30.5% | 30.4% |
Total number of genes | 113 | 113 | 113 | 113 |
Protein genes | 79 | 79 | 79 | 79 |
rRNA genes | 30 | 30 | 30 | 30 |
tRNA genes | 4 | 4 | 4 | 4 |
Duplicated genes | 19 | 19 | 19 | 19 |
Accession number | MW963339 | MZ494514 | MZ494513 | MZ494512 |
Gene Category | Gene Group | Names of Gene |
---|---|---|
Photosynthetic | Subunit of rubisco | rbcL |
Photosystem I | psaA, psaB, psaC, psaI, psaJ | |
Photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
Subunit of synthase | atpA, atpB, atpE, atpF *, atpH, atpI | |
Cytochromecompelx | petA, petB *, petD *, petG, petL, petN | |
Subunits of NADPH dehydrogenase | ndhA *, ndhB *, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
Self-replication | Transfer RNA | trnA-UGC *, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-UCC, trnG-GCC *, trnH-GUG, trnI-CAU, trnI-GAU *, trnK-UUU *, trnL-CAA, trnL-UAA *, trnL-UAG, trnfM-CAUI, trnM-CAU, trnN-GUU, trnP-UGG, trnQ-UUG, trnR-ACG, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC, trnV-UAC *, trnW-CCA, trnY-GUA |
Ribosomal RNA | rrn5, rrn4.5, rrn16, rrn23 | |
Proteins of large ribosomal subunit | rpl2 *, rpl14, rpl16 *, rpl20, rpl22, rpl23, rpl32, rpl33, rpl36 | |
Proteins of small ribosomal subunit | rps2, rps3, rps4, rps7, rps8, rps11, rps12 *, rps14, rps15, rps16, rps18, rps19, | |
RNA polymerase | rpoA, rpoB, rpoC1, rpoC2 | |
Biosynthesis | Maturase | matK |
Carbon metabolism | cemA | |
Protease | clpP * | |
Fatty acid synthesis | accD | |
Cytochrome synthesis gene | ccsA | |
Translation initiation factor | infA | |
Unknown function | Conserved open reading frames | ycf1, ycf2, ycf3 *, ycf4 |
Length | Variable Sites | Parsimony-Informative Sites | Nucleotide Diversity | |||
---|---|---|---|---|---|---|
(bp) | Number | % | Number | % | ||
LSC region | 88,705 | 316 | 0.3562 | 228 | 0.257 | 0.0022 |
IR | 26,383 | 22 | 0.0834 | 16 | 0.0606 | 0.0003 |
SSC region | 19,435 | 107 | 0.5506 | 87 | 0.4476 | 0.0036 |
Total | 160,906 | 445 | 0.2766 | 331 | 0.2057 | 0.0017 |
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Hu, G.; Wang, Y.; Wang, Y.; Zheng, S.; Dong, W.; Dong, N. New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing. Horticulturae 2021, 7, 301. https://doi.org/10.3390/horticulturae7090301
Hu G, Wang Y, Wang Y, Zheng S, Dong W, Dong N. New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing. Horticulturae. 2021; 7(9):301. https://doi.org/10.3390/horticulturae7090301
Chicago/Turabian StyleHu, Guanglong, Yiheng Wang, Yan Wang, Shuqi Zheng, Wenxuan Dong, and Ningguang Dong. 2021. "New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing" Horticulturae 7, no. 9: 301. https://doi.org/10.3390/horticulturae7090301