Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants
Abstract
:1. Introduction
2. Results and Discussion
2.1. Sequencing of the T. coccineum Genome
2.2. Size Estimation of the T. coccineum Genome
2.3. Sequence Assembly and Annotation of the T. coccineum Genome
2.4. Inter-Genus Comparative Analysis of TE Classification
2.5. Pyrethrin-Related Enzymes Encoded in the T. coccineum Genome
2.6. Synteny Analysis of Genes Encoding Pyrethrin-Related Enzymes
2.7. Functional Annotation of the T. coccineum Genes and Inter-Genus Comparative Analysis
3. Materials and Methods
3.1. Phylogenetic Analysis of Plants in This Paper
3.2. Plant Materials and Genome Sequencing
3.3. Genome Size Estimation Using Flow Cytometry
3.4. Genome Size Estimation Using K-Mer Depth Information
3.5. De Novo Assembly of Genome Sequences
3.6. Gene Prediction and Annotation
3.7. Comparative Analysis of TE Content Versus That in Other Plants
3.8. Homology Search and Synteny Analysis of Genes Encoding Pyrethrin-Related Enzymes
3.9. Comparative Analysis of Protein Superfamily Content Versus That in Other Plants
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Library | Insert Size (bp) | Read Length (Bases) | Number of Reads | Total Read Length (Bases) |
---|---|---|---|---|
PE | 350 | 151 | 5,732,398,372 | 854,270,829,961 |
MP-3kb | 3000 | 151 | 698,859,570 | 99,096,491,543 |
MP-5kb | 5000 | 151 | 750,513,382 | 107,931,325,410 |
MP-8kb | 8000 | 151 | 762,709,822 | 109,359,355,641 |
MS | 550 | 301 | 97,731,712 | 26,503,089,921 |
PB | Ave. 10,738 | 8,670,092 | 93,100,193,428 |
Contigs | Scaffolds (before Gapfilling) | Draft Genome | |
---|---|---|---|
Total number of sequence fragments | 6,500,576 | 3,061,809 | 2,836,647 |
Total length (bp) | 8,565,698,618 | 9,395,951,224 | 9,463,677,832 |
N50 (bp) | 8465 | 25,397 | 27,784 |
Length of longest contig (bp) | 149,916 | 329,693 | 331,286 |
Gaps (bp) | 0 | 777,041,487 | 724,210,424 |
GC content (%) | 34.9 | 35.1 | 35.1 |
Number of Predicted Genes | 1,582,136 |
BUSCO v5 | * C: 92.7% (Single: 70.8%, Duplicated: 21.9%) F: 5.1% M: 2.2% |
Number of predicted TEs | 772,794 |
Number of predicted genes encoding products with known protein signatures | 103,680 |
Rank | Tco | Tci | Cs | Aa | Ha | Nt | Os | At |
---|---|---|---|---|---|---|---|---|
1 | sire (25.7) | sire (33.0) | sire (32.0) | sire (21.8) | del (37.7) | del (40.4) | tat (11.4) | athila (9.54) |
2 | del (15.3) | athila (17.0) | athila (10.9) | athila (19.6) | sire (9.85) | tat (20.5) | retroviridae (8.97) | retroviridae (4.89) |
3 | athila (12.5) | del (12.0) | oryco (5.11) | del (6.57) | lentiviridae (8.72) | athila (9.87) | del (8.39) | caulimovirus (4.15) |
4 | oryco (7.25) | oryco (6.34) | lentiviridae (5.06) | oryco (4.59) | tat (6.76) | sire (3.02) | tork (4.73) | badnavirus (4.05) |
5 | tork (4.70) | lentiviridae (4.92) | del (5.03) | tork (4.01) | athila (5.17) | tork (2.80) | alpharetroviridae (4.66) | tork (3.08) |
Known Pyrethrin-Related Enzymes | Corresponding Proteins of T. coccineum | Protein Sequence Similarity |
---|---|---|
TciADH2 | Tco_0487905 | Identities = 340/378 (90%), Positives = 359/378 (95%), Gaps = 2/378 (1%) |
TciALDH1 | Tco_0682217 | Identities = 448/499 (90%), Positives = 471/499 (94%), Gaps = 1/499 (0%) |
TciCCH | Tco_0360514 | Identities = 470/498 (94%), Positives = 484/498 (97%), Gaps = 1/498 (0%) |
TciCCMT | Tco_1190813 | Identities = 358/374 (96%), Positives = 361/374 (97%), Gaps = 5/374 (1%) |
TciCDS | Tco_1315810 | Identities = 358/395 (91%), Positives = 374/395 (95%), Gaps = 0/395 (0%) |
TciGLIP | Tco_1108878 | Identities = 337/365 (92%), Positives = 348/365 (95%), Gaps = 0/365 (0%) |
TciJMH | Tco_0572988 | Identities = 450/512 (88%), Positives = 479/512 (94%), Gaps = 2/512 (0%) |
TciLOX1 | Tco_0863779 | Identities = 847/861 (98%), Positives = 853/861 (99%), Gaps = 0/861 (0%) |
TciPYS | Tco_1240348 | Identities = 465/488 (95%), Positives = 475/488 (97%), Gaps = 0/488 (0%) |
Category | IPR ID | Superfamily Name | Tco | Tci | Cs | Aa | Ha | Nt | Os | At |
---|---|---|---|---|---|---|---|---|---|---|
Biodefense | IPR036041 | Ribosome-inactivating protein | 1.96 (159) | 1.29 (98) | −1.81 (7) | −1.00 (16) | −3.07 (0) | −3.07 (0) | −0.94 (17) | −3.07 (0) |
Metabolism | IPR005848 | Urease, alpha subunit | 2.36 (108) | −0.14 (15) | −1.87 (1) | −1.46 (3) | −1.87 (1) | −0.87 (7) | −2.14 (0) | −1.87 (1) |
Metabolism | IPR036226 | Lipoxygenase, C-terminal domain | 1.86 (232) | 0.48 (86) | −0.22 (51) | −0.82 (32) | −1.12 (25) | −0.67 (36) | −1.86 (13) | −2.44 (7) |
Metabolism | IPR033966 | RuBisCO | 1.60 (42) | −0.25 (8) | 0.05 (11) | −0.15 (9) | −1.37 (1) | −0.95 (3) | −0.25 (8) | −1.15 (2) |
Metabolism | IPR032466 | Metal-dependent hydrolase | 1.48 (166) | 0.69 (94) | −1.13 (23) | −0.89 (28) | −0.32 (44) | −0.05 (54) | −1.61 (15) | −0.98 (26) |
Metabolism | IPR036849 | Enolase-like, C-terminal domain | 1.38 (71) | 0.91 (50) | −0.62 (14) | −0.55 (15) | −0.78 (12) | −0.29 (19) | −1.41 (6) | −1.29 (7) |
Metabolism | IPR036396 | Cytochrome P450 | 0.90 (1220) | 0.19 (745) | 0.16 (732) | 0.07 (688) | −0.20 (568) | −0.12 (600) | −1.05 (314) | −0.85 (361) |
Signaling | IPR035983 | HECT, E3 ligase catalytic domain | 1.22 (95) | 0.84 (72) | 0.10 (41) | −0.52 (25) | −0.90 (18) | −0.21 (32) | −1.84 (7) | −1.25 (13) |
Category | IPR ID | Superfamily Name | Tco | Tci | Cs | Aa | Ha | Nt | Os | At |
---|---|---|---|---|---|---|---|---|---|---|
Signaling | IPR039512 | RCHY1, zinc-ribbon | −1.18 (3) | −0.48 (8) | −0.09 (12) | −0.09 (12) | −0.01 (13) | 1.28 (39) | −0.72 (6) | −0.09 (12) |
Category | IPR ID | Superfamily Name | Tco | Tci | Cs | Aa | Ha | Nt | Os | At |
---|---|---|---|---|---|---|---|---|---|---|
Biodefense | IPR035992 | Ricin B-like lectins | 0.81 (44) | 1.41 (69) | −0.34 (17) | −0.05 (22) | −1.22 (7) | −0.80 (11) | −1.10 (8) | −1.48 (5) |
Biodefense | IPR036861 | Endochitinase-like | −0.13 (7) | −1.13 (1) | −0.39 (5) | −0.25 (6) | 0.53 (14) | 0.29 (11) | 0.09 (9) | 0.37 (12) |
Signaling | IPR036097 | Signal transduction histidine kinase, dimerization/phosphoacceptor domain | −0.11 (32) | 1.41 (101) | −0.62 (21) | −0.37 (26) | −0.28 (28) | 0.35 (46) | −1.74 (7) | −0.74 (19) |
Signaling | IPR024792 | Rho GDP-dissociation inhibitor domain | 0.48 (18) | 1.24 (34) | −0.14 (10) | −0.58 (6) | −0.34 (8) | −0.14 (10) | −1.04 (3) | −1.04 (3) |
Metabolism | IPR012347 | Ferritin-like | 0.72 (22) | 1.29 (35) | −0.03 (11) | −0.71 (5) | −0.57 (6) | −0.86 (4) | −1.23 (2) | −0.57 (6) |
Metabolism | IPR036909 | Cytochrome c-like domain | 0.40 (21) | 1.16 (39) | −0.50 (9) | −0.84 (6) | −0.22 (12) | −0.16 (17) | −0.82 (7) | −0.82 (7) |
Metabolism | IPR037069 | Acyl-CoA dehydrogenase/oxidase, N-terminal domain | 0.45 (22) | 1.05 (36) | −0.60 (8) | −0.30 (11) | −0.22 (12) | 0.22 (18) | −0.98 (5) | −0.84 (6) |
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Yamashiro, T.; Shiraishi, A.; Nakayama, K.; Satake, H. Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants. Int. J. Mol. Sci. 2022, 23, 7039. https://doi.org/10.3390/ijms23137039
Yamashiro T, Shiraishi A, Nakayama K, Satake H. Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants. International Journal of Molecular Sciences. 2022; 23(13):7039. https://doi.org/10.3390/ijms23137039
Chicago/Turabian StyleYamashiro, Takanori, Akira Shiraishi, Koji Nakayama, and Honoo Satake. 2022. "Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants" International Journal of Molecular Sciences 23, no. 13: 7039. https://doi.org/10.3390/ijms23137039