Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Section Observation
2.3. Genome Sequencing
2.4. RNA-Seq Library Construction and Sequencing
2.5. De Novo Sequencing and Genome Assembly
2.6. Repetitive Element Annotation and Gene Prediction
2.7. Comparative Genome Analysis
2.8. Structural Variants Analysis
2.9. GO Enrichment and Functional Annotation of Genes with SVs and PAVs
2.10. Analysis of Expansion and Contraction for Flowering-Time-Related Genes
3. Results and Discussion
3.1. Genome Sequencing and Assembly
3.2. Genome Annotation
3.3. Synteny and Phylogenetic Analysis
3.4. Variation between Luffa acutangula SG261 and Luffa cylindrica
3.5. Functional Annotation and GO Enrichment of SV and PAV Genes
3.6. Structural Variation Genes Involved in Ridge Development
3.7. Analysis of Flowering-Time-Related Genes
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Sample ID | Illumina + PacBio + Hi-C | |||
---|---|---|---|---|
Length | Number | |||
Contig (bp) | Scaffold (bp) | Contig | Scaffold | |
Total | 739,313,328 | 739,817,328 | 283 | 31 |
MAX | 37,192,690 | 64,188,378 | - | - |
mean | 2,612,414 | 23,865,075 | - | - |
A | 236,049,024 | 236,049,024 | 31.93% | 31.91% |
C | 133,750,610 | 133,750,610 | 18.09% | 18.08% |
T | 235,878,785 | 235,878,785 | 31.91% | 31.88% |
G | 133,634,909 | 133,634,909 | 18.08% | 18.06% |
N | - | 504,000 | - | 0.07% |
N50 | 18,375,156 | 56,077,004 | 15 (5.30%) | 7 (22.58%) |
N60 | 13,378,742 | 55,168,345 | 20 (7.07%) | 8 (25.81%) |
N70 | 10,763,832 | 54,241,644 | 26 (9.19%) | 9 (29.03%) |
N80 | 8,026,258 | 51,658,337 | 34 (12.01%) | 11 (35.48%) |
N90 | 4,503,403 | 51,095,587 | 46 (16.25%) | 12 (38.71%) |
Luffa cylindrica (L.) [12] | Luffa cylindrica (L.) [11] | Luffa Cylindrica [10] | Luffa acutangula [10] | Luffa acutangula SG261 | |
---|---|---|---|---|---|
Sequence method | Pacbio | Pacbio | Pacbio | Pacbio | Pacbio |
N50 (contig) (bp) | 4,815,853 | 8,800,239 | - | 110,403 | 18,375,156 |
N50 (scaffold) (bp) | 48,664,788 | 48,760,765 | 578,616 | 47,609,564 | 56,077,004 |
Genome size (Mb) | 669.7 | 656.2 | 689.8 | 735.6 | 739.8 |
Longest scaffold (bp) | 62,749,569 | 55,641,800 | 7,054,290 | 56,032,585 | 64,188,378 |
Repetitive sequence length (bp) | 416,310,000 | 419,095,893 | 391,650,000 | 456,690,000 | 536,834,300 |
Non-repeated sequence length (bp) | 253,398,411 | 237,094,093 | 298,222,192 | 278,920,612 | 202,983,028 |
BUSCO | 91.6% | 95.5% | 93.00% | 92.70% | 91.25% |
Total number of genes | 31,661 | 27,154 | 43,828 | 32,233 | 27,312 |
Average transcript (mRNA) length (bp) | - | 4184.44 | - | 1508.632356 | 1350.665312 |
Average CDS length (bp) | 1246.02 | 1160.18 | - | 1067.034598 | 1047.6968 |
Average exon length (bp) | 218.87 | 241.63 | 258,1 | 233.5 | 294.6388316 |
Average gene length (bp) | 4387.94 | 4734.773861 | 2582 | 2866 | 3404.439707 |
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Huang, A.; Feng, S.; Ye, Z.; Zhang, T.; Chen, S.; Chen, C.; Chen, S. Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development. Plants 2024, 13, 1828. https://doi.org/10.3390/plants13131828
Huang A, Feng S, Ye Z, Zhang T, Chen S, Chen C, Chen S. Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development. Plants. 2024; 13(13):1828. https://doi.org/10.3390/plants13131828
Chicago/Turabian StyleHuang, Aizheng, Shuo Feng, Zhuole Ye, Ting Zhang, Shenglong Chen, Changming Chen, and Shijun Chen. 2024. "Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development" Plants 13, no. 13: 1828. https://doi.org/10.3390/plants13131828
APA StyleHuang, A., Feng, S., Ye, Z., Zhang, T., Chen, S., Chen, C., & Chen, S. (2024). Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development. Plants, 13(13), 1828. https://doi.org/10.3390/plants13131828