Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights
Abstract
:1. Introduction
2. Materials and Methods
2.1. A. chaxingu Strain, Culture Conditions, and Nucleic Acid Preparation
2.2. Genome Sequencing and Heterozygosity Estimation
2.3. De Novo Genome Assembly and Quality Assessment
2.4. Genome Annotation
2.5. Identification of Mating-Type Locus
2.6. Phylogenomic and Evolutionary Analyses
2.7. Comparative Genomic Analysis
2.8. Transcriptome Analysis
3. Results
3.1. Genome Sequencing, T2T Assembly, and Quality Assessment
3.2. Repeat Annotation, Noncoding RNA Annotation, and Gene Prediction
3.3. Analysis of Mating-Type Genes
3.4. Prediction of Secondary Metabolite Biosynthetic Gene Clusters
3.5. Whole Genome Comparison and Syntenic Analysis
3.6. Phylogenomic Analysis and Gene Family Evolution
3.7. Gene Expression Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Type | Percent (%) of CchA | Percent (%) of CchB |
---|---|---|
Complete BUSCOs (C) | 98.50 | 98.50 |
Complete and single-copy BUSCOs (S) | 97.80 | 97.80 |
Complete and duplicated BUSCOs (D) | 0.70 | 0.70 |
Fragmented BUSCOs (F) | 0.10 | 0.10 |
Missing BUSCOs (M) | 1.40 | 1.40 |
Assembly Feature | Agrocybe chaxingu CchA | Agrocybe chaxingu CchB | Agrocybe chaxingu MP-N11 | Cyclocybe aegerita AAE-3 | Cyclocybe aegerita AAE-3-13 | Cyclocybe aegerita AAE-3-32 | Cgrocybe cylindracea ASM1337643v1 |
---|---|---|---|---|---|---|---|
Number of contigs | 13 | 13 | 4466 | 122 | 120 | 120 | 3790 |
Assembly length (Mb) | 50.60 | 51.66 | 40.30 | 44.79 | 44.74 | 44.73 | 56.49 |
Total N counts | 0 | 0 | 31,056 | 1,418,454 | 975,332 | 1,109,304 | 940,733 |
Contig N50 (Mb) | 3.95 | 3.97 | 0.0181 | 0.7684 | 0.7683 | 0.7683 | 0.5473 |
Max length (Mb) | 5.19 | 5.46 | 0.12 | 2.76 | 2.76 | 2.76 | 2.74 |
Min length (Mb) | 2.65 | 2.98 | 0.0005 | 0.0024 | 0.0033 | 0.0033 | 0.0005 |
Mean length (Mb) | 3.89 | 3.97 | 0.0090 | 0.37 | 0.37 | 0.37 | 1.49 |
Complete BUSCOs (%) | 98.50 | 98.50 | / | 97 | 97 | 94 | / |
Repeat content (%) | 16.97 | 17.97 | / | / | / | / | 12.54 |
GC (%) | 50.99 | 50.98 | 51.00 | 49.22 | 49.66 | 49.42 | 50.20 |
Assembly level | Chromosome-level | Chromosome-level | Scaffold | Scaffold | Scaffold | Scaffold | Scaffold |
Number of telomeres | 26 | 26 | 0 | 0 | 0 | 0 | 0 |
Reference | This study | This study | NCBI *: GCA_027627235.1 | [11] | [11] | [11] | [12] |
Classification | Order | Super Family | CchA | CchB | ||||
---|---|---|---|---|---|---|---|---|
Number of Elements | Length Occupied (bp) | Percentage of Sequence (%) | Number of Elements | Length Occupied (bp) | Percentage of Sequence (%) | |||
Class I (Retroelements) | 1125 | 2,633,630 | 5.21 | 1118 | 3,122,510 | 6.04 | ||
SINEs | 40 | 13,193 | 0.03 | 45 | 13,789 | 0.03 | ||
LINEs | 494 | 874,092 | 1.73 | 457 | 858,312 | 1.66 | ||
RTE/Bov-B | 0 | 0 | 0.00 | 41 | 10,852 | 0.02 | ||
L1/CIN4 | 8 | 3451 | 0.01 | 0 | 0 | 0.00 | ||
Unknown | 486 | 870,641 | 1.72 | 416 | 847,460 | 1.64 | ||
LTR elements | 591 | 1,746,345 | 3.45 | 616 | 2,250,409 | 4.36 | ||
Ty1/Copia | 200 | 214,240 | 0.42 | 133 | 212,896 | 0.41 | ||
Gypsy/DIRS1 | 391 | 1,532,105 | 3.03 | 483 | 2,037,513 | 3.94 | ||
Class II (DNA transposons) | 130 | 156,143 | 0.31 | 174 | 300,689 | 0.58 | ||
Hobo-Activator | 0 | 0 | 0.00 | 95 | 149,817 | 0.29 | ||
Tc1-IS630-Pogo | 14 | 3212 | 0.01 | 0 | 0 | 0.00 | ||
Unknown | 116 | 152,931 | 0.30 | 79 | 150,872 | 0.29 | ||
Unclassified | 6141 | 4,967,145 | 9.82 | 6886 | 5,258,353 | 10.18 | ||
Total interspersed repeats | 7396 | 7,756,918 | 15.33 | 8187 | 8,681,552 | 16.81 | ||
Rolling-circles | 205 | 514,795 | 1.02 | 128 | 275,812 | 0.53 | ||
Satellites | 1 | 87 | 0.00 | 0 | 0 | 0.00 | ||
Simple repeats | 5842 | 257,760 | 0.51 | 5979 | 262,399 | 0.51 | ||
Low complexity | 1073 | 59,876 | 0.12 | 1073 | 61,607 | 0.12 | ||
Total repeats | 14,517 | 8,589,436 | 16.97 | 15,367 | 9,281,370 | 17.97 |
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Chen, X.; Wei, Y.; Meng, G.; Wang, M.; Peng, X.; Dai, J.; Dong, C.; Huo, G. Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights. J. Fungi 2024, 10, 602. https://doi.org/10.3390/jof10090602
Chen X, Wei Y, Meng G, Wang M, Peng X, Dai J, Dong C, Huo G. Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights. Journal of Fungi. 2024; 10(9):602. https://doi.org/10.3390/jof10090602
Chicago/Turabian StyleChen, Xutao, Yunhui Wei, Guoliang Meng, Miao Wang, Xinhong Peng, Jiancheng Dai, Caihong Dong, and Guanghua Huo. 2024. "Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights" Journal of Fungi 10, no. 9: 602. https://doi.org/10.3390/jof10090602