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INTRUDUCTION: Xanthopappus subacaulis, endemic to the Qinghai-Xizang Plateau, is a perennial medicinal plant from the genus Xanthopappus of the family Asteraceae, with important economic, ecological and medicinal values. However, genomic information for this species remains limited, hindering further genetic studies and resource utilization. Determining an appropriate sequencing strategy for its whole genome is a key prerequisite for subsequent genomic studies.
RATIONALE: In order to determine the appropriate sequencing strategy for the whole genome of X. subacaulis, we analyzed and evaluated its genome size, heterozygosity, repeat and GC content using flow cytometry and genome survey analysis based on BGI sequencing.
RESULTS: Flow cytometry analyses using Opisthopappus longilobus and Solanum lycopersicum as reference genomes indicated that X. subacaulis was a diploid, with an estimated genome size of 1.94 G and 1.75 G respectively, and a DNA-C value of 0.99 pg. We generated approximately 100.3 G of clean short read sequencing data, with a GC content of 38.5%. K-mer analysis indicated that the genome size of X. subacaulis was 2 198.50 Mb, with a heterozygosity rate of 0.69%, and repeat content of 80.15%. The analysis of the long terminal repeat retrotransposons (LTR-RTs) indicated that the LTR/Copia was the most abundant LTR family, accounting for 30.72% of the whole genome, while the Gypsy family and the unknown LTRs accounted for 33.66% and 16.54%, respectively. Moreover, their peak insertion time began approximately three million years ago (Mya), with a marked amplification occurring within the last 1 Mya. These results suggested that the large-scale insertion of LTR elements was (most) likely one of the important factors leading to the genomic complexity of X. subacaulis.
CONCLUSION: This study clarifies the key genomic characteristics of X. subacaulis, which provides valuable reference data resources for subsequent genetic map construction and functional gene mining of X. subacaulis, and also lays a foundation for determining its whole-genome sequencing strategy.
Growth morphology and genomic characteristics of Xanthopappus subacaulis. (A) Growth morphology of X. subacaulis (bar=5 cm); (B) Depth and frequency distribution of K-mer and insertion time analysis of long terminal repeat retrotransposons (LTR-RTs)
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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