Abstract
Main conclusion
We report the genome assembly of P. cochinchinensis, as the first high-quality chromosome-level genome of Phyllanthaceae which is rich in medicinal plants.
Abstract
Phyllanthus cochinchinensis, a member of the Phyllanthaceae, is one of the famous medicinal plants in South China. Here, we report a de novo chromosome-level genome assembly for P. cochinchinensis using a combination of Nanopore and Illumina sequencing technologies. In total, the assembled genome consists of 284.88 Mb genomic sequences with a contig N50 of 10.32 Mb, representing ~ 95.49% of the estimated genome size. By applying Hi-C data, 13 pseudochromosomes of P. cochinchinensis were constructed, covering ~ 99.87% of the assembled sequences. The genome is annotated with 59.12% repetitive sequences and 20,836 protein-coding genes. Whole-genome duplication of P. cochinchinensis is likely shared with Ricinus communis as well as Vitis vinifera. Homologous genes within the flavonoid pathway for P. cochinchinensis were identified and copy numbers and expression level of related genes revealed potential critical genes involved in flavonoid biosynthesis. This study provides the first whole-genome sequence for the Phyllanthaceae, confirms the evolutionary status of Phyllanthus from the genomic level, and provides foundations for accelerating functional genomic research of species from Phyllanthus.
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Data availability
The datasets generated and analyzed during the current study are available in the NCBI repository (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA825722).
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Acknowledgements
This work is supported by the Natural Science Foundation of Crops Research Institute, Guangdong Academy of Agricultural Sciences (0145); the National Natural Science Foundation of China (31960064); the Special Fund for Introducing Scientific and Technological Talents of Guangdong Academy of Agricultural Sciences (R2021YJ-YB2008) and Scientific innovation strategy construction of the high-level Academy of Agriculture Science (R2019PY-JX003). We were grateful to Professor Chao-rong Tang of Hai Nan University, Professor Wei Hu of Chinese Academy of Tropical Agricultural Sciences, Professor Mao-Sheng Chen and Professor Zeng-Fu Xu of CAS Key Laboratory of Tropical Plant Resources and Sustainable Use for providing annotation file of Manihot esculenta and Jatropha curcas. We were also grateful to Professor Guang-da Tang of South China Agricultural University for identifying Phyllanthus cochinchinensis.
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Fig. S1
Results of 19-mer frequency analysis to estimate the genome size. The genome size was estimated using the frequency peak at 53 as coverage-depth. The peak at 28 is attributed to high heterozygosity. The genome size was calculated by dividing the total K-mer count by coverage-depth (16,095,655,854 / 53.95 = 298,343,945) (PDF 345 KB)
Fig. S2
Distribution of Ks values within or between P. cochinchinensis and other seven malpighiales species. (PDF 214 KB)
Fig. S3
Inter-genomic comparison of P. cochinchinensis vs R. communis (left); P. cochinchinensis vs P. trichocarpa (right). (PDF 5436 KB)
Fig. S4
Genomic syntenic depth ratio analysis. (PDF 438 KB)
Fig. S5
Measurement of flavonoid compounds in stems and leaves. Significant difference (P-value< 0.001) was marked by ***. (PDF 306 KB)
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Zhang, W., Xu, S., Gu, Y. et al. The first high-quality chromosome-level genome assembly of Phyllanthaceae (Phyllanthus cochinchinensis) provides insights into flavonoid biosynthesis. Planta 256, 109 (2022). https://doi.org/10.1007/s00425-022-04026-7
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DOI: https://doi.org/10.1007/s00425-022-04026-7