Chromosomal-level genome of the Pinus massoniana 'Minlin WY36'

Sun, W.-H.; Zhang, F.; Zhao, X.; Li, Z.; Liu, K.-W.; Wu, S.; Guo, Y.; Hu, X.; Zeng, M.; Wang, L.; Zhou, C.-Y.; Chen, D.; Zheng, R.; Wu, X.; Peng, D.-H.; Ma, L.; Wang, Z.-W.; Lan, W.; Chen, H.; Zou, S.; Tsai, W.-C.; Van de Peer, Y.; Liu, Z.-J.; Lan, S.

doi:10.1101/2025.06.23.660646

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bioRxiv · 10.1101/2025.06.23.660646

Chromosomal-level genome of the Pinus massoniana 'Minlin WY36'

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Abstract

Owing to conifers complex and large genomes, it is challenging to construct a comprehensive reference genome and conduct evolutionary and genomic research. Here, we present the chromosome-level assembly of Pinus massoniana Minlin WY36, a pioneering conifer species used for afforestation, timber production, and oleoresin extraction. The genome size was determined to be 23.41 Gb, with a contig N50 value of 1.15 Mb and a scaffold N50 value of 2.02 Gb. A total of 23.16 Gb of reads (98.93% of the assembled genome) were anchored and oriented onto 12 pseudochromosomes, with chromosome lengths from 1.47 to 2.29 Gb. A total of 32,144 protein-coding genes were predicted, of which 27,173 (84.54%) were functionally annotated. The P. massoniana Minlin WY36 genome consists of 79.41% (18.57 Gb) repetitive sequences, among which long terminal repeat sequences (LTR) were the most abundant. Through comparative genomic analysis, we found that the unique and significantly expanded genes in P. massoniana Minlin WY36 were enriched in the metabolism related to resin synthesis. This study offers valuable insights into conifer evolution and contributes resources for further investigations of conifer adaptation and developmental processes.

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Sun, W.-H., Zhang, F., Zhao, X., Li, Z., Liu, K.-W., Wu, S., Guo, Y., Hu, X., Zeng, M., Wang, L., Zhou, C.-Y., Chen, D., Zheng, R., Wu, X., Peng, D.-H., Ma, L., Wang, Z.-W., Lan, W., Chen, H., Zou, S., Tsai, W.-C., Van de Peer, Y., Liu, Z.-J., Lan, S.. 2025-06-26. Chromosomal-level genome of the Pinus massoniana 'Minlin WY36'. https://doi.org/10.1101/2025.06.23.660646

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