BEIJING, China —The rare and endangered tree species Phoebe zhennan (commonly known as "golden-thread nanmu") is a unique timber tree of the family Lauraceae endemic to China. It is naturally distributed in Chongqing, Guizhou, Hubei, Hunan, Sichuan, and Yunnan. The wood is highly valued for its golden luster, fragrance, and durability. However, due to historical over‑harvesting and habitat loss, its wild resources have sharply declined. It is now listed as a second-class nationally protected wild plant in China and as Vulnerable on the IUCN Red List. Previous genetic studies mostly relied on low‑throughput markers such as SSR and AFLP; although these revealed some population structure, they had insufficient resolution. Recently, chromosome‑level genome assemblies have become available, but conventional non‑haplotype‑resolved assemblies cannot distinguish allelic variation from haplotype‑specific structural variants, hindering in‑depth analyses of evolutionary and adaptive mechanisms.
Researchers from the Forestry Science Research Institute of Guizhou Province and Guizhou University used the largest P. zhennan specimen (with a trunk diameter of 2.84 m) in Qinggangpo, Sinan County, Guizhou Province, as the study material. They successfully constructed the first haplotype‑resolved chromosome‑level genome for this species, obtaining two complete haplotypes – HapA (956.20 Mb) and HapB (910.89 Mb). Each was anchored to 12 chromosomes, with scaffold N50 values of 86.27 Mb and 77.12 Mb, respectively. A total of 33,757 and 33,651 protein‑coding genes were annotated, with BUSCO completeness scores of 99.1% and 98.9%, respectively. The proportions of repetitive sequences were 75.95% and 70.83%, respectively. These metrics collectively indicate a high‑quality reference genome.
In addition, the research team performed the first haplotype‑resolved whole‑genome structural variation analysis in P. zhennan , identifying a total of 112 inversions, 2,371 translocations, approximately 6.06 million single nucleotide polymorphisms (SNPs), 345,000 insertions, and 349,000 deletions. Functional enrichment analysis revealed that genes located within structural variation regions were significantly enriched in biological pathways related to DNA damage response and stress responses, suggesting that these regions may play important roles in environmental adaptation of P. zhennan . The study also identified a haplotype‑specific translocation region between Chr04 and Chr05, which contains 14 protein‑coding genes warranting further functional investigation.
This work provides a high‑precision reference genome for subsequent research in population genetics, molecular breeding, and conservation genomics. At the same time, it lays an important foundation for comparative genomics of the Lauraceae, evolution of repetitive sequences, and investigation of chromosomal structural variations.
Original Source:
Ting Zou, Rong-Rong Yan, Hong Luo, Heng-Feng Jia, Yun-Li Jiang, Guo-Xiong Hu. 2026. Haplotype-resolved chromosomal-level genome assembly of the endangered tree Phoebe zhennan . J Syst Evol. https://doi.org/10.1111/jse.70089
Keywords:
conservation genomics, chromosome-level assembly, haplotype-resolved genome, Lauraceae, Nanmu, Phoebe zhennan.
Author’s Institution:
Guizhou Academy of Forestry. College of Life Sciences, Guizhou University
About JSE:
Journal of Systematics and Evolution (JSE) is a peer-reviewed, bi-monthly international English-language journal dedicated to the understanding of biodiversity and evolution. Papers in any of the following and related fields will be considered: systematics and biodiversity conservation, paleobiology and biogeography, adaptation, speciation and domestication, evolutionary genomics and Evo-Devo, theory and methods in evolutionary biology.
Journal of Systematics and Evolution
Haplotype-resolved chromosomal-level genome assembly of the endangered tree Phoebe zhennan
3-Jul-2026