Researchers from BGI-Research and collaborating institutions (Southwest Forestry University; Xi’an Jiaotong University; South China Botanical Garden; and Chinese Academy of Sciences, Shanghai) have recently assembled high-quality, chromosome-scale genome sequences for 11 economically and ecologically important timber trees. These species are from the mahogany, rosewood, teak, and balsa families.
This achievement is of great significance to current research in the field and also lays a foundation for future research on genetic resources with similar characteristics, as well as for genetic improvement in other species. The findings were published in Scientific Data, a peer-reviewed, open-access journal published by Nature Research. Scientific Data focuses on descriptions of datasets and research that advance the sharing and reuse of scientific data.
The Chromosome-scale genomes series of the four research papers.
The newly sequenced species include Swietenia macrophylla and Khaya senegalensis (mahoganies), Dalbergia sissoo (Indian rosewood), Ochroma pyramidale (balsa), Mesua ferrea (Ceylon ironwood), Tectona grandis (teak), Pterocarpus santalinus (red sandalwood), Pterocarpus macrocarpus (Burma padauk), Dalbergia cochinchinensis (Thailand rosewood), Dalbergia cultrata, and Senna siamea.
The study is part of the 10,000 Plant Genomes Project（10KP）initiative, which is dedicated to creating plant genomic resources that serve scientific research, societal needs, and environmental sustainability. The samples were collected from the Ruili Botanical Garden and Xishuangbanna Tropical Botanical Garden in Yunnan, China.
The study found that the heartwood of these tree species is not only dense and durable but also emits a fragrance in some of the new wood, thereby adding to its high decorative and practical value. These trees yield high-value decorative wood that is used in quality furniture, musical instruments, and luxury products. Several species also possess medicinal properties. However, many have suffered population declines due to overexploitation.
Dr. Sunil Kumar Sahu, a research scientist from BGI-Research, said: “The high-quality genomic data generated in this study have been made freely available and are anticipated to serve as a valuable genetic resource. This availability is crucial for promoting comparative genomic analyses and gaining a deeper understanding of wood properties in non-model woody species.”
The assembled genomes provide a valuable genetic resource to support conservation as well as molecular breeding efforts to improve desirable traits. They also enable comparative analyses to uncover genomic factors influencing commercially relevant wood properties, such as density, strength, color, and durability. The researchers utilized a combination of conformation sequencing strategies to produce contiguous and accurate chromosome-scale genome assemblies. The assembly results show excellent continuity and completeness. Additionally, elucidating the genetic basis of commercially prized attributes in threatened species, such as P. santalinus, will strengthen conservation efforts and help relieve harvesting pressures on wild populations.
Most species displayed elevated gene counts compared to their closely related plant relatives with previously published genomes. This difference may reflect the challenges associated with assembling the repetitive regions typical of tree genomes. It also highlights the utility of using certain sequencing strategies to improve gene space representation. Over 97% of the predicted genes showed homology support from protein databases, although many lacked specific functional annotations, representing targets for further research.
Dr. Liu Huan, Chief Scientist at BGI-Research, stated: “Although quite a few tree genomes have been published, and the general wood formation and genome architecture have been extensively discussed in model timber tree species like poplar, oak, and eucalyptus, the tree species sequenced in this study exhibit distinct wood properties. This suggests that the novelties in this research differ from those in other published tree genome studies.”
The chromosome-scale assemblies significantly enhance genome resources for valuable timber trees. They provide genomic frameworks to uncover traits associated with wood properties, environmental adaptation, growth, and disease resistance.
By identifying genes associated with heartwood, these assemblies may aid in tree improvement efforts and help shorten breeding cycles. Additionally, their relatively complete gene inventories can facilitate research into the biosynthesis of medicinal compounds. These high-quality genomes provide tools to promote the ecologically sustainable utilization of precious tree species, and realize their potential to enhance climate resilience in managed forests.
Read the research articles:
https://www.nature.com/articles/s41597-023-02593-2
https://www.nature.com/articles/s41597-023-02420-8
https://www.nature.com/articles/s41597-023-02707-w
https://www.frontiersin.org/articles/10.3389/fpls.2023.1218515/full