Chromosome-scale genomes of commercially important mahoganies, Swietenia macrophylla and Khaya senegalensis.

Mahogany species (family Meliaceae) are highly valued for their aesthetic and durable wood. Despite their economic and ecological importance, genomic resources for mahogany species are limited, hindering genetic improvement and conservation efforts. Here we perform chromosome-scale genome assemblies of two commercially important mahogany species: Swietenia macrophylla and Khaya senegalensis. By combining 10X sequencing and Hi-C data, we assemble high-quality genomes of 274.49 Mb (S. macrophylla) and 406.50 Mb (K. senegalensis), with scaffold N50 lengths of 8.51 Mb and 7.85 Mb, respectively. A total of 99.38% and 98.05% of the assembled sequences are anchored to 28 pseudo-chromosomes in S. macrophylla and K. senegalensis, respectively. We predict 34,129 and 31,908 protein-coding genes in S. macrophylla and K. senegalensis, respectively, of which 97.44% and 98.49% are functionally annotated. The chromosome-scale genome assemblies of these mahogany species could serve as a vital genetic resource, especially in understanding the properties of non-model woody plants. These high-quality genomes could support the development of molecular markers for breeding programs, conservation efforts, and the sustainable management of these valuable forest resources.

Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis).

Wood is the most important natural and endlessly renewable source of energy. Despite the ecological and economic importance of wood, many aspects of its formation have not yet been investigated. We performed chromosome-scale genome assemblies of three timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis) which exhibit different wood properties such as wood density, hardness, growth rate, and fiber cell wall thickness. The combination of 10X, stLFR, Hi-Fi sequencing and HiC data led us to assemble high-quality genomes evident by scaffold N50 length of 55.97 Mb (O. pyramidale), 22.37 Mb (M. ferrea) and 14.55 Mb (T. grandis) with >97% BUSCO completeness of the assemblies. A total of 35774, 24027, and 44813 protein-coding genes were identified in M. ferrea, T. grandis and O. pyramidale, respectively. The data generated in this study is anticipated to serve as a valuable genetic resource and will promote comparative genomic analyses, and it is of practical importance in gaining a further understanding of the wood properties in non-model woody species.

The chromosome-scale genomes of Dipterocarpus turbinatus and Hopea hainanensis (Dipterocarpaceae) provide insights into fragrant oleoresin biosynthesis and hardwood formation.

Dipterocarpaceae are typical tropical plants (dipterocarp forests) that are famous for their high economic value because of their production of fragrant oleoresins, top-quality timber and usage in traditional Chinese medicine. Currently, the lack of Dipterocarpaceae genomes has been a limiting factor to decipher the fragrant oleoresin biosynthesis and gain evolutionary insights into high-quality wood formation in Dipterocarpaceae. We generated chromosome-level genome assemblies for two representative Dipterocarpaceae species viz. Dipterocarpus turbinatus Gaertn. f. and Hopea hainanensis Merr. et Chun. Our whole-genome duplication (WGD) analysis revealed that Dipterocarpaceae underwent a shared WGD event, which showed significant impacts on increased copy numbers of genes related to the biosynthesis of terpene, BAHD acyltransferases, fatty acid and benzenoid/phenylpropanoid, which probably confer to the formation of their characteristic fragrant oleoresin. Additionally, compared with common soft wood plants, the expansion of gene families was also found to be associated with wood formation, such as in CESA (cellulose synthase), CSLE (cellulose synthase-like protein E), laccase and peroxidase in Dipterocarpaceae genomes, which might also contribute to the formation of harder, stronger and high-density timbers. Finally, an integrative analysis on a combination of genomic, transcriptomic and metabolic data from different tissues provided further insights into the molecular basis of fragrant oleoresins biosynthesis and high-quality wood formation of Dipterocarpaceae. Our study contributes the first two representative genomes for Dipterocarpaceae, which are valuable genetic resources for further researches on the fragrant oleoresins and superior-quality timber, genome-assisted breeding and improvement, and conservation biology of this family.

The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway.

Clausena lansium (Lour.) Skeels (Rutaceae), recognized as wampee, is a widely distributed fruit tree which is utilized as a folk-medicine for treatment of several common diseases. However, the genomic information about this medicinally important species is still lacking. Therefore, we assembled the first genome of Clausena genus with a total length of 310.51 Mb and scaffold N50 of 2.24 Mb by using 10× Genomics technology. Further annotation revealed a total of 34,419 protein-coding genes, while repetitive elements covered 39.08% (121.36 Mb) of the genome. The Clausena and Citrus genus were found to diverge around 22 MYA, and also shared an ancient whole-genome triplication event with Vitis. Furthermore, multi-tissue transcriptomic analysis enabled the identification of genes involved in the synthesis of carbazole alkaloids. Altogether, these findings provided new insights into the genome evolution of Wampee species and highlighted the possible role of key genes involved in the carbazole alkaloids biosynthetic pathway.

Dissecting the genome of star fruit (Averrhoa carambola L.).

Averrhoa carambola is commonly known as star fruit because of its peculiar shape, and its fruit is a rich source of minerals and vitamins. It is also used in traditional medicines in countries such as India, China, the Philippines, and Brazil for treating various ailments, including fever, diarrhea, vomiting, and skin disease. Here, we present the first draft genome of the Oxalidaceae family, with an assembled genome size of 470.51 Mb. In total, 24,726 protein-coding genes were identified, and 16,490 genes were annotated using various well-known databases. The phylogenomic analysis confirmed the evolutionary position of the Oxalidaceae family. Based on the gene functional annotations, we also identified enzymes that may be involved in important nutritional pathways in the star fruit genome. Overall, the data from this first sequenced genome in the Oxalidaceae family provide an essential resource for nutritional, medicinal, and cultivational studies of the economically important star-fruit plant.

[Incidence and risk factors of HIV infection among sero-negative spouses of HIV patients in Dehong prefecture of Yunnan province].

OBJECTIVE: To study the HIV incidence and risk factors among sero-negative spouses of HIV patients in Dehong prefecture of Yunnan province. METHODS: A cohort of sero-negative spouses of the HIV patients had been developed and followed up since November, 2005. HIV new infections and related behaviors had been investigated every six months. RESULTS: By the end of June, 2008, 790 sero-negative spouses of HIV patients had been recruited, of whom 702 were followed-up for at least one time. During the total 1202.35 person-years, 31 new HIV infections were identified, with an overall incidence of 2.58/100 person-years. The HIV incidence rates were 2.22/100 person-years in 2006, 2.95/100 person-years in 2007 and 2.74/100 person-years in 2008. Data from the Cox proportional hazard regression model indicated that those who resided in Yingjiang county [hazard ratio (HR) = 4.37, 95%CI: 1.48 - 12.90, P = 0.008], ever using drugs (HR = 3.49, 95%CI: 1.09 - 11.18, P = 0.035), or having an HIV-infected spouse who never exposed to antiretroviral treatment (HR = 3.60, 95%CI: 1.41 - 9.16, P = 0.007) were at higher risk for HIV infection. CONCLUSION: Sero-negative spouses of HIV patients in Dehong prefecture of Yunnan province had a relatively high incidence of HIV new infection during 2006-2008. More efforts should put on those people living in these areas, having a history of drug use or having an HIV-infected spouse who had never been exposed to antiretroviral treatment.

[Incidence and risk factors on HIV infection among injection drug users in Dehong prefecture area of Yunnan province].

OBJECTIVE: To determine the incidence and risk factors on HIV infection among injection drug users (IDU) in Dehong prefecture area of Yunnan province. METHODS: An epidemiological cohort of HIV-negative IDU had been developed and followed since October, 2004. HIV new infections and related behaviors had been investigated every six months. RESULTS: By the end of 2008, 760 HIV-negative IDU had been recruited and followed for a total of 1153.6 person-years. 47 new HIV infections were identified, with an overall incidence of 4.07/100 person-years during the follow-up period. The HIV incidence was 4.45/100 person-years during 2004 - 2006, 4.50/100 person-years in 2007 and 2.54/100 person-years in 2008. Both the behavior of drug injection and the HIV incidence among the cohort had substantially decreased during the follow-up period. Multiple regression analysis using Cox proportional hazard model indicated that people with Jing-po ethnicity (Hazard ratio, HR = 2.56, 95%CI: 1.06 - 6.19) and other minorities except for Dai (HR = 3.26, 95%CI: 0.89 - 11.96) were at higher risk for HIV infection than the people with Han ethnicity. People injecting drugs with (HR = 2.27, 95%CI: 0.98 - 5.25) or without (HR = 5.27, 95%CI: 2.25 - 12.34) needle sharing were at higher risk for HIV infection than those reporting having no drug injection behavior during the follow-up period. CONCLUSION: Both the behavior of drug injection and the HIV incidence among former IDU in Dehong prefecture area of Yunnan province had been decreasing during the four years. However, needle sharing remained the most important risk factor for HIV new infection among IDUs. IDUs with different ethnicities seemed to have different risks towards HIV infection.