Materials and methods Plant materials, DNA extraction and genome sequencingįresh Q. acutissima, laying the foundation for novel genes discovery and ultimately contributing to the development of novel properties for the species breeding programs. Our results are expected to improve our understanding of the evolution and diversification of genes in Q. We performed structural gene annotation, repetitive sequences identification, and executed comparative genomics with other plant genomes. acutissima genome was sequenced and de novo assembled using PacBio long reads, Hi-C reads, and Illumina short reads. acutissima native populations is crucial, and the understanding of the species genome-wide evolution, gene function, and molecular breeding are important elements to supporting these goal ( Greene and Morris, 2001). Thus, planning breeding and conservation programs for Q. acutissima forest ecosystems have been degraded due to human disturbance, threatening the species genetic resources ( Aldrich et al., 2003 Zhang et al., 2013). acutissima is mainly focused on propagation, eco-physiology, selection, and genetic diversity ( Dong, 2008 Wang et al., 2009 Liao, 2012 Zhang et al., 2013). acutissima timber provides excellent building material and charcoal production in many Asian countries, including China, Japan, and Korea ( Zhang et al., 2013). acutissima is usually mixed or secondary monocultures, which are also distributed in a scattered manner in harsh environments ( Aldrich et al., 2003 Zhang et al., 2013). acutissima Carruth is widely distributed in East Asia, especially in southeast China (18° - 41° N, 91° - 123☎) ( Li et al., 2018 Yang et al., 2019). acutissima have been published, the continuity of the assembly still needs improvement ( Fu et al., 2022).Īs an important ecological and economic tree species, Q. However, only four species with whole genome sequences have been published, including Q. glauca, and 10 other Quercus plastomes ( Li et al., 2021). Within the Quercus genera, the evolutionary profiles of plastid genomes have been elucidated in Q. The subgenera Quercus includes five groups (sections): Ponticae, Virentes, Protobalanus (intermediate Oak), Quercus (white oak), and Lobatae (red oak), while Cerris includes three groups (sections): Ilex, Cerris and Cyclobalanopsis ( Denk et al., 2017). According to molecular classification, the genera Quercus has been divided into two subgenera, Quercus and Cerris ( Denk and Grimm, 2010 Denk et al., 2017 Deng et al., 2018 Hipp et al., 2018). Oaks have various utilities, including timber, bioenergy, and dyes production ( Sasaki et al., 2014 Wu et al., 2014 Li et al., 2018). acutissima genome not only promises to accelerate the species molecular biology studies and breeding, but also promotes genome level evolutionary studies.Īs one of the largest genera in Fagaceae, Quercus (oak) contains more than 400 widely distributed species in Asia, Europe, Africa, and North America ( Simeone et al., 2016). variabilis were differentiated around 3.6 million years ago, and showed no evidence of species-specific whole genome duplication.Ĭonclusion: The assembled and annotated high-quality Q. Ab initio, homology-based and RNA sequence-based gene prediction identified 29,889 protein-coding genes, of which 82.6% could be functionally annotated. The repetitive sequences constituted 55.63% of the genome, among which long terminal repeats were the majority and accounted for 23.07% of the genome. Results: We generated a 957.1 Mb genome with a contig N50 of 1.2 Mb and scaffold N50 of 77.0 Mb. Methods: Here, we combined PacBio long reads, Hi-C, and Illumina short reads to assemble Q. Introduction: Quercus acutissima is an economic and ecological tree species often used for afforestation of arid and semi-arid lands and is considered as an excellent tree for soil and water conservation. 3Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada.2Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, China.1National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.Dan Liu 1,2 Xiaoman Xie 2 Boqiang Tong 2 Chengcheng Zhou 1 Kai Qu 1 Haili Guo 2 Zhiheng Zhao 1 Yousry A.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |