Genomic characteristics of critically endangered Chimonobambusa hirtinoda C.S. Chao & K.M. Lan

Abstract

With its unique square-shaped culm, Chimonobambusa hirtinoda C.S. Chao & K.M. Lan is a critically endangered species, and its natural habitat is solely restricted to Doupeng Mountain in Guizhou, China. Two small-insert libraries from C. hirtinoda were constructed and sequenced. Approximately 127.83 Gb of highquality reads were generated and assembled into 9,320,997 contigs with a N50 length of 213bp, thereby producing 8,867,344 scaffolds with total length of 2.01 Gb. An estimated genome size of C. hirtinode was 2.86 Gb on the basis of k-mer frequency analysis, with the GC content of 45.40%. The repeat rate and heterozygous ratio were 74.11 and 1.48% in C. hirtinoda genome, respectively. Finally, 65,398 SSR loci were identified in the assembled contigs, including 58.66% tri-nucleotide, 27.42% di-nucleotide, 7.94% tetranucleotide, 3.67% penta-nucleotide, and 2.31% hexa-nucleotide. Results of this study are useful not only for ecological conservation of C. hirtinoda, but also for phylogenetic studies. Introduction As an important non-timber forest resource, Bambusoideae includes 115 genera and more than 1400 species, most of which are primarily distributed in Asia, South America and Africa. The subfamily Bambusoideae is the unique one that embraces woody members in the grass family (Poaceae) (Gu et al. 2016). Woody bamboos are of notable cultural and economic significance and have a long cultivation and utilization history, providing food and raw materials for construction and manufacturing all around the world. About 2.5 billion people rely on it economically and the annual trade value has exceeded 2.5 billion US dollars (Peng et al. 2013). The subfamily Bambusoideae in China comprises 37 genera with 500 species, many species play important roles in their ecosystems (Zhang et al. 2011). Because of their remarkable growth rate, infrequent reproduction and long flowering intervals, woody bamboos are very interesting but taxonomically challenging taxa (Zhang et al. 2011, Peng et al. 2013), with potentials for economic development and scientific research. Chimonobambusa Makino (Bambusoideae, Poaceae), consisting of more than 30 taxa, are primarily distributed in China, Japan, Vietnam and Myanmar. C. hirtinoda belongs to Sect. Oreocalamus of the genus. Its internodes are usually slightly 4-angled, with a fulvous tomentose ring below each node. C. hirtinoda is a critically endangered species in China, and its natural distribution is solely restricted to Doupeng Mountain in Guizhou. Due to human interference activities such as bamboo shoot harvesting, the only C. hirtinoda population is declining (Su et al. 2016a,b), and this species is now listed as an IUCN critically endangered plant (http://www. incnredlist.org/search). So far, the study of C. hirtinoda remains as a blank sheet. With the fast development of next-generation sequencing (NGS) technology and the completion of the Moso bamboo (Phyllostachys edulis) whole-genome sequencing (Peng et al. 2013), increasing availability of genome and transcriptome data provide new insights on bamboo genetics and *Author for correspondence: [email protected]. College of Forestry, Nanjing Forestry University, Nanjing 210037, China. China National Bamboo Research Center, Hangzhou 310012, China.