Abstract
Chusquea culeou is one important ornamental bamboo in gardens to form a substantial clump of greenery. At present, the genetic data of this species are scarce. In this study, we produced the complete chloroplast (cp) genome of C. culeou by genome skimming. The complete cp genome is 138,137 base-pairs (bp) in size, with a large single copy region (LSC) of 81,671 bp and a small single copy region (SSC) of 12,858 bp which are separated by a pair of inverted repeats (IRs) of 21,804 bp. The genome contained a total of 132 genes, including 84 protein-coding genes, 40 transfer RNAs and 8 ribosomal RNAs. There were 12 intron-containing genes. The GC content of the cp genome is 38.8% and protein-coding regions make up 43.5% of this cp genome. Phylogenomic analysis strongly supported C. culeou locating in the neotropical woody bamboos lineage, being closely related to C. liebmannii and C. circinata.
Chusquea culeou É.Desv. is an evergreen bamboo native to South America and now widely cultivated in temperate regions for its frost-tolerance (Judziewicz et al. Citation1999). Unfortunately, the wild populations of C. culeou have been largely diminished over the past decades due to the excessive deforestation. The DNA sequence data of this bamboo is very scarce at present (Fisher et al. 2014). In this study, we generated and characterized the complete chloroplast (cp) genome of C. culeou using the genome-skimming method (Zhang and Chen Citation2016), providing essential resource for conservation and utilization of this valuable bamboo.
Total genomic DNA was extracted from fresh leaves of C. culeou grown in Kunming Botanic Garden in Kunming, Yunnan province of China. The voucher specimen was deposited at the Herbarium of Kunming Institute of Botany, Chinese Academy of Sciences (accession number KMBG1218). Illumina paired-end (PE) DNA library was prepared and sequenced in Beijing Genomics Institute (BGI) in Shenzhen, China. We assembled the cp genome using CLC Genomics Workbench v7.5 (CLC Bio, Aarhus, Denmark), following previous studies (Wang et al. Citation2018a). The assembled cp genome was then annotated by DOGMA (Wyman et al. Citation2004), coupled with manual check and adjustment.
The cp genome of C. culeou (GenBank accession MH410122) is 138,137 base-pairs (bp) in size with a typical quadripartite structure: one large single copy region (LSC) of 81,671 bp and one small single copy region (SSC) of 12,858 bp being separated by two inverted repeats (IRs) of 21,804 bp. This cp genome has 132 genes, including 84 protein-coding genes, 8 ribosomal RNA genes and 40 transfer RNA genes. We found nine distinct protein-coding genes (atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rps12, rps16) contained one intron each and only one gene (ycf3) had two introns. Protein-coding regions (CDS) occupy 43.5% of C. culeou cp genome and the overall GC content of this cp genome is 38.8%. As expected, the C. culeou cp genome shows a highly conserved genome structure of tropical woody bamboos (Bambusoideae: Bambuseae) (Wysocki et al. Citation2015).
The phylogenomic analysis was conducted based on 28 Bambusoideae cp genomes using RAxML v.8.2.8 (Stamatakis Citation2014). The position of C. culeou in the clade of neotropical woody bamboos was highly supported (). The five sampled Chusquea taxa clustered together and robustly resolved as (C. spectabilis, (Chusquea sp., (C. culeou, (C. liebmannii, C. circinata)))). The phylogenetic relationships among the sampled Bambuseae species were clearly resolved as well, in agreement with previous studies (Zhang et al. Citation2018; Wang et al. Citation2018b).
Figure 1. Maximum likelihood tree resulted from 28 Bambusoideae chloroplast genomes. Coloured branches indicate the neotropical and paleotropical bamboo lineages. The position of Chusquea culeou is shown in bold. Values above nodes are bootstrapping support values.
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References
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