Characterization of the complete chloroplast genome of Alsophila gigantea (Cyatheaceae), an ornamental and CITES giant tree fern

Abstract

We characterized the complete chloroplast genome of Alsophila gigantea (Cyatheaceae), an ornamental and CITES giant tree fern. Its genome size is 161,679 bp in length, containing a large single copy (LSC) of 92,315 bp and a small single copy (SSC) of 21,702 bp separated by a pair of inverted repeat regions (IRs) of 23,831 bp. The overall GC contents of the chloroplast genome are 41.4%. A total of 133 genes are annotated, comprising 89 protein-coding genes, 33 tRNA, eight rRNA, and three pseudogenes. ML phylogenetic tree indicates that A. gigantea is sister to A. podophylla.

Keywords:

• Alsophila gigantea
• an ornamental and CITES giant tree fern
• chloroplast genome
• phylogenetic analysis

Alsophila gigantea, known as Cyathea gigantea, is a giant tree fern belonging to Cyatheaceae (Zhang and Nishida 2013). Its erect trunk is 2–5 meter tall with remnants of older leaf bases. The stipe is covered with dark brown and glossy scales. The species mainly grows in moist open areas in dense forests at an altitude up to 1200 m in India, Sri Lanka, Burma, Thailand, Laos, Vietnam, and southern China (Zhang and Nishida 2013). Similar to other species of Alsophila, A. gigantea is not only used as a source of starch, but also its frond is used for growing epiphytic orchids (Kiran et al. 2012). As an ornamental fern with a loose crown of leaves, it has been included in Appendix II of CITES (2017) due to illegal collection. In addition, A. gigantea forms a complex with other morphologically similar species of Alsophila such as A. glabra, A. podophylla, and A. subdubia (Large and Braggins 2004). Hence, acquirement of its whole chloroplast genome sequence will contribute to determine the relationship between these taxa.

In this study, the sample was collected from South China Botanical Garden, Chinese Academy of Sciences (23°11′3.56″N, 113°21′43.28″E) and deposited in Herbarium of Sun Yat-sen University (SYS; voucher: SS Liu 201618). Total genomic DNA was extracted from young leaves using Tiangen Plant Genomic DNA Kit (Tiangen Biotech Co., Beijing, China) and further broken into approximately 300 bp fragments. After ligated barcode adaptors, a paired-end library was constructed and sequenced using Illumina Hiseq 2500 platform (Illumina Inc., San Diego, CA).

In total, 12,053,058 raw reads were obtained. After low-quality reads and adapters were trimmed by Trimmomatic (Bolger et al. 2014), remaining 11,109,827 high-quality clean reads were de novo assembled to complete chloroplast genome by Velvet v1.2.07 (Zerbino and Birney 2008). Gaps were filled by PCR-based methods. The genes were annotated using DOGMA (Wyman et al. 2004) and tRNAscan-SE (Schattner et al. 2005) with the default configuration and were further manually curated against the plastome of A. spinulosa (NC_012818). The complete chloroplast genome sequences of A. gigantea were aligned with 11 species from leptosporangiates including Diplopterygium glaucum as an outgroup using MAFFT v7.311 (Katoh and Standley 2013). A maximum likelihood (ML) phylogenetic tree was constructed using raxmlGUI version 1.5b (https://sourceforge.net/projects/raxmlgui/) (Silvestro and Michalak 2012) with 1000 bootstrap replicates.

The plastome of A. gigantea was found to possess a total length 161,679 bp with 41.4% GC content (Genbank accession number: MH603068). It is a typical quadripartite structure containing a large single copy (LSC) of 92,315 bp and a small single copy (SSC) of 21,702 bp separated by a pair of inverted repeat regions (IRs) of 23,831 bp. A total of 133 genes were annotated, comprising 89 protein-coding genes, 33 tRNA, eight rRNA, and three pseudogenes. Among them, 13 have two copies. Except three genes with two introns (ycf3, clpP, and rps12), 14 genes harbor an intron (ndhB, rps16, atpF, rpoC1, petB, petD, rpl16, rpl2, ndhA, trnG-UCC, trnV-UAC, trnA-UGC, trnI-GAU, and trnL-CAA). ML phylogenetic tree indicates that A. gigantea is sister to A. podophylla with high bootstrap support value (Figure 1).

Figure 1. Maximum likelihood (ML) tree based on complete chloroplast genomes from 12 leptosporangiate ferns and one outgroup (Diplopterygium glaucum).

Disclosure statement

The authors declare no conflict of interests. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [31370364, 31570652, 31670200, 31770587, and 31872670], the Natural Science Foundation of Guangdong Province, China [2016A030313320 and 2017A030313122], Science and Technology Planning Project of Guangdong Province, China [2017A030303007], Project of Department of Science and Technology of Shenzhen City, Guangdong, China [JCYJ20160425165447211, JCYJ20170413155402977, and JCYJ20170818155249053], and the Science and Technology Planning Project of Guangzhou City, China [201804010389].