Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)

Abstract

Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981-85,983 bp, a small single copy region of 18,182-18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)-most of them autapomorphies-were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.

Keywords: Asteliaceae; Chloroplast; Cushion plants; Genetic variability; Magellanic moorland; Organellar genome; Plastome; South America.

Figure 1. The chloroplast genome map of Astelia pumila specimen AEX.3 (see Table 1).

Genes shown on the outside of the outer circle are transcribed clockwise, while genes shown on the inside are transcribed counterclockwise. The positions of the large (LSC) and small single copy (SSC) regions, as well as of the inverted repeats (IRs), are indicated on the inner circle.

Figure 2. Maximum Likelihood tree, based on whole chloroplast genome sequences, to illustrate the phylogenetic position of A. pumila within Asparagales.

Alstroemeria aurea (Liliales, Alstroemericeae) served as outgroup. Numbers indicate node support (based on 1,000 bootstrap replicates). NCBI GenBank accession numbers: A. aurea, KC968976; V. planifolia, KJ566306; D. nobile, KX377961; C. aloifolium, NC_021429; A. pumila, MH752983; I. gatesii, NC_024936; A. maculata, KX377523; A. coddii, KX790363; A. prattii, MG739457; A. cepa, NC_024813; E. latifolius, NC_025305; A. officinalis, KY364194; N. atopocarpa, KX931462; M. bicolor, NC_035970; P. sibiricum, KT695605; P. verticillatum, KT722981; A. monspeliensis, KX790360 ; H. parviflora, NC_032703; Y. brevifolia, NC_032711 ; M. biflora, KX822778; O. biflora, NC_032709; B. japonica, KX822775; A. kirkii, NC_032697.