Elatostema qinzhouense (Urticaceae), a new species from limestone karst in Guangxi, China

Ethics statement

All the collecting locations of the new species reported in this study are outside any natural conservation area and no specific permissions were required for these locations. Since the species are currently undescribed, they are not currently included in the China Species Red List (Wang & Xie, 2004). Our field studies did not involve any endangered or protected species. No specific permits were required for the present study.

Nomenclature

The electronic version of this article in Portable Document Format (PDF) will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants (ICN), hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. In addition, new names contained in this work which have been issued with identifiers by IPNI will eventually be made available to the Global Names Index. The IPNI can be accessed and the associated information contained in this publication viewed through any standard web browser using the web address http://ipni.org/. The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central, and CLOCKSS.

Morphological examination

We used the morphological species concepts of Wei, Monro & Wang (2011), Fu et al. (2014), Wang (2014) and Fu et al. (2017a) to distinguish and compare taxa, placing emphasis on peduncle bract shape and length, the number, morphology and arrangement of the bracts comprising the receptacle-like involucre, the number of bracteoles per flower and leaf lamina length/width ratios. Material was examined using an Olympus SZX16 binocular microscope (Japan) and Plan Apo lens at × 10 and × 90 magnifications (Wei, Monro & Wang, 2011). For achene morphology, we also made scanning electron micrograph (SEM) observations. Fruiting material was collected from specimens, dried, and mounted using double-sided adhesive tape and coated with gold using a sputter coater. The fruit were then observed and photographed under a ZEISS EVO18 scanning electron microscope. At least five achenes were used to determine their size and surface ornamentation.

Extinction threat assessment

An extinction threat assessment was undertaken for the new species described here using IUCN criteria (IUCN, 2001; IUCN, 2019). Calculations of the extent of occurrence (EOO) and area of occupation (AOO) were undertaken using the online conservation assessment tool GeoCATAT (Bachman et al., 2011). The AOO was calculated using a cell width of 2 km as recommended by IUCN (2019).

Genomic DNA extraction and sequencing

Leaf material for DNA extraction was dried using silica gel (Chase & Hills, 1991). Genomic DNA was extracted using a modified CTAB protocol (Chen et al., 2014) and assessed by agarose gel electrophoresis. The total gDNA sample was sent to Majorbio (http://www.majorbio.com/, China) for library construction and next-generation sequencing. Short-insert (350 bp) paired-end read libraries preparation and 2 × 150 bp sequencing were performed on an Illumina (HiSeq4000) genome analyzer platform. Approximately 2 Gb of raw data for the new species was filtered using the FASTX-Toolkit to obtain high-quality clean data by removing adaptors and low-quality reads (http://hannonlab.cshl.edu/fastx_toolkit/download.html).

Plastid genome and ribosomal DNA (rDNA) assembly and annotation

Clean reads were paired and imported in Geneious Prime (Kearse et al., 2012). For plastid genome assembly, the clean reads were mapped to published plastid genome sequence as reference (Fu et al., 2019c) using the Fine Tuning option in Geneious Prime (iterating set as 10 times) to exclude nuclear and mitochondrial reads. Then, de novo assembly was performed using Geneious Prime with a medium-low sensitivity setting to assemble plastid genome sequence. The generated contigs was mapped by the clean reads using the Fine Tuning option in Geneious Prime (iterating set as 10 times) to fill gaps. Contigs were able to be concatenated using the Repeat Finder option implemented in Geneious Prime until a ∼130 kb contig (including SSC, IR and LSC) being built. The Inverted repeat (IR) region was determined by the Repeat Finder option in Geneious Prime and was reverse copied to obtain the complete plastid genome. The annotation approach of plastid genome was performed using CPGAVAS2 and PGA (Qu et al., 2019; Shi et al., 2019). The process of rDNA assembly is generally same to plastid genome assembly with the exception of different reference (Gryta et al., 2017) and iterating as none. The annotation approach of rDNA was performed using Annotate option in Geneious Prime.

Phylogenetic analyses

We generated a phylogeny using sequences data from previous phylogenies of Elatostema s.l. (Tseng et al., 2019). We extracted three DNA regions (ITS, trnH-psbA and psbM-trnD) from assembled rDNA and complete plastid genome sequences, respectively of the new species and downloaded most of the sequences data used in Tseng et al. (2019) from Genbank (details see Table S1). This resulted in 107 taxa (116 accessions) of Elatostema s.l. as ingroup and three species, belonging to Lecanthus, Poikilopermum and Debregeasia, as outgroup. Three datasets (ITS, trnH-psbA and psbM-trnD) were aligned independently using multiple alignment using fast Fourier transform (MAFFT) version 7.0 (Katoh & Standley, 2013) with default settings, followed by manual adjustment. The two best supported tree topologies from maximum likelihood (ML) analyses of cpDNA and nrITS were visually compared for topological incongruence. A conflict in tree topologies of each tree was considered significant when incongruent topologies both received bootstrap values ≥ 80% (Monro, 2006; Tseng et al., 2019). As there was no significant incongruence between two datasets (Tseng et al., 2019), phylogenies were reconstructed based on the combined dataset using ML and Bayesian inference (BI). The BI and ML analyses were performed followed Tseng et al. (2019).

Cytological experiments

Stem cuttings of the new species were grown in tap-water in a culture room. Actively growing root tips were harvested after 3–4 weeks. Cytological examination followed Fu et al. (2017b). The best metaphase plates were photographed using an imager microscope with a camera attachment. At least 3–5 cells from 3–5 root tips of the new species at somatic metaphase were counted to determine the chromosome numbers.

Characteristics of the complete plastid genome and ribosomal DNA

The complete plastid genome and ribosomal DNA (rDNA) sequences of Elatostema qinzhouense comprised 150,398 bp (Fig. 1) and 5,804 bp, respectively. The characteristics and statistics of plastid genome and rDNA were summarized in Tables 1 and 2.

Phylogenetic reconstruction

The characteristics and statistics of the datasets used in this study are presented in Table 3. BI and ML analyses of dataset of three DNA regions (ITS, trnH-psbA and psbM-trnD) resulted in the same tree topologies that both indicate the new species recovering in the clade of Elatostema (PP = 1, BP = 100%) and sister to E. hezhouense W.T. Wang, Y.G. Wei & A.K. Monro (PP = 1, BP = 100%) (Fig. 2).

Chromosome characteristics

The chromosome number of Elatostema qinzhouense was observed to be 2n = 26. The chromosome size fell into the range 1.45–3.33 µm, suggesting slight size variation. Detailed karyotype analysis was not possible because the chromosomes were small and had unclear centromeres (Fig. 3).

Taxonomic treatment

Elatostema qinzhouense L.F. Fu, A.K. Monro & Y.G. Wei, sp. nov. (Figs. 4 and 5 and S1)

IPNI

Type. China. Guangxi: cultivated material in Guilin Botanical Garden harvested on 24 March 2017, wild-collected, from Taiping Town, Lingshan County, Qinzhou City, 22.408N, 108.835E (WGS84), elev. 124 m, 26 May 2014, Pan B and Ma HS P1184 (holotype IBK (IBK00426150!); isotype K (K000798321!)).

Diagnosis. Most similar to Elatostema hezhouense from which it differs by the smaller size of leaf laminae (10–45 × 6–15 mm vs. 55–115 × 20–25 mm), fewer and smaller staminate peduncle bracts (1, 1 mm vs. 2, 3.5 mm), longer pistillate peduncle bract (0.900 mm vs. 0.375 mm) and a larger achene (0.86–0.94 × 0.27–0.30 mm vs. 0.6 × 0.25 mm) (see Table 4).

Description. Perennial herb, epipetric, monoecious. Not tuber forming. Stem 150–270 × 1–2 mm, erect to arching, branched, drying finely sulcate, furfuraceous, glabrous, with internodes 6–27 mm. Stipules solitary, opposite the leaf at each node, persistent, 2–3 × 0.75–1.5 mm, narrowly lanceolate, glabrous. Leaves distichous, alternate, petioles 1–1.5 × 0.5 mm, glabrous; laminae 10–45 × 6–15 mm, length:width ratio 1.6–3.5:1, asymmetrically oblanceolate or falcate, chartaceous, 5-nerved, the secondary nerves 4–6 pairs, 30–45° to the midrib; upper surface drying green, furfuraceous, glabrous, cystoliths densely scattered, fusiform, 0.2–0.5 mm; lower surface drying yellow-green, furfuraceous glabrous, sparsely brown glandular, cystoliths absent; base asymmetrical, broader-half auriculate, narrower-half cuneate; margin serrate-dentate, teeth 3–5 mm apart; apex acuminate. Staminate and pistillate inflorescences borne on the same stems concurrently. Staminate inflorescences solitary, 5–7 mm, bearing 2–4 flowers in a receptacle-like involucre; peduncle ca 0.9 × 0.5 mm, glabrous, bracteate; bract 1 mm, deltate; receptacle ca 2.5 × 1 mm, oblong, not lobed, glabrous, subtended by marginal bracts, marginal bracts 6, unequal, outer major bracts 2, inner minor bracts 4; major bracts 4–5 mm, broadly ovate, the apex corniculate, minor bracts ca 5 mm, ovate. Staminate flowers 2.5–3 × 2 mm, white, pedicellate, pedicel 1.5–2.0 mm; bracteoles 2, equal, 2–3 mm, narrowly lanceolate or linear; tepals 4 or 5, the subapical appendage 1.0 mm, corniculate, green. Pistillate inflorescences solitary, 5–6 mm, bearing more than 40 flowers in a pedunculate receptacle-like involucre; peduncle ca 1.0 × 0.8 mm, glabrous, bracteate; bracts 0.9 mm, deltate, furfuraceous; receptacle-like involucre 1–1.5 × 2.5–3.0 mm, subquadrate, not lobed, glabrous, subtended by marginal bracts, the bracts unequal, dark green, furfuraceous, major bracts 2, 1.2–1.5 mm, broadly ovate, with a raised dorsal midrib, the apex corniculate, minor bracts 8, 1.0–1.2 mm, ovate, the apex corniculate. Pistillate flowers pedicellate; pedicel subsessile; bracteoles 2, equal, 1.0–1.3 mm, narrowly lanceolate or linear. Infructescences as pistillate inflorescences; achene 0.86–0.94 × 0.27–0.30 mm, length:width ratio 3.07–0.31:1, oblongoid, pale brown, with 8 narrow longitudinal ridges.

Distribution and habitat. Elatostema qinzhouense is known from a single locality in Lingshan County, Qinzhou City, Guangxi, China. E. qinzhouense is likely calcicolous and grows under evergreen broad-leaved forest on limestone hills. Flowering from December to March, fruiting from March to April.

Etymology. Elatostema qinzhouense is named after the type locality, Qinzhou City, Guangxi Zhuang Autonomous Region, China.

Vernacular name.钦州楼梯草 (Chinese name).

Additional specimen examined (paratype). China. Guangxi: cultivated material in Guilin Botanical Garden harvested on 27 January 2019, wild-collected, from Taiping Town, Lingshan County, Qinzhou City, 22.408N, 108.835E (WGS84), elev. 124 m, 26 May 2014, Pan B and Ma HS P1184 (paratypes BJFC!, CSH!, PE!).

Conservation Assessment. Elatostema qinzhouense is known from a single locality (AOO 4 km², criteria B2). At this locality the population of this species comprises ca 200 mature individuals (criteria D1). The only observed population is at the edge of agricultural land on a small limestone hill, which, although deforested in the past, appears not to be actively disturbed. According to IUCN (2001) and IUCN (2019) E. qinzhouense could be considered Critically Endangered (CR) according to criteria D1 and B2. Botanically, this part of Guangxi is relatively poorly explored and so it may be that other populations exist that have yet to be observed. Given the frequency of point-endemics in the genus the opposite is also possible. Given the lack of imminent threat and this species resilience to past deforestation, and the frequency of point-endemics amongst karst-associated Elatostema suggesting that this species may not have been subject to a large reduction in population size we re-appraise E. qinzhouense as Endangered (EN).