Corresponding author: Bing-Hua Chen (
Academic editor: N. Holstein
Zhang M, Zhang X-H, Shi S, Chen B-H (2023)
The subfamily
Typically,
This paper describes a new species of
The morphological description of the new species was based on the study of specimens collected in 2019 from various locations. A Stereoscopic Zoom Microscope (Carl Zeiss, Axio zoom. v.16, Germany), equipped with an attached digital camera (Axiocam), and a Digital caliper were used to record the sizes of the morphological characters. Field observations provided habitats and phenology for the new species.
In this study, total DNA was extracted from fresh leaves of the new species using a DNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). Purified total DNA of the new species was fragmented, and genome skimming was performed using next-generation sequencing technologies on the Illumina Novaseq 6000 platform. The sequencing was conducted by Berry Genomics Co. Ltd. (Beijing, China) using 150 bp paired-end reads with a 480 bp insert size, resulting in 11.58 GB of reads.
The phylogenetic position of the new species was determined through the analysis of nrITS and whole plastome sequences. The nrITS (ITS1-5.8S-ITS2) was assembled using GetOrganelle v1.7.5, with -R of 7 and k-merset of “35, 85, 115”. The embplant_nr library was selected as the reference genome database, then annotated and visualized using Geneious v2021.2.2.
The paired-end reads were filtered and assembled into a complete plastome using a GetOrganelle v1.7.5.0 (
The phylogenetic relationship was constructed using Maximum likelihood (ML) analyses with the combined nrITS sequence. In total, 92 samples of
To construct a phylogenetic tree based on plastome sequences, a total of 33 plastome sequences of
The online tool IRscope (
The complete chloroplast genome of
Gene contents in the plastid genome of
Category, group of genes | Gene names |
---|---|
Photosynthesis: | |
Subunits of photosystem I | |
Subunits of photosystem II | |
Subunits of NADH dehydrogenase | |
Subunits of cytochrome b/f complex | |
Subunits of ATP synthase | |
Large subunit of rubisco |
|
Subunits photochlorophyllide reductase | – |
Self-replication: | |
Proteins of large ribosomal subunit | |
Proteins of small ribosomal subunit | |
Subunits of RNA polymerase | |
Ribosomal RNAs | |
Transfer RNAs | |
Other genes: | |
Maturase |
|
Protease | |
Envelope membrane protein |
|
Acetyl-CoA carboxylase |
|
c-type cytochrome synthesis gene |
|
Translation initiation factor |
|
Genes of unknown function: | |
Conserved hypothetical chloroplast ORF |
Notes: Gene*: Gene with one introns; Gene**: Gene with two introns; Gene(2): Number of copies of multi-copy genes.
Representative cp genome of
The plastome of
Statistics on the basic features of the plastid genomes of
Species | Accession No. | Number of Genes | Length (bp) | GC Content (%) | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
PCGs |
|
|
Total | LSC | SSC | IR | Total | LSC | SSC | IR | ||
|
|
79 | 29 | 4 | 161,303 | 90,559 | 18,956 | 25,894 | 36.75 | 34.58 | 30.79 | 42.71 |
|
|
80 | 30 | 4 | 161,385 | 90,660 | 18,927 | 25,899 | 36.77 | 34.61 | 30.83 | 42.71 |
|
|
79 | 29 | 4 | 161,322 | 90,551 | 18,977 | 25,897 | 36.73 | 34.57 | 30.71 | 42.71 |
|
|
80 | 31 | 4 | 161,304 | 90,585 | 18,959 | 25,897 | 36.72 | 34.57 | 30.68 | 42.70 |
|
|
80 | 29 | 4 | 161,420 | 90,407 | 19,255 | 25,879 | 36.76 | 34.58 | 31.01 | 42.71 |
|
|
80 | 29 | 4 | 161,476 | 90,731 | 18,987 | 25,879 | 36.75 | 34.58 | 30.88 | 42.71 |
|
|
80 | 31 | 4 | 161,020 | 90,596 | 19,160 | 25,632 | 36.71 | 34.53 | 30.83 | 42.77 |
|
|
80 | 31 | 4 | 161,184 | 90,524 | 19,052 | 25,804 | 36.73 | 34.55 | 30.78 | 42.74 |
|
|
75 | 27 | 4 | 161,974 | 90,523 | 18,239 | 26,606 | 36.70 | 34.58 | 30.86 | 42.30 |
|
|
80 | 31 | 4 | 161,178 | 90,558 | 19,096 | 25,762 | 36.78 | 34.61 | 30.83 | 42.78 |
|
|
80 | 31 | 4 | 161,349 | 90,616 | 18,969 | 25,882 | 36.79 | 34.63 | 30.92 | 42.71 |
|
|
81 | 30 | 4 | 161,171 | 90,466 | 18,939 | 25,883 | 36.75 | 34.61 | 30.71 | 42.71 |
A chloroplast genome identification analysis was performed on the 12
The present study confirmed
Phylogenetic tree of 33 complete plastid sequences derived from the
Phylogenetic tree of 92 sequences based on nrITS genes. The boldness of the branches indicates RAxML bootstrap probabilities (BP). Three species of
Morphological differences between
Characters |
|
|
---|---|---|
Leaf margin | Acute teeth; 7–10 pairs | Obtuse teeth; 3–6 pairs |
Leaf surface | Glabrous on both upper and lower surfaces, only biaxially retaining fascicled hairs on axil of veins | Glabrous on both upper and lower surfaces, only biaxially retaining fascicled hairs on axil of veins |
Leaf shape | Oblanceolate, ovate-elliptic | Ovate, obovate, elliptic, or obovate-elliptic |
Leaf blade size (cm) | 3.7–9.8 ×1.1–3.2 | 4.0–9.0 ×1.0–4.0 |
Petiole length | 0.5–1.3 cm long | 0.5–1.5 cm long |
Number of secondary veins | 9–13 (–15) pairs | 7–10 (–11) pairs |
Fruiting stalk length | Almost sessile | Almost sessile |
Cupule | Usually solitary, few in clusters of 2 or 3 (–4), 0.5–0.7 cm high by 2.2–2.7 cm in diam. | Solitary (or 2), 0.7–1.1 cm high by 2.3–3.2 cm in diam. |
Cupule outside | Very faintly visible hairs | Faintly visible hairs |
Scale arrangement | Imbricate | Imbricate |
Nut size | 1.4–1.8 cm high by 1.5–2.6 cm in diam. | 1.8–2.4 cm high by 2.3–3.3 cm in diam. |
Nut enclosure by cupule | Enclosing ca.1/4–1/3 of the nut | Enclosing basal part of nut |
Basal scar of the nut | Margin concave but center convex, ca 1.7 cm in diam. | Margin concave but center ± convex, ca 2.0 cm in diam. |
Infructescence length | 1.5–4.0 cm long | 2.0–3.0 cm long |
China. Fujian Province, Fuzhou City, Minhou County, Dahu town, Niumu Mountain, forest margins,
Trees usually less than 8 m tall, evergreen. Branchlets densely grayish yellow tomentose, soon glabrescent. Bud scales compact, densely covered with grayish yellow silky short hairs. Leaf blade oblanceolate or ovate-elliptic, 3.7–9.8 × 1.1–3.2 cm, leathery, concolorous, apex acuminate to caudate, ca. 9 mm long, base cuneate and inaequilateral, margin with 7–10 acute teeth except basally entire, abaxially with tufts of hairs along veins; midvein adaxially puberulent; secondary veins 7–16 on each side of midvein, adaxially slightly impressed; tertiary veins slender, evident. Petiole 0.5–1.3 cm, tomentose, soon glabrescent. Rachis of inflorescences densely tawny tomentose. Inflorescences male, or androgynous, 2–6, in leaf axils toward base of branchlets or in a dense paniculate cluster on subterminal shoots, erect; rachis of male inflorescences, 5.6 cm long; flowers usually 3 in dichasial clusters; perianth 6-lobed; stamens 12. Female flowers 4–11, borne on basal part of androgynous inflorescences, perianth 6-lobed, styles 3, 3 mm. Infructescences 1.4–4.3 cm; rachis 4.5 mm thick, glabrescent, lenticellate. Cupule usually 1(or in clusters of 2–3–(4)), saucer-shaped, 4.6–7.4 mm × 2.2–2.7 cm, enclosing ca. 1/4–1/3 of nut, wall 1.0–2.5 mm thick; bracts imbricate, broadly triangular, covered with grayish brown, shortly tomentose hairs, midvein ridged. Nut depressed globose, 1.0–1.9 × 1.5–2.6 cm, glabrous, apex flat, wall 3.3–6.9 mm thick and horny; scar 1.5–1.9 cm in diam., margin concave but center convex.
Distribution of
Florescence May to June, fruiting season September to October of the following year.
Chinese name: 大湖柯 (da hu ke). The epithet dahuensis (大湖) refers to Dahu town, Minhou County, Fujian Province where this new species was found.
The following morphological characteristics were used to classify the species, including the acute teethed leaf blade margins, a concave nut scar, and cupules that do not completely enclose the nut. There are four other plants share similar characteristics with
During our fieldwork from 2017 to 2022, fruit-bearing large trees of
Phylogenetic analysis was completed on the whole chloroplast genomes, and nrITS sequences of the
The new species has an overall morphology similar to
As a result of its simple, stable genetic structure and ease of sequencing, the chloroplast genome has become increasing popular for species identification, phylogeny reconstruction, demographic history tracing and species divergence studies (
The chloroplast genome of the new species was compared with the other members of
1 | Female flower solitary |
|
– | Female flowers in clusters of (2 or)3(–5) |
|
2 | Nut covered with appressed minute hairs |
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– | Nut glabrous |
|
3 | Leaf blade margin with 7–10 acute teeth; cupules enclosing 1/4–1/3 of nut |
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– | Leaf blade margin with 3–6 obtuse teeth; cupules enclosing the bottom of nut |
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4 | Young leaf blade abaxially with tufts of stellate hairs at axils of veins, wall 6–10 mm thick |
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– | Young leaf blades covered with appressed minute hairs, wall 10–14 mm thick |
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5 | Leaf blade margin lobate-dentate |
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– | Leaf blade margin entire or rarely with 1–3 teeth near apex |
|
This work was financially supported by Special Project of Orchid Survey of National Forestry and Grassland Administration (contract no. 2020-07), the Sub-project VI of National Program on Key Basic Research Project (Grant No. 2015FY110200), the National Special Fund for Chinese medicine resources Research in the Public Interest of China (Grant No.2019-39), the Natural Science Foundation of Fujian Province (2020J05037 to MZ), the Foundation of Fujian Educational Committee (JAT190089 to MZ), and the scientific research innovation program “Xiyuanjiang River Scholarship” of College of Life Sciences, Fujian Normal University (22FSSK018).
Supplementary data
tables and figures
The information of the phylogenetic analysis of the species used in the present study (nrITS). Note: “-” indicate the data is not yet public. The information of the phylogenetic analysis of the species used in the present study (plastid genome). Comparison of the LSC, SSC and IR regions among twelve chloroplast genomes of