Strong Bootstrap Values Research Articles

First Report of Powdery Mildew Caused by Podosphaera xanthii on Sphagneticola trilobata in Hainan Province, China.

Sphagneticola trilobata (L.) Pruski is a perennial creeping herb of the Asteraceae family, which is native to South America. It was introduced into Southern China as a groundcover in the 1970s (Zhang et al. 2023). Now it is mainly used for folk medicine to treat various kinds of inflammatory, incuding joint pain, rheumatic diseases, arthritis, in addition to treating persistent wounds, ulcers, and edemas (Gonçalves et al. 2022). In February and November 2023, powdery mildew symptoms were observed on 60% of S. trilobata plants on the Hainan Medical University campus (19° 58' 53″ N; 110° 19' 47″ E) in Haikou, Hainan Province, China. Powdery mildew colonies covered the leaf surfaces and stems of affected plants, causing discoloration and defoliation. Mycelia were superficial and hyphal appressoria were nipple-shaped. Conidiophores (n =30) were unbranched, cylindrical, 74 to 161 × 10 to 14 µm, and produced three to five immature conidia in chains with a crenate outline. Foot cells (n =30) were cylindrical, straight or sometimes curved at the base, and 27 to 56 µm long. Conidia (n =100) were ellipsoid-ovoid to doliiform, 17 to 30 ×14 to 28 µm (length/width ratio = 1.1 to 1.9), with well-developed fibrosin bodies, and produced germ tubes from the lateral position. Based on these morphological characteristics, the pathogen was provisionally identified as Podosphaera xanthii (Braun and Cook 2012). The teleomorph was not observed. A specimen was deposited in the Hainan Medical University Plant Pathology Herbarium as HMST-23. To confirm the genus identification and ascertain a putative species, genomic DNA was extracted from mycelium, conidiophores, and conidia using a fungal DNA kit (Omega Bio-Tek, USA). The rDNA internal transcribed spacer (ITS) region was amplified with primers ITS1/ITS4 (White et al. 1990) and sequenced directly. The resulting 577-bp sequence was deposited in GenBank (accession no. OR784549). A BLASTn search in GenBank of this sequence showed 100% similarity with the ITS sequences of P. xanthii isolates from China (MT260063, MN203658, OP765400, and MT739423), Thailand (LC270780), and Vietnam (KM260731, KM260730, and KR779870). Additionally, the 28S rDNA region was amplified using the primer pairs NL1 and NL4 (O´Donnell 1993; accession no. OR784550). This region shared 100% similarity with P. xanthii isolates (LC371334, LC270782, AB936277, and OP765401) as well. Powdery mildew from Hainan sample belonged to the P. xanthii group with strong bootstrap values support 99% in maximum likelihood phylogenetic tree based on ITS and 28S gene sequences. To confirm pathogenicity, five healthy potted plants of S. trilobata were inoculated by gently pressing a powdery mildew-infected leaf onto 15 young leaves. Five non-inoculated plants served as controls. All plants were maintained in a greenhouse at 24 to 30°C, 70% relative humidity, with a 16-h photoperiod. After 7 days, inoculated leaves showed powdery mildew symptoms whereas no symptoms were observed on control plants. The fungal colonies observed on inoculated plants were morphologically identical to those found on the originally infected leaves collected from Hainan Province. Based on the morphological characteristics and molecular identification, the fungus was identified as P. xanthii. In different countries and regions, P. xanthii has been previously reported on S. trilobata in Taiwan (Yeh et al. 2021). To our knowledge, this is the first record of P. xanthii infecting S. trilobata in Hainan Province, China. S. trilobata is often planted as an ornamental plant on both sides of the road, and we are concerned that it may serve as a new host, spreading this pathogen to other economic crops.

Phylogenetic Relationship of Diadema: Emphasis on The Two Distinct Clades of D. Setosum With The Inclusion of Long Spine Black Sea Urchin From Malaysian Borneo

Diadema urchins (family Diadematidae) are ecologically important bioindicators of coral reef ecosystems and seagrass beds. Diadema urchins which are widely distributed and broadcast spawners, have been frequently utilized as model invertebrate species for zoogeography research of the Indo-West Pacific region. So far, Malaysian Borneo, located at the geographic center of Maritime Southeast Asia, has been under-sampled. This study aims to fill this sampling gap and provide the first record of Diadema setosum from Malaysian Borneo using genetic diagnostics to conclusively establish the clade-level identity of the species. According to Cytochrome Oxidase I gene analysis, Diadema is monophyletic. Seven species of Diadema namely Diadema palmeri, Diadema clarki, Diadema mexicanum, Diadema antillarum, Diadema paucispinum, Diadema africanum, and Diadema savignyi, formed their subclades with strong bootstrap values, demonstrating interspecific variation. The findings of this study provide further evidence for the presence of two distinct monophyletic clades, with all D. setosum individuals forming a monophyletic clade that later split into two distinct subclades, dividing Red Sea population (D. setosum-b) and Indo-West Pacific populations (D. setosum-a), supported by a significant genetic divergence value ranging from 6.3% to 9.1%. This study also revealed notable levels of nucleotide and population subdivision between the D. setosum from the Indo-West Pacific and the Red Sea populations (Nst = 0.891; Fst = 0.886) with a low number of migrants per generation (Nm = 0.065). This may suggest geographic isolation due to ecological factors preventing each other from surviving in the territory of the other, or that the two clades of D. setosum were a separate species. Additional morphological and molecular analysis is required in the future to ascertain the level of divergence and further resolve the taxonomic confusion within the genus Diadema.

Phenotypic and genotypic diversity of root nodule bacteria from wild Lathyrus and Vicia species in Gaziantep, Turkey.

This study identified the phenotypic and genotypic characteristics of the bacteria that nodulate wild Lathyrus and Vicia species natural distribution in the Gaziantep province of Turkey. Principle component analysis of phenotypic features revealed that rhizobial isolates were highly resistant to stress factors such as high salt, pH and temperature. They were found to be highly sensitive to the concentrations (mg/mL) of the antibiotics neomycin 10, kanamycin, and tetracycline 5, as well as the heavy metals Ni 10, and Cu 10, and 5. As a result of REP-PCR analysis, it was determined that the rhizobial isolates were quite diverse, and 5 main groups and many subgroups being found. All of the isolates nodulating wild Vicia species were found to be related to Rhizobium sp., and these isolates were found to be in Clades II, III, IV, and V of the phylogenetic tree based on 16S rRNA. The isolates that nodulated wild Lathyrus species were in Clades I, II, IV, V, VI, VII, and VIII, and they were closely related to Rhizobium leguminasorum, Rhizobium sp., Phyllobacterium sp., Serratia sp., and Pseudomonas sp. According to the genetic analyses, the isolates could not be classified at the species level, the similarity ratio was low, they formed a distinct group that was supported by strong bootstrap values in the phylogenetic tree, and the differences discovered in the network analysis revealed the diversity among the isolates and gave important findings that these isolates may be new species.

Phylogenetic Relationships of Isognomon (Lightfoot, 1786) Oysters from North Sulawesi, Indonesia

The Isognomon (Lightfoot, 1786) is a genus of oysters found in various coastal ecosystems throughout the world. Along with other bivalves, it performs significant ecological functions in marine ecosystems by providing food and habitat for fish and invertebrate habitats, filtering water, and protecting shorelines. Taxonomic classification of the Isognomon oyster can be challenging due to the varied or cryptic phenotypic characters, particularly shell characters. In this study, two specimens with different shell characters of Isognomon oyster were collected from mangrove waters in Likupang, North Sulawesi, Indonesia, and subjected to molecular analysis to determine their identity. The mitochondrial cytochrome C oxidase subunit I (COI) gene was utilized as a primer for this purpose, and the genetic distance and phylogenetic position of the two specimens were determined by comparing them with the GenBank database. The Basic Local Alignment Search Tool (BLAST) revealed that the two specimens were of belonged to Isognomon ephippium, with a similarity of 99.84%. The genetic distance between the two specimens was calculated using the Tamura Nei model and found to be 0.00, while the genetic distance between I. ephippium and other species in the Isognomon genus ranged from 0.00 to 0.14. The results of the Neighbor Joining (NJ) tree analyses showed that the two specimens clustered together with I. ephippium, which was divided into two distinct clades with a strong bootstrap value of 100 at the node

First Report of Powdery Mildew Caused by Podosphaera xanthii on Vernonia cinerea in China.

Vernonia cinerea (L.)Less. is an annual herbaceous plant of the Asteraceae family, which is widely distributed throughout Southeast Asia, India, and the tropical and subtropical regions of China. This herb is known to contain various bioactive compounds and is commonly used in traditional system of medicine in China and India (Singh et al. 2021). During the spring of 2022 and 2023, powdery mildew symptoms were observed on 70% of V. cinerea plants on the Hainan Medical University campus (19° 58' 53″ N; 110° 19' 47″ E) in Haikou, Hainan Province, China. Powdery mildew colonies covered the leaf surfaces and stems of affected plants, causing discoloration and defoliation. Mycelia were superficial and hyphal appressoria were nipple-shaped. Conidiophores (n =30) were unbranched, cylindrical, 104 to 188 × 11 to 15 µm, and produced three to five immature conidia in chains with a crenate outline. Foot cells (n =30) were cylindrical, straight or sometimes curved at the base, and 32 to 57 µm long. Conidia (n =100) were ellipsoid-ovoid to doliiform, 19 to 45 ×16 to 26 m (length/width ratio = 1.2 to 2.4), with well-developed fibrosin bodies, and produced germ tubes from the lateral position. Based on these morphological characteristics, the pathogen was provisionally identified as Podosphaera xanthii (Braun and Cook 2012). The teleomorph was not observed. A specimen was deposited in the Hainan Medical University Plant Pathology Herbarium as HMVC-22. To confirm the genus identification and ascertain a putative species, genomic DNA was extracted from mycelium, conidiophores, and conidia using a fungal DNA kit (Omega Bio-Tek, USA). The rDNA internal transcribed spacer (ITS) region was amplified with primers ITS1/ITS4 (White et al. 1990) and sequenced directly. The resulting 577-bp sequence was deposited in GenBank (accession no. OP765400). A BLASTn search in GenBank of this sequence showed 100% similarity with the ITS sequences of P. xanthii isolates from China (MT260063, MT739423 and MT131253), Thailand (LC270780), and Vietnam (KM260731). Additionally, the 28S rDNA region was amplified using the primer pairs NL1 and NL4 (O´Donnell 1993; accession no. OP765401). This region shared 100% similarity with P. xanthii isolates (LC371333, LC270780, and AB936277) as well. Powdery mildew from Hainan sample belonged to the P. xanthii group with strong bootstrap values support 99% in maximum likelihood phylogenetic tree based on ITS and 28S gene sequences. To confirm pathogenicity, five healthy potted plants of V. cinerea were inoculated by gently pressing a powdery mildew-infected leaf onto 15 young leaves. Five non-inoculated plants served as controls. All plants were maintained in a greenhouse at 24 to 30°C, 70% relative humidity, with a 16-h photoperiod. After 7 days, inoculated leaves showed powdery mildew symptoms whereas no symptoms were observed on control plants. The fungal colonies observed on inoculated plants were morphologically identical to those found on the originally infected leaves collected from Hainan Province. Based on the morphological characteristics and molecular identification, the fungus was identified as P. xanthii. In different countries and regions, Erysiphe cichoracearum has been previously reported on some Vernonia species, including V. Galamensis from southern parts of Ethiopia (Hundesa and Mekonnen 2017). To our knowledge, this is the first record of P. xanthii infecting V. cinerea in China. We are concerned that the pathogen could become a threat to the widespread planting of V. cinerea in the future.

The complete chloroplast genome sequence of Ligustrum foliosum (Oleaceae), a species endemic to the Ulleungdo Island, Korea

We determined the complete chloroplast genome sequence of Ligustrum foliosum Nakai, an endemic species of Korea. The plastome was 165,731 bp long, with a large single copy (90,009 bp), a small single copy (11,448 bp), and a pair of inverted repeats (32,137 bp). Moreover, 113 genes were encoded, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis of 18 species using concatenated 78 protein-coding genes (excluding one pseudogene) revealed that L . foliosum is most closely related to L. quihoui , having strong bootstrap values. This study is the first report of the chloroplast genome of L . foliosum and provides important information for future phylogenetic studies on Ligustrum and distinguishing closely related species of Ligustrum .

Two new species of Xanthagaricus from Punjab, Pakistan

Many basidiomata collected during a fungal survey of the Indus Riverbed revealed two new taxa in the genus Xanthagaricus. Phylogenetic analyses of the Internal Transcribed Spacers (ITS) & ribosomal Large Subunit (28S) have confirmed that these new species (namely Xanthagaricus punjabensis & Xanthagaricus kotadduensis) form a separate clade with a strong bootstrap value from the closest species of Xanthagaricus. The closest taxon to Xanthagaricus punjabensis is X. Thailandensis, while Xanthagaricus kotadduensis is closely related to X. omanicus. Xanthagaricus punjabensis is unique due to its umbonate disc, dull orange to light yellow lamellae, gray rhizomorphic mycelial mat at the base of stipe, presence of annulus, globose to subglobose basidiospore, narrowly utriform to utriform cheilocystidia, and clavate to broadly clavate caulocystidia. Our second new taxon, X. Kotadduensis, can be characterized by the absence of annulus, utriform to knobbed cheilocystidia, and oblong caulocystidia. Our results strongly support the placement of the new taxa within the genus Xanthagaricus and provide a unique insight into the phylogenetic relationships within this genus. With this addition, the number of known species of Xanthagaricus from Pakistan becomes three.

Identification and screening of enzymatic abilities of Ktedonobacteria from forest soil of Cisolok Geothermal Area, Indonesia

Abstract. Rachmania MK, Ningsih F, Sari DCAF, Eshananda Y, Sakai Y, Yabe S, Yokota A, Sjamsuridzal W. 2022. Identification and screening of enzymatic abilities of Ktedonobacteria from forest soil of Cisolok Geothermal Area, Indonesia. Biodiversitas 23: 4686-4695. This study aimed to provide information on culturable Ktedonobacteria from forest soil in the Cisolok geothermal area and their potential as enzyme producers. Twelve ktedonobacterial isolates were obtained from this study and identified based on full-sequence of the 16S rRNA gene. Seventeen isolates (including five isolates from previous studies) were used for enzymatic screening and phylogenetic analyses. Screening of amylolytic (0.5% soluble starch) and cellulolytic (0.5% carboxymethylcellulose) (CMC) activities from ktedonobacterial isolates was performed on a ten-fold diluted R2A agar medium, and were incubated at 30 °C for 21 days. The EzBioCloud search revealed that all isolates showed low sequence similarities with Dictyobacter aurantiacus S-27T (97.82 to 98.18%) as their closest related species. The phylogenetic tree showed that all isolates belong to the genus Dictyobacter (family Dictyobacteraceae of the class Ktedonobacteria). All isolates formed a monophyletic group and were placed as the sister clade to D. aurantiacus, as supported by a very strong bootstrap value (99%). Screening of amylolytic and cellulolytic abilities showed that most isolates (88.23%) were able to degrade both 0.5% starch and 0.5% CMC as substrates. This study revealed the presence of Ktedonobacteria with amylolytic and cellulolytic abilities in the forest soil of Cisolok geothermal area.

Structural Characterization and Comparative Analyses of the Chloroplast Genome of Eastern Asian Species Cardamine occulta (Asian C. flexuosa With.) and Other Cardamine Species.

Cardamine flexuosa is considered to be two separate species in the Cardamine genus based on their geographical distribution: European C. flexuosa and Eastern Asian C. flexuosa. These two species have not shown any morphological differences to distinguish each other. Recently, the Eastern Asian species has been regarded as Cardamine occulta by their ecological habitats. Therefore, we are interested in analyzing the C. occulta chloroplast genome and its characteristics at the molecular level. Here, the complete chloroplast (cp) genome of C. occulta was assembled de novo with next-generation sequencing technology and various bioinformatics tools applied for comparative studies. The C. occulta cp genome had a quadripartite structure, 154,796 bp in size, consisting of one large single-copy region of 83,836 bp and one small single-copy region of 17,936 bp, separated by two inverted repeats (IRa and IRb) regions of 26,512 bp. This complete cp genome harbored 113 unique genes, including 80 protein-coding genes, 29 tRNA, and four rRNA genes. Of these, six PCGs, eight tRNA, and four rRNA genes were duplicated in the IR region, and one gene, infA, was a pseudogene. Comparative analysis showed that all the species of Cardamine encoded a small variable number of repeats and SSRs in their cp genome. In addition, 56 divergences (Pi > 0.03) were found in the coding (Pi > 0.03) and non-coding (Pi > 0.10) regions. Furthermore, KA/KS nucleotide substitution analysis indicated that thirteen protein-coding genes are highly diverged and identified 29 amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggested that C. occulta has a closer genetic relationship to C. fallax with a strong bootstrap value. The identified hotspot regions could be helpful in developing molecular genetic markers for resolving the phylogenetic relationships and species validation of the controversial Cardamine clade.

The complete chloroplast genome sequence of medicinal plant Centipeda minima (Compositae)

The complete chloroplast genome sequence of Centipeda minima (L.) A. Braun et Aschers (Compositae) has been characterized by Illumina pair-end sequencing. The chloroplast genome is 152,351 bp in length, including a pair of inverted repeats (IRs) of 25,004 bp (12.1%) and a large single copy (LSC) and a small single copy (SSC) region of 83,972 bp (55.1%) and 18,371 bp (32.8%), respectively. The chloroplast genome includes 127 genes, which contain 83 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. The nucleotide composition is asymmetric (31.1% A, 18.5% C, 19.0% G, 31.4% T). The overall GC content of C. minima chloroplast genome is 37.5%. Phylogenetic analysis illustrates that C. minima is closely related to other Asteraceae species, including Helianthus annuus subsp. texanus, Tithonia diversifolia and Xanthium sibiricum with a strong bootstrap value of 100.

First genetic record and the phylogenetic relationship of Osteochilus spilurus (Cyprinidae: Labeoninae ) originating from Bangka and Belitung Islands, Indonesia

Abstract. Kurniawan A, Hariati AM, Kurniawan A, Wiadnya DGR. 2021. First genetic record and the phylogenetic relationship of Osteochilus spilurus (Cyprinidae: Labeoninae) originating from Bangka and Belitung Islands, Indonesia. Biodiversitas 22: 794-802. Osteochilus spilurus is a freshwater fish from Southeast Asia. Species identification for this fish in Indonesia is still solely limited to morphological characteristics. Therefore it is highly important to validate using short DNA sequences that have been proven to be fast, effective, and accurate. Fish specimens were collected from Lenggang river in Belitung island, and Lebak river in Bangka island, Indonesia. Mitochondrial cytochrome b gene (cyt b, 408 bp) was amplified and sequenced. We collected fish specimens from Lenggang River in Belitung Island and Lebak River in Bangka Island, Indonesia. The results suggested that individuals from both islands are clustered together with a strong bootstrap value (100%) in a monophyletic clade. The specimens deposited at NCBI as the first Indonesian genetic records. They have a sister lineage to individuals from Sabah, Malaysia, although supported by a low bootstrap value. While geographical connection during the Pleistocene period allowed wide distribution of the species, differences in the evolutionary processes of historical biogeography and environmental changes are the predicted cause of the low genetic similarity. These findings can be used as a sequence reference and basic information for conservation of this species.

The complete chloroplast genome of Foonchewia coriacea (Rubioideae: Rubiaceae): a monotypic species endemic to Guangdong, China

Foonchewia coriacea, a monotypic genus of the Rubiaceae, is endemic to China. Its complete chloroplast genome was determined to be 153,114 bp in length and the GC content was 37.90%. The sequence includes a large single-copy region of 83,978 bp, a small single-copy region of 18,290 bp, and the inverted region is 25,423 bp in length. It contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum likelihood (ML) and Bayesian inference (BI) analyses revealed F. coriacea was closely related to Dunnia sinensis with strong bootstrap values, belonging to the subfamily Rubioideae.

Dissection for Floral Micromorphology and Plastid Genome of Valuable Medicinal Borages Arnebia and Lithospermum (Boraginaceae).

The genera Arnebia and Lithospermum (Lithospermeae-Boraginaceae) comprise 25–30 and 50–60 species, respectively. Some of them are economically valuable, as their roots frequently contain a purple-red dye used in the cosmetic industry. Furthermore, dried roots of Arnebia euchroma, A. guttata, and Lithospermum erythrorhizon, which have been designated Lithospermi Radix, are used as traditional Korean herbal medicine. This study is the first report on the floral micromorphology and complete chloroplast (cp) genome sequences of A. guttata (including A. tibetana), A. euchroma, and L. erythrorhizon. We reveal great diversity in floral epidermal cell patterns, gynoecium, and structure of trichomes. The cp genomes were 149,361–150,465 bp in length, with conserved quadripartite structures. In total, 112 genes were identified, including 78 protein-coding regions, 30 tRNA genes, and four rRNA genes. Gene order, content, and orientation were highly conserved and were consistent with the general structure of angiosperm cp genomes. Comparison of the four cp genomes revealed locally divergent regions, mainly within intergenic spacer regions (atpH-atpI, petN-psbM, rbcL-psaI, ycf4-cemA, ndhF-rpl32, and ndhC-trnV-UAC). To facilitate species identification, we developed molecular markers psaA- ycf3 (PSY), trnI-CAU- ycf2 (TCY), and ndhC-trnV-UAC (NCTV) based on divergence hotspots. High-resolution phylogenetic analysis revealed clear clustering and a close relationship of Arnebia to its Lithospermum sister group, which was supported by strong bootstrap values and posterior probabilities. Overall, gynoecium characteristics and genetic distance of cp genomes suggest that A. tibetana, might be recognized as an independent species rather than a synonym of A. guttata. The present morphological and cp genomic results provide useful information for future studies, such as taxonomic, phylogenetic, and evolutionary analysis of Boraginaceae.

The complete plastid genome of Bauhinia variegata L. var. variegata (Leguminosae)

Bauhinia variegata L. var. variegata is a popular ornamental tree in the tropical and subtropical region. We herein report and characterize the complete plastid genome of B. variegata var. variegata in an effort to provide genomic resources for genetic utilization. The complete plastome is 155,415 bp in length and contains the typical quadripartite structure, including two inverted repeat (IR) regions of 25,549 bp, a large single-copy (LSC) region of 86,110 bp and a small single-copy (SSC) region of 18,207 bp. 130 genes are annotated, including 85 protein-coding genes, 37 transfer RNA genes, and four unique ribosomal RNA genes. The phylogenetic analysis based on the plastomes from B. variegata var. variegata and 12 previously reported species of Cercidoideae suggested a sister-relationship between B. variegata var. variegata and B. × blakeana with a strong bootstrap value.

Characterization of the complete chloroplast genome of Caesalpinia sappan L. (Leguminosae)

Caesalpinia sappan L. is a widely cultivated medicinal plant. As a first report in this genus, we presented the complete chloroplast genome of C. sappan using genome skimming of paired-end NGS data. The total length of the chloroplast genome was 160,192 bp and contained a typical quadripartite structure including one large single-copy (LSC) region (89,726 bp), one small single copy (SSC) region (18,358 bp) and a pair of inverted repeats (IR) regions (26,054 bp). The GC content of this genome was 36.0%. The whole genome contained 127 genes including 83 protein-coding genes, 36 tRNA genes, and eight rRNA genes. ML analysis revealed C. sappan was closely related to Haematoxylum brasiletto with strong bootstrap values belonging to the subfamily Caesalpinioideae of Leguminosae.

The first complete chloroplast genome of Gentiana rigescens and its phylogenetic position in Gentianaceae

Gentiana rigescens Franch. ex Hemsl. (Gentianaceae) is an endangered medicinal plant endemic to the southwest of China. The chloroplast (cp) genome of G. rigescens was 146,891 bp in length, with a large single-copy (LSC) region of 79,377 bp, a small single-copy (SSC) region of 17,026 bp, and a pair of inverted repeats (IRs) of 25,244 bp, forming a typical quadripartite structure. A total of 130 genes were annotated from the cp genome of G. rigescens, including 85 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. Phylogenetic analysis indicated that G. rigescens was closely related to G. tonggolensis with strong bootstrap values belonging to the subfamily Gentianoideae.

Complete genome and phylogenetic analysis of Agrimonia pilosa ldb

Agrimonia pilosa Ldb., a herbaceous plant, has been used in Chinese medicines as anti-haemorrhagic, anthelmintic and anti-inflammatory agent. In this study, the complete chloroplast (cp) genome sequence of A. pilosa was first reported. The cp genome is 155,188 bp in length, with two inverted repeat (IR) regions of 25,965 bp, the large single copy (LSC) region of 84,521 bp and the small single copy (SSC) region of 18,737 bp. A total of 129 genes were predicted, including 84 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The phylogenetic analysis suggested that A. pilosa is more closely related to Sanguisorba filiformis with strong bootstrap values belonging to the subfamily Rosoideae.

The complete chloroplast genome of Dunnia sinensis (Rubiaceae): a monotypic species endemic to Guangdong, China

Dunnia sinensis, a monotypic genus of the Rubiaceae, is an Endangered species endemic to China. Its complete chloroplast genome was determined to be 154,909 bp in length and the GC content was 37.80%. The sequence includes a large single-copy region of 84,894 bp, a small single-copy region of 16,973 bp, and the inverted region of 26,521 bp in length. It contains 130 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ML and BI analyses revealed D. sinensis was closely related to Galium mollugo and Leptodermis scabrida with strong bootstrap values belonging to the subfamily Rubioideae.

Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis.

Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was determined using the Illumina HiSeq 2500 platform. The complete chloroplast genome of C. sclerophylla is 160,497 bp long, including a pair of inverted repeat (IR) regions (25,675 bp) separated by a large single-copy (LSC) region of 90,255 bp and a small single-copy (SSC) region of 18,892 bp. The overall GC content of the chloroplast genome is 36.82%. A total of 131 genes were found; of these, 111 genes are unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the smaller chloroplast genome of C. sclerophylla compared to three congeneric species. Sequence analysis indicated that the LSC and SSC regions are more divergent than IR regions within Castanopsis; furthermore, greater divergence was found in noncoding regions than in coding regions. The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. Furthermore, these findings will be valuable for future studies of genetic diversity and enhance our understanding of the phylogenetic evolution of Castanopsis.

Characterization of the complete chloroplast genome of medicinal tea tree (Melaleuca alternifolia)

Melaleuca alternifolia is commonly known as the medicinal tea tree. The complete chloroplast (cp) genome sequence is 160,104 bp in length, with a quantitative molecule structure comprising two copies of inverted repeats (IRa and IRb) of 26,737 bp separated by a large single copy (LSC) of 88,151bp, a small single copy (SSC) of 18,479 bp. A total of 131 genes were identified including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes and two pseudogene (Ψycf1, ΨinfA), respectively. Phylogenomic analysis suggests that M. alternifolia is closely related to the rest species of Myrtaceae with strong bootstrap values.