cpDNA Sequences Research Articles

Phylogeographic patterns match the floristic subdivisions: The diversification history of a widespread herb in subtropical China.

Subtropical China is dominated by evergreen broad-leaved forests (EBLFs) and is acknowledged as a critical region for its high floristic richness and endemism. Understanding of evolutionary mechanisms of such global biodiversity hotspots comes almost exclusively from long-lived tree species. Herbaceous plants represent critical biodiversity components in forests, however, the diversification history of understory herbs in subtropical EBLFs remain poorly understood. Here, we investigated the phylogeographic patterns and demographic history of Oreocharis auricula, a widespread perennial herb endemic to the EBLFs of subtropical China. Both cpDNA sequences and single-copy nuclear genes were used to investigate the genetic variation among 657 individuals from 68 populations. Evidences from molecular dating, demographic history construction, and species distribution modeling were also combined to infer the phylogeography and evolutionary history of O. auricula. Strong phylogeographic signals have been congruently observed using nuclear and plastid DNA markers, with the diversification patterns generally consistent with the recognized floristic subdivisions of subtropical China. Notably, we revealed an important phylogeographic barrier along the Nanling mountain range, which is also around a climatic transition at 24-26°N latitude in subtropical China, separating the south monsoon subtropical EBLFs from the mid-subtropical EBLFs. Demographic expansion and significant niche divergence were detected among the extant lineages, which may have diverged during the early Pleistocene. The inherent characteristics of understory herbs with limited dispersal and short generation time intensify the genetic divergence response of O. auricula to abiotic forces, contributing to the profound phylogeographic imprints of mountains and climate in such herbaceous flora. To further substantiate the generality of the identified patterns, it is paramount to extend phylogeographic investigations to other understory herbaceous taxa in subtropical China. These results have expanded our understanding of the diversification processes of subtropical forests in China.

Dryopteris microlepioides, a new synonym of Trichoneuron microlepioides (Dryopteridaceae)

When reviewing the species diversity of Dryopteridaceae from Vietnam, we noticed the name Dryopteris microlepioides Christensen (1934: 102) is taxonomically uncertain and to be treated (Hassler 1994–2024). Dryopteris microlepioides was described based on two collections from northern Vietnam and was thought to be a distinct species superficially resembling Microlepia speluncae (Linnaeus 1753: 1093) Moore (1857: 93) (Christensen 1934). Since its publication in 1934, this name had been neglected by authors who treated Dryopteris Adanson (1763: 20) for the fern flora or species diversity of Vietnam (e.g., Tardieu-Blot & Christensen 1938, 1941; Pham 1999; Phan 2010). At the first sight of the type specimens of D. microlepioides, the senior author (SYD) was aware of D. microlepioides representing the same taxon with Trichoneuron microlepioides Ching (1965: 119) described from southern Yunnan, China, because this taxon is morphologically unique by having the microlepioid frond habit (especially with copious pale hairs on both surfaces) and the dryopterioid sori (reniform, medial on abaxial surface of lamina) (Fig. 1). Phylogenetically, the sample of this species from northern Vietnam, which was identified as T. microlepioides by Liu et al. (2016), was resolved to be sister to Polystichopsis (Smith 1875: 217) Holttum (1947: 147) in Dryopteridaceae subfam. Polybotryoideae based on the analysis of three cpDNA sequences (rbcL, atpA, and atpB) (Liu et al. 2016). In recent years, we also collected this taxon in northern Vietnam (paratype locality of D. microlepioides) and southern Yunnan, China, and conducted phylogenetic analysis based on cpDNA genome (not presenting here). Our analysis resolved one sample from Vietnam (Dong 4598) and two collections from Yunnan (Dong 4801 and Zuo 5093) clustered together, identifying no any significant difference between them. The three samples in the phylogenetic tree formed a sister relationship in high supporting values with Polystichopsis as the result in Liu et al. (2016). This result provides further evidence supporting the same species of D. microlepioides Christensen (1934) with T. microlepioides Ching (1965).

Systematic position of Rivina humilis var. humilis, R. humilis var. bracteata and R. bengalensis based on nrDNA ITS and cpDNA rbcL & trnH-psbA sequence data

The ITS and cpDNA sequences were obtained for three taxa of the family Phytolaccaceae, viz. Rivina bengalensis S.C.Srivast. & T.K.Paul, R. humilis L. var. humilis, and R. humilis var. bracteata D.Maity, Sonia Mitra, Manasi Mandal & Maiti. The MLtree strongly supports the Rivina humilis clade, which includes R. bengalensis and R. humilis var. bracteata. The synonymization of R. bengalensis is supported by both molecular and morphological data. The accessions of Rivina humilis var. bracteata group together in the R. humilis clade, but the results also show inter-population variation, which primarily supports the varietal status of the taxon. The broadly oblanceolate bracts which is abruptly narrowed from middle or above middle into a long subulate to narrowly triangular, acuminate apical lobe make the variety distinct from typical R. humilis. The combined rbcL and trnH-psbA dataset reveal congruent result for the sequenced Rivina spp. Present study is the first report on molecular systematics of R. humilis from India.

From forest to savanna and back to forest: Evolutionary history of the genus Dimorphandra (Fabaceae).

The tree genus Dimorphandra (Fabaceae), which contains 26 species divided into three subgenera, was studied using DNA sequence data from six chloroplast genome regions (cpDNA) and the nuclear internal transcribed spacer (ITS). The analyses, which included Bayesian phylogenies and haplotype networks, ancestral area reconstructions, and ecological niche modeling, allowed for exploring the evolutionary history of Dimorphandra. Within the subgenus Phaneropsia, the cpDNA sequence data were more closely-related to species from the genus Mora, while the ITS sequence data displayed a closer phylogenetic relationship with the subgenus Pocillum. This incongruence may be due to incomplete lineage sorting associated with ancient polymorphisms. The Amazonian Dimophandra lineages were highly polymorphic and divergent, while those from the Cerrado and the Atlantic Forest had low levels of polymorphisms. The Amazon likely gave rise to the Dimophandra lineage that produced the Cerrado species, while a Cerrado lineage likely gave rise to the Atlantic Forest species. Habitat shifts were identified as a key factor in shaping the late evolutionary history of Dimorphandra.

Glacial history of Saxifragawahlenbergii (Saxifragaceae) in the context of refugial areas in the Western Carpathians.

Despite the wealth of data available for mountain phylogeography, local-scale studies focused on narrow endemic species remain rare. Yet, knowledge of the genetic structure of such species biogeographically linked to a restricted area is of particular importance to understand the history of the local flora and its diversity patterns. Here, we aim to contribute to the phylogeographical overview of the Western Carpathians with a genetic study of Saxifragawahlenbergii, one of the most characteristic endemic species of this region. We sampled populations from all discrete parts of the species' distribution range to apply sequencing of selected non-coding cpDNA and nuclear ribosomal DNA (ITS) regions, as well as Amplified Fragment Length Polymorphism (AFLP) fingerprinting. First, while ITS sequences showed weak diversification, the genetic structure based on cpDNA sequences revealed two well-differentiated groups of haplotypes. One of them is restricted to the main center of the distribution range in the Tatra Mountains (Mts), while the second group included a series of closely related haplotypes, which in most cases were unique for particular isolated groups of populations in peripheral mountain ranges and in the south-eastern part of the Tatra Mts. AFLP fingerprinting also revealed a pattern of divergence among populations, while only partly corroborating the division observed in cpDNA. Taking into account all the data, the pattern of genetic structure, supported by the high levels of unique genetic markers in populations, may reflect the historical isolation of populations in several local refugia during the last glacial period. Not only the center of the range in the Tatra Mts, but also other, neighboring massifs (Malá Fatra, Nízke Tatry, Chočské vrchy, Muránska planina), where populations are characterized by separate plastid DNA haplotypes, could have acted as separate refugia.

Chloroplast genome of Justicia procumbens: genomic features, comparative analysis, and phylogenetic relationships among Justicieae species.

Justicia procumbens L. is a traditional medicinal plant that is widely distributed in China. However, little is known about the genetic diversity and evolution of this genus, and no genomic studies have been carried out on J. procumbens previously. In this study, we aimed to assemble and annotate the first complete chloroplast genome (cpDNA) of J. procumbens and compare it with all previously published cpDNAs within the tribe Justicieae. Genome structure and comparative and phylogenetic analyses were performed. The 150,454bp-long J. procumbens cpDNA has a circular and quadripartite structure consisting of a large single copy, a small single copy, and two inverted repeat regions. It contains 133 genes, of which 88 are protein-coding genes, 37 are tRNA genes, and eight are rRNA genes. Twenty-four simple sequence repeats (SSRs) and 81 repeat sequences were identified. Comparative analyses with other Justicieae species revealed that the non-coding regions of J. procumbens cpDNA showed greater variation than did the coding regions. Moreover, phylogenetic analysis based on 14 cpDNA sequences from Justicieae species showed that J. procumbens and J. flava were most closely related. This study provides valuable genetic information to support further research on the genetic diversity and evolutionary development of the tribe Justicieae.

Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced

Vicia sepium (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese V. sepium lineage has been considered to have been introduced separately from Europe. Here, we examined whether the species was introduced or not on the basis of cpDNA sequences and genome-wide SNPs from Japanese and overseas samples. Both the cpDNA haplotype network and the nuclear DNA phylogenetic tree showed that Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA phylogenetic tree also showed that each lineage is clearly monophyletic, genetic admixture of the genetic cluster dominated in the Hokkaido lineage was also detected in the Mt. Ibuki lineage. Population divergence analysis showed that the two lineages diverged during the last glacial period. The Mt. Ibuki lineage showed a sudden population decline 300–400 years ago, indicating that some anthropogenic activity might be involved, while the Hokkaido lineage showed a gradual population decline from 5000 years ago. Consequently, these two lineages show low current genetic diversity compared with overseas lineages. These results show that the Japanese V. sepium is not introduced but is native.

Phylogeography and chromosome number variation in Micranthes nelsoniana and related species (Saxifragaceae) in Northeast Asia

Abstract Micranthes nelsoniana possesses multiple different variants and numerous chromosomes. Based on the internal transcribed spacer (ITS) and chloroplast (cp)DNA sequences, the phylogeography of M. nelsoniana and its relatives in Northeast Asia was investigated, with extensive sampling around the Kuril Islands. The Arctic–Asian continent and a clade of marginal islands were the two main groupings that comprised the ITS phylogenetic tree. The island clade was separated into five well-supported clades: Kamchatka and Hokkaido highlands, Kuril–Aleutian Islands, southern Kuril Islands, Japanese archipelago, and Primorye region. Micranthes fusca was found in Japan and in the southern Kuril Islands. It is a separate species that created several types of hybrids between M. nelsoniana in the centre of the Kuril Islands based on a comparison of the ITS and cpDNA networks. Micranthes nelsoniana and M. ohwii appear to have hybridized in the northern Kuril Islands. Cytological investigation on the local species of M. nelsoniana showed that the chromosomal numbers are: 2n = 24, 26, 28, 30, 50, and 80. Among them, two usual numbers to this area, 2n = 24 and 50, appear to encourage interspecific gene exchange. The genomes of Hokkaido plants with high chromosome counts were cloned, revealing that they contained genes of both continental and marginal origins. This study revealed the crucial role of marginal islands along Northeast Asia in the genetic diversity of M. nelsoniana and related species.

Time‐calibrated phylogeny of Daphne (Thymelaeaceae): Pre‐mediterranean temporal origin of the sclerophyllous Daphne gnidium

AbstractThe sclerophyllous syndrome is characterized by well‐defined traits (evergreen coriaceous leaves, inconspicuous flowers, and fleshy fruits). It has been hypothesized that lineages displaying the sclerophyllous syndrome show lower speciation rates than non‐sclerophyllous lineages after the establishment of the mediterranean climate. Daphne gnidium displays sclerophyllous traits and some differentiation into three subspecies (gnidium, mauritanica, maritima), but the spatio‐temporal origin of this taxonomic group is unknown due to the lack of a time‐calibrated phylogeny of the whole genus. Here, we inferred phylogenetic relationships and divergence times of Daphne (32 species, 238 samples) and other genera of Thymelaeaceae (16 genera, 38 species, 34 samples) using the internal transcribed spacer (ITS), which revealed that the current circumscription of Daphne is profoundly polyphyletic because some species are nested within the genera Wikstroemia and Edgeworthia. In contrast, D. gnidium formed a well‐supported clade as recognized in taxonomic accounts (subgenus Spachia). We found morphological and phylogenetic support for Daphne mauritanica as a monophyletic lineage sister to D. gnidium. Divergence between D. gnidium and D. mauritanica appears to have predated the establishment of seasonally dry conditions, which supports a pre‐mediterranean temporal origin of the lineage. A phylogeographical analysis within D. gnidium based on 66 nrDNA (ITS) and 84 cpDNA (rps16, trnV) sequences agreed with the low differentiation of the species in the Pleistocene despite its large distribution range. Altogether, D. gnidium illustrates one more example of the sclerophyllous syndrome with no speciation after the onset of the mediterranean climate.

Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses

BackgroundSium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced.ResultsThe Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029–155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61–67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported.ConclusionsThe plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.

Phylogeography of alpine plant Parnassia wightiana (Celastraceae)

Parnassia wightiana Wall. ex Wight & Arn., a perennial herb, is an alpine plant distributed across three biodiversity hotspots in China. This species offers an excellent study system to analyze the distribution pattern and genetic structure of high mountainous plant populations. Three chloroplast DNA (cpDNA) regions ( rpl32- t rnL, trnL-F, and trnS-G) from 442 individuals of 39 populations and internal transcribed spacers (ITS) from 418 individuals of 38 populations were sequenced and analyzed. We identified a total of 26 haplotypes based on the concatenated sequences of cpDNA and a total of 36 based on ITS sequences. A hierarchical analysis of molecular variance indicated significant phylogeographic structure among populations. Mismatch analysis of multipeak and Tajima’s D neutral test demonstrated Parnassia wightiana populations within China had not experienced abrupt expansion recently. The allopatric fragmentation resulted in the geographic isolation due to environmental heterogeneity, producing a high proportion of private haplotypes in the distribution of Parnassia wightiana within China.

A new distribution record of Lemna turionifera (Araceae, Lemnoideae) in Korea

Here we confirm the first accurate distributional record of Lemna turionifera Landolt (Lemnoideae, Araceae) in Korea. The nomenclator, Elias Landolt (1926–2013), had collected the species in Korea, but to date, there have been no other identifiers of this species. A Lemna species collected from Andong showed the key characters of L. turionifera: pigmented fronds, consistently-sized papillae along the middle vein, purple-colored root base, and turion forming. The cpDNA sequence of the atpF-atpH intergenic spacer of our Lemna sample was identical or quite similar (99.6%–100%) to those found in Landolt's collection. Although we could not find flowers, fruits, or seeds during a field survey, after 15 days of indoor incubation, we were able to observe the flowering of L. turionifera. The flower was protogynous, and the spathe was reddish.

Species boundaries within the recently diverged South American monocot‐like Eryngium (Apiaceae, Saniculoideae) based on biogeographic, climatic, morphological, and molecular data: E. cerradense, a new species from Paraguay

AbstractThe species of Eryngium with a monocot‐like habit are among the most taxonomically complex. They show low phenotypic and molecular differentiation due to their recent, rapid, and reticulate speciation during the Quaternary period. In this study, we evaluate the boundaries of the monocot‐like Eryngium regnellii and a closely related entity from the grasslands in the Cerrado of Paraguay. We integrated evidence from multiple data sources to test species delimitation: we estimated the phylogenetic position of both entities within Eryngium based on ITS nrDNA and cpDNA sequences; we carried out univariate and multivariate morphometric analyses to test statistically significant differences and to recognize morphological diagnostic characters; we also analyzed geographic distribution, habitat, and bioclimatic variables to evaluate divergence in environmental niche, and finally, we used Bayesian coalescent‐based delimitation approaches to test genetic structure. Divergence in morphology, environmental niche, and genetic structure between E. regnellii and the lineage from Paraguay support the hypothesis of evolutionary independence among these two lineages. Therefore, based on an integrative approach, we recognize and describe a new species from Paraguay: Eryngium cerradense.

The evolutionary history of rice azaleas (Rhododendron tschonoskii alliance) involved niche evolution to a montane environment.

The formation of isolated montane geography on islands promotes evolution, speciation, and then radiation if there are ecological changes. Thus, investigating evolutionary histories of montane species and associated ecological changes may help efforts to understand how endemism formed in islands' montane floras. To explore this process, we investigated the evolutionary history of the Rhododendron tschonoskii alliance, which grows in montane environments of the Japanese archipelago and the Korean Peninsula. We studied the five species in the R. tschonoskii alliance and 30 outgroup species, using genome-wide single-nucleotide polymorphisms and cpDNA sequences, in association with environmental analyses. The monophyletic R. tschonoskii alliance diverged since the late Miocene. Species in the alliance currently inhabit a cold climatic niche that is largely different from that of the outgroup species. We observed clear genetic and niche differentiations between the taxa of the alliance. The association of the alliance's evolution with the formation of cooler climates on mountains indicates that it was driven by global cooling since the mid-Miocene and by rapid uplift of mountains since the Pliocene. The combination of geographic and climatic isolation promoted high genetic differentiation between taxa, which has been maintained by climatic oscillations since the Quaternary.

Genetic variability and phylogenetic relationships of Begonia multangula based on atpB-rbcL non-coding spacer of cpDNA sequences

Abstract. Warseno T, Efendi M, Chasani AR, Daryono BS. 2022. Genetic variability and phylogenetic relationships of Begonia multangula based on atpB-rbcL non-coding spacer of cpDNA sequences. Biodiversitas 23: 5491-5501. Begonia (Begoniaceae) belongs to Section Platycentrum-Sphenanthera Group which has a wide distribution from Sumatra to the Lesser Sunda Islands and Sulawesi. Information on B. multangula genetic variability and intraspecies relationships based on molecular characters is critical for developing appropriate strategies in conservation biology, breeding activities, and many other applied fields. The genetic variability and interspecific relationships of B. multangula in Indonesia were investigated using sequence data from the atpB-rbcL intergenic spacer (IGS) cpDNA regions. The atpB-rbcL IGS fragment was amplified using atpB-1 as the forward primer and rbcL-1 as the reversed primer. Genetic variations were found in the length of the sequence and nucleotide divergences in the atpB-rbcL IGS region. The genetic distance between 822 fixed sites ranged from 0 to 0.61%. Eighteen of the 822 sites (99.27%) analyzed were invariable, six sites (0,73%) were variable consisting of 4 singleton variable sites and two parsimony informative sites, and twelve sites were gaps. The phylogenetic relationships generated by B. multangula based on the atpB-rbcL IGS sequence analysis indicated the genetic variation and divided it into two clades. However, the clustering pattern of B. multangula specimens resulting from molecular analysis based on atpB-rbcL IGS sequences did not show the geographic clustering grouping pattern.

Genetic variability and phylogenetic relationships of Begonia multangula based on atpB-rbcL non-coding spacer of cpDNA sequences

Abstract. Warseno T, Efendi M, Chasani AR, Daryono BS. 2022. Genetic variability and phylogenetic relationships of Begonia multangula based on atpB-rbcL non-coding spacer of cpDNA sequences. Biodiversitas 23: 5491-5501. Begonia (Begoniaceae) belongs to Section Platycentrum-Sphenanthera Group which has a wide distribution from Sumatra to the Lesser Sunda Islands and Sulawesi. Information on B. multangula genetic variability and intraspecies relationships based on molecular characters is critical for developing appropriate strategies in conservation biology, breeding activities, and many other applied fields. The genetic variability and interspecific relationships of B. multangula in Indonesia were investigated using sequence data from the atpB-rbcL intergenic spacer (IGS) cpDNA regions. The atpB-rbcL IGS fragment was amplified using atpB-1 as the forward primer and rbcL-1 as the reversed primer. Genetic variations were found in the length of the sequence and nucleotide divergences in the atpB-rbcL IGS region. The genetic distance between 822 fixed sites ranged from 0 to 0.61%. Eighteen of the 822 sites (99.27%) analyzed were invariable, six sites (0,73%) were variable consisting of 4 singleton variable sites and two parsimony informative sites, and twelve sites were gaps. The phylogenetic relationships generated by B. multangula based on the atpB-rbcL IGS sequence analysis indicated the genetic variation and divided it into two clades. However, the clustering pattern of B. multangula specimens resulting from molecular analysis based on atpB-rbcL IGS sequences did not show the geographic clustering grouping pattern.

The complete chloroplast genome of ‘biasong’ (Citrus micrantha Wester), a native species from the Southern Philippines

‘Biasong’ (Citrus micrantha), native to the Southern Philippine Islands, is an important cultivated fruit tree but has no published plastome sequence. We assembled and characterized the C. micrantha chloroplast genome from accession in the germplasm collection of the Institute of Crop Science, University of the Philippines Los Baños. The complete chloroplast (cp) genome sequence is 159,928-bp long with 128 coding genes comprising 83 mRNA genes, 37 tRNA genes, and eight rRNA genes. Out of the mRNA genes, 45 genes code for photosynthesis, 30 genes code for self-replication, and five genes code for other functions. A phylogenetic analysis of the assembled genome, along with 24 Citrus species and three other Rutaceae species, identified Citrus aurantiifolia as its closest relative with available complete cpDNA sequence.

Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics

Rosa lucieae is one of the famous wild ancestors of cultivated roses and plays a very important role in horticultural research, but there is still a lack of research on the R. lucieae chloroplast genome. In this study, we used the Illumina MiSeq platform for sequencing, assembly, and annotation to obtain the R. lucieae chloroplast genome sequencing information and compared genomics, selection stress analysis, and phylogenetic analysis with 12 other chloroplast genomes of Rosa. The R. lucieae cpDNA sequence has a total length of 156,504 bp, and 130 genes are annotated. The length of all 13 studied chloroplast genomes is 156,333~157,385 bp. Their gene content, gene sequence, GC content, and IR boundary structure were highly similar. Five kinds of large repeats were detected that numbered 100~116, and SSR sequences ranged from 78 to 90 bp. Four highly differentiated regions were identified, which can be used as potential genetic markers for Rosa. Selection stress analysis showed that there was significant positive selection among the 18 genes. The phylogenetic analysis of R. lucieae and R. cymose, R. maximowicziana, R. multiflora, and R. pricei showed the closest relationship. Overall, our results provide a more comprehensive understanding of the systematic genomics and comparative genomics of Rosa.

A New Deep-Water Epilithic Green Alga, Ulvella lacustris, from an Alpine Brackish Lake in Qinghai–Tibet Plateau

Ulvella species are widely distributed in ocean and freshwater habitats and from high latitudes to the tropics. However, no species of this genus have been found in the Qinghai–Tibetan Plateau. In the present study, five rock specimens were collected from the bottom of Qinghai Lake at a depth of about 15–28 m, from which three unialgal strains were isolated. These strains were characterized by prostrate pseudoparenchyma, irregular or radial branch filaments, and mono- or polystromatic discs or rosettes formed by consecutive filaments, with thalli that can grow up to 180 um in length, suggesting that they may be Ulvella species. Phylogenetic analysis based on 18S rDNA and tufA cpDNA sequences revealed that the isolates formed a strong branch among other Ulvella species and were closely related to Ulvella leptochaete and Ulvellawaernii. This result was also confirmed by neighbor-joining tree inference based on ITS2 secondary structure. Unlike other members of Ulvella, the isolated strain was characterized by its unique habitat, field morphology of thallus, size of vegetative cells, and number of pyrenoids. Based on these morphological differences, the phylogenetic analysis, and the comparison of ITS2 secondary structure with relative species, the strain isolated in this study was proposed to be a novel Ulvella sp. The alga was found on the bottom of brackish lakes on the Qinghai–Tibetan Plateau, which meant that our sampling range needed to be expanded further.

The complete chloroplast genome of Vitex trifolia L. (Lamiaceae)

The three-leaved chaste tree (Vitex trifolia) is a medicinal and ornamental plant widely distributed from East Africa to the Pacific but has no complete chloroplast genome sequence. We assembled and characterized the V. trifolia accession from the germplasm collection of the Institute of Crop Science, University of the Philippines Los Baños. The complete plastome sequence is 154,444-bp long with 131 coding genes comprising 87 mRNA genes, 36 tRNA genes, and 8 rRNA genes. A phylogenetic analysis of the assembled genome, together with nine other Lamiaceae species, identified V. rotundifolia as its closest relative with available complete cpDNA sequence. The clustering also supports the genotypic similarity of the species belonging to trifolia group of the genus Vitex.