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Aim Rapid and accurate species identification is the foundation for biodiversity assessment. DNA barcoding has been shown to be an effective tool to overcome the taxonomic impediment to facilitate biodiversity conservation in temperate forests. However, this tool has rarely been considered for use in tropical forests. This study aims to investigate the utility and species resolution of DNA barcoding in a subtropical region. Location The Dinghushan National Nature Reserve (DNNR) in China. Methods A DNA barcoding database was constructed for 531 trees present in the DNNR. We used a phylogenetic method (neighbour-joining trees) and sequence similarity (all-to-all BLASTn searches) to evaluate the utility and species resolution of five DNA barcode regions (rbcL, matK, ITS, ITS2 and trnH-psbA), both singly and in combinations of two or three region. Results The combination of rbcL + matK + ITS had the highest species resolution (94.19%). However, when considering the difficulty of sequence recoverability, rbcL + ITS2 performed best (64.64%). Species resolution for large genera containing more than two species was substantially lower than that for small genera with one and two species per genus. Local small spatial scales (1-ha quadrats) resulted in moderately improved species resolution (70.82% for rbcL + ITS2) compared to larger spatial scales (20 and 1133 ha). We document incongruent signals between nuclear and cpDNA regions and the challenges associated with barcoding large genera inherent to subtropical floras. Main conclusions This study considerably expands the global DNA barcode database for subtropical trees. Based on cost-effectiveness and the trade-off between sequence recovery and species resolution, we suggest that the rbcL + ITS2 barcode combination is an effective tool for documenting plant diversity in the DNNR. This study also sheds some light on the limitations and challenges for the application of barcoding to conservation biogeography in subtropical forests.

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

Jewel orchid is the common name of several orchid species which can be alike in morphological characteristics, but variable in medicinal properties. At present, two DNA barcode loci, namely, maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL), are intensively utilized for plant identification. However, the discrimination effectiveness of these loci is variable among plant species. This study was carried out to compare the identifying efficacy of these two loci on jewel orchid population collected throughout Vietnam. The results revealed that 21 jewel orchid accessions studied were segregated into four different species with significant variations. The discrimination power of matK and rbcL markers in this jewel orchid study displayed different efficiency level. The rbcL gene has higher distinguishing potential than either matK gene alone or the combination of both genes. The findings of this project could provide valuable information that is necessary for classification, plant origin identification, breeding, and conservation program of jewel orchid in Vietnam.

The flowering plant family Proteaceae is putatively of Gondwanan age, with modern and fossil lineages found on all southern continents. Here we test whether the present distribution of Proteaceae can be explained by vicariance caused by the break-up of Gondwana. Africa, especially southern Africa, Australia, New Zealand, South America, New Caledonia, New Guinea, Southeast Asia, Sulawesi, Tasmania. We obtained chloroplast DNA sequence data from the rbcL gene, the rbcL-atpB spacer, and the atpB gene from leaf samples of forty-five genera collected from the field and from living collections. We analysed these data using Bayesian phylogenetic and molecular dating methods, with five carefully selected fossil calibration points to obtain age estimates for the nodes within the family. Four of eight trans-continental disjunctions of sister groups within our sample of the Proteaceae post-date the break-up of Gondwana. These involve independent lineages, two with an Africa-Australia disjunction, one with an Africa-South America disjunction, and one with a New Zealand-Australasia disjunction. The date of the radiation of the bird-pollinated Embothriinae corresponds approximately to the hypothesized date of origin of nectar-feeding birds in Australia. The findings suggest that disjunct distributions in Proteaceae result from both Gondwanan vicariance and transoceanic dispersal. Our results imply that ancestors of some taxa dispersed across oceans rather than rafting with Gondwanan fragments as previously thought. This finding agrees with other studies of Gondwanan plants in dating the divergence of Australian, New Zealand and New Caledonian taxa in the Eocene, consistent with the existence of a shared, ancestral Eocene flora but contrary to a vicariance scenario based on accepted geological knowledge.

In this study, DNA barcoding and phylogenetic analysis of five Prunus armeniaca L. genotypes (Cataloglu, Hacihaliloglu, Hasanbey, Hudayi, and Kabaasi) grown in Malatya/Türkiye were conducted using chloroplast DNA (cpDNA) mat K and rbc L regions. The cpDNA mat K region was amplified using mat K472F and mat K1248R primers, while the rbc L region was amplified with rbc LaF and rbc LaR primers. The matK and rbcL sequences were utilized to assess nucleotide ratios, genetic distance, and nucleotide diversity (π). The neighbor- joining (NJ) tree including other Prunus species from NCBI was created. In addition, physiochemical and 3-D analysis of mat K and rbc L proteins were performed. As a result, π = 0.000549 for mat K sequence and π = 0.002657 for rbc L sequence were determined. NJ (neighbor joining) phylogenetic trees formed with both mat K and rbc L sequences were found to be compatible with each other. The mat K and rbc L gene regions were found to be suitable for phylogenetic analysis.

Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal ( https://fernphy.github.io ) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.

Ruppia cf. maritima is one of the few native Hawaiian brackish water flowering plants, but its identity has never been examined using genetic analysis. The ability of this seagrass to tolerate a wide range of salinities and temperatures is reflected in its morphological variability among locations worldwide. Three populations on the island of Hawai‘i were sampled, and molecular analyses of the nuclear gene ITS and two chloroplast genes trnH-psbA and rbcL were used to examine the identity of Hawaiian Ruppia. Concatenated analyses showed that the populations contained little intra- or interpopulation variability, and indicated greatest genetic similarity to specimens from Japan, India, Vietnam, and Africa. Slight variations in tree topologies were present among the individual nuclear and two plastid markers; however, all Hawaiian specimens nested within other sequences reported as R. maritima. Molecular phylogenetic analyses demonstrate that there are multiple clades of samples from around the world labeled as R. maritima, and that the Hawaiian samples are allied with one of these clades. The geographic isolation and geologic age of each Hawaiian island, as well as the disjunct distribution of Ruppia populations among islands and within each island suggest a multiplex biogeography and evolutionary history of Hawaiian Ruppia.

The new species Hypnea corona Huisman & Petrocelli is described to accommodate specimens from Australia, New Zealand, Italy, and Japan that were previously included in the Hypnea cornuta complex but were shown by recent molecular studies to represent a species-level clade. Hypnea corona produces distinctive stellate, starch-filled propagules that are easily dislodged and serve as vegetative reproductive structures. However, similar structures are found in closely related species and thus H. corona is distinguished primarily by unique rbcL barcode sequences.

A phylogenetic tree is an arrangement that can describe kinship data in the form of a branched tree. In the field of forestry, identification using morphological data is difficult because it takes a long time and the fruit and flower seasons are uncertain. Another alternative that can be used to create a phylogenetic tree is to use secondary data. This study aims to explore the availability of GeneBank sequence data for tree species at the Universitas Sumatera Utara and create a phylogenetic tree to see their relationships based on rbcL markers. The results showed that the highest sequence of trees on the USU campus using the rbcL gene was 86.8%. In the reconstruction of the phylogeny tree, the boostrap value is above 70%, and tree species are grouped according to the same family.

Improving global yields of important agricultural crops is a complex challenge. Enhancing yield and resource use by engineering improvements to photosynthetic carbon assimilation is one potential solution. During the last 40 million years C 4 photosynthesis has evolved multiple times, enabling plants to evade the catalytic inadequacies of the CO 2 -fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco). Compared with their C 3 ancestors, C 4 plants combine a faster rubisco with a biochemical CO 2 -concentrating mechanism, enabling more efficient use of water and nitrogen and enhanced yield. Here we show the versatility of plastome manipulation in tobacco for identifying sequences in C 4 -rubisco that can be transplanted into C 3 -rubisco to improve carboxylation rate ( V C ). Using transplastomic tobacco lines expressing native and mutated rubisco large subunits (L-subunits) from Flaveria pringlei (C 3 ), Flaveria floridana (C 3 -C 4 ), and Flaveria bidentis (C 4 ), we reveal that Met-309-Ile substitutions in the L-subunit act as a catalytic switch between C 4 ( 309 Ile; faster V C , lower CO 2 affinity) and C 3 ( 309 Met; slower V C , higher CO 2 affinity) catalysis. Application of this transplastomic system permits further identification of other structural solutions selected by nature that can increase rubisco V C in C 3 crops. Coengineering a catalytically faster C 3 rubisco and a CO 2 -concentrating mechanism within C 3 crop species could enhance their efficiency in resource use and yield.