rbcL Gene Research Articles

Description of the new species Mallomonas okhapkinii (Synurales, Chrysophyceae) based on morphological and molecular data

This paper describes a new species of Mallomonas discovered in a swamp area in Russia. The species was identified based on scale morphology, examined using scanning and transmission electron microscopy, and subjected to molecular analysis. The new species, Mallomonas okhapkinii sp. nov., belongs to the section Planae and is most similar in scale and bristle ultrastructure to M. matvienkoae sensu stricto. Phylogenetic analysis, performed using a concatenated dataset of nuclear-encoded small subunit rRNA and plastid-encoded rbcL genes, revealed that the strains of the new species form a distinct clade with high statistical support, closely related to the clade of M. paragrandis and M. sorohexareticulata. This species was found in only one habitat.

Plant Diversity Research in Shangqiu Yellow River Ancient Course National Forest Park, China

The Shangqiu Yellow River Ancient Course National Forest Park, the only national forest park in China created entirely from man-made forests, plays a critical role in ecological conservation. Our research employed plot surveys and quantitative ecological methods, including a diversity index analysis and importance value analysis, to investigate the diversity of arboreal, shrub, and herbaceous plants. This study revealed the composition and distribution of plant communities and analyzed invasive species. It identified dominant plant families, genera, and species and evaluated the types, distribution, and characteristics of invasive plants. We documented 70 families, 177 genera, and 254 species, highlighting that local environmental factors and human activities significantly affect the composition and distribution of plant communities. The presence of 29 invasive plant species poses a risk to the ecosystem. We constructed a phylogenetic tree of the plant community based on rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit) gene sequences, revealing the evolutionary relationships among species, and evaluated the community’s stability using the NTI (nearest taxon index) and NRI (net relatedness index). This research aims to provide a scientific foundation for conserving plant diversity and promoting sustainable development, and it can inform ecological protection and biodiversity studies in similar regions.

Evidence for the proposal that Palisada corallopsis and P. furcata (Ceramiales, Rhodophyta) are conspecific

Abstract Palisada corallopsis has a widely reported distribution in the western and eastern Atlantic and some areas of the Indo-Pacific Ocean, whereas P. furcata has a more restricted distribution, reported only from Brazil and Cuba. Palisada corallopsis and P. furcata were collected from their type localities, Havana, Cuba and Ceará, Brazil, respectively, and compared by morphological and molecular analyses using rbcL and COI-5P genes. The molecular results placed the sequences from the type locality of both species in the same clade, showing low genetic divergence, 0.95 % for rbcL and 1.6 % for COI-5P. Morphologically, the species share similar habits, with branchlets bi-to trifurcated, cortical cells that may be arranged as a palisade and connected by secondary pit-connections. Our detailed morphological observations, including examination of the type specimens, and molecular analyses demonstrate that P. corallopsis and P. furcata are conspecific, P. furcata being a later taxonomic synonym of P. corallopsis.

Three new species of the genus ‘Carteria’ (Chlamydomonadales, Chlorophyceae) with the proposal of correct generic names

ABSTRACT ‘Carteria’ is a genus of quadriflagellate chlamydomonadalean green algae, however this genus is not thought to be a monophyletic group. In this study, we investigated nine strains of ‘Carteria’ newly isolated from China by morphological comparisons and molecular phylogeny of 18S rDNA and rbcL genes. Five strains could be identified as existing ‘Carteria’ species. Four strains with clearly different morphology and independent phylogenetic positions compared with the described ‘Carteria’ species were identified as three new species. Since the original type species, Carteria cordiformis, has been recognized as a prasinophyte alga, the generic name Carteria cannot be applied to other species previously assigned to ‘Carteria’. Six ‘Carteria’ species (including three new species) and one Pseudocarteria species of Carteria-Clade I were transferred to the genus Corbierea, and the description of this genus was emended. A new genus, Staurocarteria gen. nov. was proposed for Carteria-Clade II.

Microbial mechanisms for CO2 and CH4 emissions in Robinia pseudoacacia forests along a North–South transect in the Loess Plateau

Forest soil microbes play a crucial role in regulating atmospheric-soil carbon fluxes. Environmental heterogeneity across forest types and regions may lead to differences in soil CO2 and CH4 emissions. However, the microbial mechanisms underlying these emission variations are currently unclear. In this study, we measured CO2 and CH4 emissions of Robinia pseudoacacia forests along a north–south transect in the Loess Plateau. Using metagenomic sequencing, we investigated the structural and functional profiles of soil carbon cycling microbial communities. Results indicated that the forest CO2 emissions of Robinia pseudoacacia was significantly higher in the north region than in the south region, while the CH4 emission was oppositely. This is mainly attributed to changes in gene abundance driven by soil pH and moisture in participating carbon degradation and methane oxidation processes across different forest regions. The gene differences in carbon fixation processes between regions primarily stem from the Calvin cycle, where the abundance of rbcL, rbcS, and prkB genes dominates microbial carbon fixation in forest soils. Random forest models revealed key genes involved in predicting forest soil CO2 emissions, including SGA1 and amyA for starch decomposition, TYR for lignin decomposition, chitinase for chitin decomposition, and pectinesterase for pectin decomposition. Microbial functional characterization revealed that interregional differences in CH4 emissions during methane metabolism may originate from methane oxidation processes, and the associated gene abundances (glyA, ppc, and pmoB) were key genes for predicting CH4 emissions from forest soils. Our results provide new insights into the microbial mechanisms of CO2 and CH4 emissions from forest soils, which will be crucial for accurate prediction of the forest soil carbon cycle in the future.

DNA barcoding, pollen and seed characteristics for documentation of four monocot Mediterranean endemic plant species in Egypt

Endemic taxa are critical constituents in the flora of most parts of the world. Recently, most of these taxa have become exposed to extinction. This study aims to increase understanding of four monocot Mediterranean threatened endemic taxa in Egypt (Allium mareoticum Bornm. & Gauba, Bromus aegyptiacus Tausch, Muscari salah-eidii (Täckh. & Boulos) Hosni, Pancratium arabicum Sickenb.) by description of their pollen and seed and authentication of DNA barcoding using rbcL and matK genes. Twenty field visits were conducted from March 2017 till April 2023 including different localities through Mediterranean area for covering the presence of these species. Characterization of pollen grains and seeds were examined using a light (LM) and scanning electron microscopes (SEM). DNA barcoding was carried out for documentation of the four species. Maturase K (matK) and ribulose-bisphosphate carboxylase (rbcL) were used as primers for PCR amplification and gene sequencing. The two genes were successful in identifying Allium mareoticum, Bromus aegyptiacus, and Muscari salah-eidii at the genus level and Pancratium arabicum at both species and genus levels for rbcL marker, and the genus level for matK marker. This study is considered a leading study for new barcodes of (A) mareoticum, (B) aegyptiacus, and M. salah-eidii which were initially made available to the NCBI.

In Silico Evaluation of rbcL, matK, and psbA-trnH Regions on the Genus Spatholobus (Fabaceae)

Spatholobus is a genus that belongs to the Fabaceae that is known to contain various bioactive compounds and distributed across Asia, including Indonesia. However, exploration of Spatholobus in Indonesia is still rare. Therefore, DNA barcoding is used to support the exploration and conservation of Spatholobus in Indonesia. However, there is no universal marker that can be used across all plant species. In addition, there are still few studies related to DNA barcoding within the genus Spatholobus. The purpose of this study was to evaluate the rbcL, matK, and intergenic spacer psbA-trnH regions in silico that can be used as DNA barcodes for the genus Spatholobus. This study began with a sequence search on the NCBI database including the rbcL, matK, and intergenic spacer psbA-trnH genes in the genus Spatholobus and Phaseolus coccineus as the outgroup. Each sequence was then aligned with ClustalW. Then, a phylogenetic tree was constructed using the Maximum-Likelihood (ML) with 1000× bootstrap. As a result, the rbcL, matK, and psbA-trnH regions can be used as markers for DNA barcoding in the genus Spatholobus with different specifications. The rbcL and matK can be used to distinguish Spatholobus at the genus level, while the psbA-trnH can be used to distinguish Spatholobus at the species level.

Ploidy levels in diverse picocyanobacteria from the Baltic Sea.

In nature, the number of genome or chromosome copies within cells (ploidy) can vary between species and environmental conditions, potentially influencing how organisms adapt to changing environments. Although ploidy levels cannot be easily determined by standard genome sequencing, understanding ploidy is crucial for the quantitative interpretation of molecular data. Cyanobacteria are known to contain haploid, oligoploid, and polyploid species. The smallest cyanobacteria, picocyanobacteria (less than 2 μm in diameter), have a widespread distribution ranging from marine to freshwater environments, contributing significantly to global primary production. In this study, we determined the ploidy level of genetically and physiologically diverse brackish picocyanobacteria isolated from the Baltic Sea using a qPCR assay targeting the rbcL gene. The strains contained one to four genome copies per cell. The ploidy level was not linked with phylogeny based on the identity of the 16S rRNA gene. The variation of ploidy among the brackish strains was lower compared to what has been reported for freshwater strains and was more similar to what has been reported for marine strains. The potential ecological advantage of polyploidy among picocyanobacteria has yet to be described. Our study highlights the importance of considering ploidy to interpret the abundance and adaptation of brackish picocyanobacteria.

Impact of Molecular Identification of Palm leaves on the preservation and conservation of Palm Leaves-Tala patra Manuscripts

Palm leaves manuscripts preservation is the main target of this research work. Therefore, this research study aimed at molecular identification of palm leaves by DNA Barcoding to assess the potential level on manuscript preservation. This study aims to amplify the rbcL and matK genes in palm leaves collected from different regions of Bangalore. The DNA was isolated by CTAB method and the amplification was done by PCR analysis. DNA barcoding proved to be an efficient tool for proper discrimination of the related species by generating standers that can be used universally. rbcL: A gene found in the chloroplast genome, encoding a large subunit of the enzyme ribulose-bisphosphate carboxylase. matK: Another chloroplast gene coding for maturase K, involved in splicing group II introns. The discrimination is done by accurately sequencing the standard gene region in a very short time (Hebert et al., 2003). rbcL and matK have been having most recommended and vasty studied DNA barcodes for plants, as they are proved by PWG (Pair wise group) to be potential standardized barcodes for plant DNA barcoding. These barcodes are used to properly identify and discriminate any native or foreign plant species (Maloukh et al., 2017). This work guides us the impact/role of molecular identification-DNA Barcoding of palm leaves on the preservation of Palm leaves manuscripts

Dasysiphonia adriatica sp. nov. (Delesseriaceae, Rhodophyta), a new red algal species from the North Adriatic Sea (Mediterranean Sea)

Dasysiphonia is a genus of the family Delesseriaceae (Rhodophyta) including 9 taxonomically accepted species, among which only the non-indigenous Dasysiphonia japonica has been documented from the Adriatic Sea (Mediterranean). This invasive species is native to Hokkaido Island (Japan) and was introduced to Europe and the Mediterranean Sea through imports of the commercial Pacific oyster Magallana gigas. In this study, we describe a new species belonging to the genus Dasysiphonia, collected in the Mediterranean Sea. This new taxon was sampled in Slovenian coastal waters; its thalli were analysed using both molecular and morphological approaches and it was compared with the other known species. Moreover, samples of the invasive D. japonica were collected from different Venice Lagoon (Italy) sites and used for comparison with the new taxon. The phylogenetic reconstruction, based on the plastid rbcL gene, clearly distinguished the new Slovenian entity from all the known Dasysiphonia species, including the ones recently transferred from the sister genus Dasya. These results indicate that the Slovenian samples represent a new species, hereby named Dasysiphonia adriatica sp. nov.

Composition and temporal dynamics of the phytoplankton community in Laizhou Bay revealed by microscopic observation and rbcL gene sequencing

Laizhou Bay, a major breeding ground for economic marine organisms in the northern waters of China, is facing rapid environmental degradation. In this study, field surveys in this area were conducted in the spring, summer, and autumn of 2020. Microscopic observation and RuBisCO large subunit (rbcL) gene analysis were employed to understand the community structure and temporal dynamics of phytoplankton. The phytoplankton community structures detected by the two methods showed significant differences. Microscopic observation revealed the dominance of dinoflagellates in spring that shifted to the dominance of diatoms in summer and autumn. However, rbcL gene sequencing consistently identified diatoms as dominant throughout all three seasons, with their relative abundance showing an increasing trend. Conversely, the relative abundance of the second- and third-most abundant taxa, namely, haptophytes and ochrophytes, decreased as the seasons transitioned. rbcL gene sequencing annotated more species than microscopy. It could detect haptophytes and cryptophytes, which were overlooked by microscopy. In addition, rbcL gene sequencing detected a remarkable amount of Thalassiosira profunda, which was previously unidentified in this sea area. However, it appeared to underestimate the contribution of dinoflagellates considerably, with most taxa being only identified through microscopic identification. The two methods jointly identified 28 harmful algal bloom taxa with similar detection quantities but substantial differences in species composition. Phytoplankton communities were influenced by temperature, salinity, and nutrients. The results of this work suggest that a combination of multiple techniques is necessary for a comprehensive understanding of phytoplankton.

Insights into malaria vectors–plant interaction in a dryland ecosystem

Improved understanding of mosquito–plant feeding interactions can reveal insights into the ecological dynamics of pathogen transmission. In wild malaria vectors Anopheles gambiae s.l. and An. funestus group surveyed in selected dryland ecosystems of Kenya, we found a low level of plant feeding (2.8%) using biochemical cold anthrone test but uncovered 14-fold (41%) higher rate via DNA barcoding targeting the chloroplast rbcL gene. Plasmodium falciparum positivity was associated with either reduced or increased total sugar levels and varied by mosquito species. Gut analysis revealed the mosquitoes to frequently feed on acacia plants (~ 89%) (mainly Vachellia tortilis) in the family Fabaceae. Chemical analysis revealed 1-octen-3-ol (29.9%) as the dominant mosquito attractant, and the sugars glucose, sucrose, fructose, talose and inositol enriched in the vegetative parts, of acacia plants. Nutritional analysis of An. longipalpis C with high plant feeding rates detected fewer sugars (glucose, talose, fructose) compared to acacia plants. These results demonstrate (i) the sensitivity of DNA barcoding to detect plant feeding in malaria vectors, (ii) Plasmodium infection status affects energetic reserves of wild anopheline vectors and (iii) nutrient content and olfactory cues likely represent potent correlates of acacia preferred as a host plant by diverse malaria vectors. The results have relevance in the development of odor-bait control strategies including attractive targeted sugar-baits.

DNA Extraction and PCR Optimization of Coffea arabica L. and Coffea canephora Pierre ex A. Froehner

DNA isolation is an important step for further molecular analysis. Coffee plants contain polysaccharides, polyphenols, and secondary metabolites which can contaminate the results of DNA isolation. This study was conducted to isolate DNA from arabica and robusta coffee leaves using a modified CTAB method and PCR optimization for amplification of matK and rbcL genes. DNA was isolated using buffers (CTAB 10%, PVP 1%, β-mercaptoethanol 1%, Tris-HCl 1M, NaCl 5M, and EDTA 0.5%), and eluted with TE-RNase. Genomic DNA of ten coffee plants was successfully isolated with concentrations ranging from 33-146 nm/µL with purity (A260/A280) 1.7-1.9. Based on the genomic DNA isolated, matK and rbcL genes were amplified with initial denaturation conditions of 94°C (for 1 minute of matK and 4 minutes of rbcL) followed by 35 cycles of denaturation at 94°C for 30 seconds, annealing (adjusted to each primer), and extension at 72°C for 1 minute. The optimal PCR conditions were effective to amplify matK (900 bp) and rbcL (600 bp) genes. Thus, the modified DNA isolation method and PCR optimization can be used as an efficient tool for further molecular analysis of Coffea arabica L. and Coffea canephora Pierre ex A. Froehner.

The Diatom Diversity and Ecological Status of a Tufa-Depositing River through eDNA Metabarcoding vs. a Morphological Approach-A Case Study of the Una River (Bosnia and Herzegovina).

Tufa deposits in karst rivers are unique habitats created by mutual interactions between specific environmental and biotope features and inhabited by diatoms as a highly abundant and diverse algal group. This pilot study aimed to investigate the diversity of diatom communities on tufa depositing habitats and assess the Una River's ecological status using a comparative molecular and morphological approach for diatom identification. The 312 base pairs of the rbcL gene were barcoded and analyzed using MiSeq reads and amplicon sequence variants (ASVs) obtained by the DADA2 pipeline. The reference database Diat.barcode v7 was used for taxonomic assignment. The morphological identification of the diatoms was carried out in parallel. In total, the combined dataset revealed 46 taxa identified at genus rank, 125 on the subgenus, and 145 on combined taxonomy rank. The metabarcoding approach mostly leads to a lower number of identified taxa at species rank (58 in molecular vs. 119 in optical inventory), resulting in higher values of beta diversity and heterogeneity in diatom assemblages in samples obtained by morphological approach. Despite the high percentage of taxonomically not assigned diatom ASVs to the species rank, high Shannon diversity index values and a similar number of taxa per locations compared to the morphological approach were obtained. Taxa Achnanthidium minutissimum (Kützing) Czarnecki, Achnanthidium pyrenaicum (Hustedt) H.Kobayasi, Amphora pediculus (Kützing) Grunow, Diatoma vulgaris Bory, Navicula cryptotenella Lange-Bertalot, and Navicula tripunctata (O.F.Müller) Bory were identified at all locations in both inventories. Although limited consistency in the diatom abundances between the two inventory datasets was found, a similar grouping of samples was observed connected to the river's longitudinal gradient. The data obtained using molecular approach in most sites indicated a mostly lower ecological status (good or moderate) compared to the data obtained from the morphological approach (high, good, and moderate). The potential of environmental DNA (eDNA) diatom metabarcoding for water monitoring and diversity studies is undeniable, but to fully realize the benefits of these methods in the future, it is essential to standardize protocols and expand the reference database for species found in specific habitats, such as tufa deposits.

Molecular Identification Validates Morphological Identification of Javanese Cardamom from Banyumas in Central Java, Indonesia

Cardamom is one of the prominent plants with significant economic value in the Banyumas Regency, Central Java, Indonesia. Although Javanese cardamom is traditionally categorized under Amomum compactum, the morphological variations observed create ambiguity about its exact species status. DNA barcoding using the maturase K (matK) and ribulose-bisphosphate carboxylase (rbcL) genes is proven as a reliable technique to elucidate the taxonomic status of morphological variable plant cultivars. This study aimed to characterize cardamom from Banyumas Regency using morphological and molecular approaches for taxonomic status identification and genetic diversity evaluation. The matK and rbcL genes were selected as genetic markers and sequenced using a bidirectional sequencing technique. Morphological examination showed significant color variations at the cardamom stem base. All samples had high genetic identities to reference species in databases and were supported by high query cover and zero e-values. Therefore, molecular characterization, alongside geographic distribution assessment, established that this plant belongs to a single species, Amomum compactum. Additionally, the analysis conducted showed a low level of genetic diversity, as evidenced by haplotype and nucleotide diversity. Low-level genetic diversity provides additional data to convince that cardamon in Banyumas Regency belongs to a single species. These results are essential data in seed selection for further cultivation.

A First Approach for the In Vitro Cultivation, Storage, and DNA Barcoding of the Endangered Endemic Species Euonymus koopmannii.

Euonymus koopmannii is a rare and protected species in Kazakhstan, valued for its ecological role in soil stabilization and its ornamental properties. This study presents the first use of micropropagation and phylogenetic analysis for the endemic plant E. koopmannii. Seedlings of E. koopmannii proved to be more effective than internodes as primary explants for plant micropropagation of in vitro culture, with a multiplication coefficient of 28.5 from seedlings and 6.1 from internodes. On MSR I medium supplemented with 0.5 mg/L IBA and 0.05 mg/L IAA, a higher success rate of 67% was achieved for root formation of test tube-grown E. koopmannii plants. Using mannitol as an osmotic agent at a concentration of 8 mg/L prolonged the storage time of E. koopmannii under slow growth conditions when compared to CCC and abscisic acid. Phylogenetic relationships and species identification were analyzed using four DNA-barcoding markers, comparing E. koopmannii with species from NCBI. All candidate barcoding markers showed sufficient levels of interspecific genetic variation among Euonymus species. In addition, ITS region and rbcL gene sequences effectively distinguished E. koopmannii from other species. These results provide fundamental information that will be valuable for future biotechnological and molecular studies.

Description of Two New Species of Stauroneis Ehrenberg (Naviculales, Bacillariophyceae) from the Russian Far East Using an Integrative Approach.

Stauroneis (Naviculales, Bacillariaceae) are widespread, mostly in fresh-water habitats, and account for 343 species. They are described mainly on the basis of morphology and morphometric traits. These characteristics vary during life cycles and may overlap between species, making their identification difficult. We isolated two strains of naviculoid diatoms and examined them using an integrative approach (phylogenetic, morphological, ultrastructural data, and life cycle). Phylogenetic analyses based on chloroplast rbcL gene data showed affinity of the new strains to the genus Stauroneis. Our algae share morphological features typical of Stauroneis but differ from similar species in minimal valve length measurements, valve apex shape, and minimal number of striae in 10 μm. Two strains are distinct from each other in maximal valve length and width, partially valve shape, the number of areolae in 10 μm, and cingulum structure. It was revealed that the strains reproduce via isogamy. Three species delimitation methods (ASAP, PTP, and GMYC) also confirmed that the two closely related new strains represent distinct species. Based on molecular data and phenotypic traits examined within the framework of an integrative approach, we describe two new isolates as Stauroneis urbani sp. nov. and Stauroneis edaphica sp. nov.

Differential association of key bacterial groups with diatoms and Phaeocystis spp. during spring blooms in the Southern Ocean.

Interactions between phytoplankton and heterotrophic bacteria significantly influence the cycling of organic carbon in the ocean, with many of these interactions occurring at the micrometer scale. We explored potential associations between specific phytoplankton and bacteria in two size fractions, 0.8-3 µm and larger than 3 µm, at three naturally iron-fertilized stations and one high nutrient low chlorophyll station in the Southern Ocean. The composition of phytoplankton and bacterial communities was determined by sequencing the rbcL gene and 16S rRNA gene from DNA and RNA extracts, which represent presence and potential activity, respectively. Diatoms, particularly Thalassiosira, contributed significantly to the DNA sequences in the larger size fractions, while haptophytes were dominant in the smaller size fraction. Correlation analysis between the most abundant phytoplankton and bacterial operational taxonomic units revealed strong correlations between Phaeocystis and picoeukaryotes with SAR11, SAR116, Magnetospira, and Planktomarina. In contrast, most Thalassiosira operational taxonomic units showed the highest correlations with Polaribacter, Sulfitobacteria, Erythrobacter, and Sphingobium, while Fragilariopsis, Haslea, and Thalassionema were correlated with OM60, Fluviicola, and Ulvibacter. Our in-situ observations suggest distinct associations between phytoplankton and bacterial taxa, which could play crucial roles in nutrient cycling in the Southern Ocean.

Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake.

Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes (MAGs) from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.

DNA barcoding, inter-specific and inter-generic variation studies on South Indian scaly tree ferns (Cyathea sp.pl.) using chloroplast rbcL gene

DNA barcoding is an effective identification tool for tree ferns with heteromorphic generations with morphologically simple gametophytic phase. A complete reference dataset which includes coverage of the target local flora is necessary for accurate identification. Three different Cyathea sp.pl. were investigated to test the utility of plastid DNA barcode regions rbcL with the intention of developing an identification system for native pteridophytes. In addition, the inter-specific and inter-generic variations among the Cyathea sp.pl. were also focused. BLAST analysis revealed the similar rbcL sequences related to C. nilgirensis Holttum, C. gigantea (Wallich ex Hook. f.) Holttum and C. crinita (Hook.) Copel and a sum of 143 sequences viz., Cyathea sp.pl. (121), Gymnosphaera sp.pl.(4), Sphaeropteris sp.pl. (1) and Alsophila sp.pl. (17). The sequences of 143 plants were retrieved from GenBank in FASTA format. The sequences were aligned using multiple sequence alignment tool MUSCLE. The inter-specific and inter-generic distance percentage were calculated using Maximum Likelihood, Minimum Evolution, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) and Neighbor-Joining method. The analyses were constructed using MEGA X software. The rbcL gene provided sequence variation with its strong resolving power. This study demonstrates the overall effectiveness of DNA barcodes for species identification of tree fern genus Cyathea in the pteridophyte flora of Southern Western Ghats.