A new cyanobacterial genus Altericista and three species, A. lacusladogae sp. nov., A. violacea sp. nov., and A. variichlora sp. nov., described using a polyphasic approach.

Several strains of unicellular cyanobacteria from the culture collection of St. Petersburg State University, St. Petersburg, Russia (CALU), which were preliminary identified as Synechocystis sp., are reclassified in the new genus Altericista. Three new species are proposed, A. lacusladogae, A. violacea, and A. variichlora. The last species produces accessory chlorophylls d and f in cultures illuminated by far-red light, an attribute rarely observed in cyanobacteria, especially in unicellular strains. This genus is morphologically similar to Synechocysis having coccoid cells that divide in two successive planes at right angles, containing no sheath or capsule, and having the lamellar system represented by peripheral concentric thylakoids. Altericista shows ecological, biochemical, and physiological characters unlike those in Synechocystis and has the distinguishing phenotypic characters as follows: freshwater, non-halotolerant ecotype; palmitate and α-linoleate as major fatty acids; and the ability to photoacclimate, including several types of complementary chromatic adaptation. Genetic differences from Synechocystis sp. include 16S rRNA, rpoC1, and rbcL gene sequences, as well as sequence and folding of 16S-23S ITS.

DNA Sequencing of Type Material Reveals Pneophyllum marlothii comb. nov. from South Africa and P. discoideum comb. nov. (Chamberlainoideae, Corallinales, Rhodophyta) from Argentina.

A partial rbcL sequence from the type material of Spongites discoideus from southern Argentina showed that it was distinct from rbcL sequences of South African specimens to which that name had been applied based on morpho-anatomy. A partial rbcL sequence from an original syntype specimen, herein designated the lectotype, of Lithophyllum marlothii, type locality Camps Bay, Western Cape Province, South Africa, was identical to rbcL sequences of South African field-collected specimens assigned to S. discoideus. Based on phylogenetic analyses of rbcL and/or psbA sequences, both of these species belong in Pneophyllum and are transferred there as P. discoideum comb. nov. and P. marlothii comb. nov. The two species exhibit a distinct type of development where thick, secondary, monomerous disks are produced from thin, primary, dimerous crusts. Whether this type of development represents an example of convergent evolution or is characteristic of a clade of species within Pneophyllum remains to be resolved.

An rbcL mRNA-binding protein is associated with C3 to C4 evolution and light-induced production of Rubisco in Flaveria.

Nuclear-encoded RLSB protein binds chloroplastic rbcL mRNA encoding the Rubisco large subunit. RLSB is highly conserved across all groups of land plants and is associated with positive post-transcriptional regulation of rbcL expression. In C3 leaves, RLSB and Rubisco occur in all chlorenchyma cell chloroplasts, while in C4 leaves these accumulate only within bundle sheath (BS) chloroplasts. RLSB's role in rbcL expression makes modification of its localization a likely prerequisite for the evolutionary restriction of Rubisco to BS cells. Taking advantage of evolutionarily conserved RLSB orthologs in several C3, C3-C4, C4-like, and C4 photosynthetic types within the genus Flaveria, we show that low level RLSB sequence divergence and modification to BS specificity coincided with ontogeny of Rubisco specificity and Kranz anatomy during C3 to C4 evolution. In both C3 and C4 species, Rubisco production reflected RLSB production in all cell types, tissues, and conditions examined. Co-localization occurred only in photosynthetic tissues, and both proteins were co-ordinately induced by light at post-transcriptional levels. RLSB is currently the only mRNA-binding protein to be associated with rbcL gene regulation in any plant, with variations in sequence and acquisition of cell type specificity reflecting the progression of C4 evolution within the genus Flaveria.

Seasonal recruitment and survival strategies of Palisada cervicornis comb. nov. (Ceramiales, Rhodophyta) in coral reefs.

As marine tropical ecosystems deteriorate and lose biodiversity, their communities are shifting to being dominated by a few species, altering ecosystem's functioning and services. Macroalgae are becoming dominant on coral reefs, and are frequently observed outcompeting corals. Turf algal assemblages are the base of energy flow in these systems and one of the most abundant types of macroalgae on coral reefs, but little is known about their biology and diversity. Through molecular and morphological analyses, we identified the turf-forming species Laurencia cervicornis, and by studying seasonal recruitment and the impact of herbivorous fishes on its abundance, we describe its survival strategy. The molecular analyses used a total of 45 rbcL gene sequences including eight current genera within the Laurencia complex and two new sequences of L. cervicornis and strongly support the new combination of Palisada cervicornis comb. nov. In addition, a detailed morphological characterization including the description of reproductive structures is provided. Palisada cervicornis was seen recruiting in all seasons but was typically in low abundance. Specimens grown on tiles in fish exclosure cages were devoured in less than 4 h when offered to fishes. Even though many species of the Laurencia complex have chemicals that deter herbivory, species within the genus Palisada lack feeding deterrents and thus are highly palatable. We suggest that P. cervicornis is a palatable species that seems to survive in the community by obtaining a size-refuge from herbivory within turf communities.

Evolution of RLSB, a nuclear-encoded S1 domain RNA binding protein associated with post-transcriptional regulation of plastid-encoded rbcL mRNA in vascular plants.

BACKGROUND: RLSB, an S-1 domain RNA binding protein of Arabidopsis, selectively binds rbcL mRNA and co-localizes with Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) within chloroplasts of C3 and C4 plants. Previous studies using both Arabidopsis (C3) and maize (C4) suggest RLSB homologs are post-transcriptional regulators of plastid-encoded rbcL mRNA. While RLSB accumulates in all Arabidopsis leaf chlorenchyma cells, in C4 leaves RLSB-like proteins accumulate only within Rubisco-containing bundle sheath chloroplasts of Kranz-type species, and only within central compartment chloroplasts in the single cell C4 plant Bienertia. Our recent evidence implicates this mRNA binding protein as a primary determinant of rbcL expression, cellular localization/compartmentalization, and photosynthetic function in all multicellular green plants. This study addresses the hypothesis that RLSB is a highly conserved Rubisco regulatory factor that occurs in the chloroplasts all higher plants. RESULTS: Phylogenetic analysis has identified RLSB orthologs and paralogs in all major plant groups, from ancient liverworts to recent angiosperms. RLSB homologs were also identified in algae of the division Charophyta, a lineage closely related to land plants. RLSB-like sequences were not identified in any other algae, suggesting that it may be specific to the evolutionary line leading to land plants. The RLSB family occurs in single copy across most angiosperms, although a few species with two copies were identified, seemingly randomly distributed throughout the various taxa, although perhaps correlating in some cases with known ancient whole genome duplications. Monocots of the order Poales (Poaceae and Cyperaceae) were found to contain two copies, designated here as RLSB-a and RLSB-b, with only RLSB-a implicated in the regulation of rbcL across the maize developmental gradient. Analysis of microsynteny in angiosperms revealed high levels of conservation across eudicot species and for both paralogs in grasses, highlighting the possible importance of maintaining this gene and its surrounding genomic regions. CONCLUSIONS: Findings presented here indicate that the RLSB family originated as a unique gene in land plant evolution, perhaps in the common ancestor of charophytes and higher plants. Purifying selection has maintained this as a highly conserved single- or two-copy gene across most extant species, with several conserved gene duplications. Together with previous findings, this study suggests that RLSB has been sustained as an important regulatory protein throughout the course of land plant evolution. While only RLSB-a has been directly implicated in rbcL regulation in maize, RLSB-b could have an overlapping function in the co-regulation of rbcL, or may have diverged as a regulator of one or more other plastid-encoded mRNAs. This analysis confirms that RLSB is an important and unique photosynthetic regulatory protein that has been continuously expressed in land plants as they emerged and diversified from their ancient common ancestor.

A segment of rbcL gene as a potential tool for forensic discrimination of Cannabis sativa seized at Rio de Janeiro, Brazil.

Cannabis sativa, known by the common name marijuana, is the psychoactive drug most widely distributed in the world. Identification of Cannabis cultivars may be useful for association to illegal crops, which may reveal trafficking routes and related criminal groups. This study provides evidence for the performance of a segment of the rbcL gene, through genetic signature, as a tool for identification for C. sativa samples apprehended by the Rio de Janeiro Police, Brazil. The PCR amplified and further sequenced the fragment of approximately 561 bp of 24 samples of C. sativa rbcL gene and showed the same nucleotide sequences, suggesting a possible genetic similarity or identical varieties. Comparing with other Cannabaceae family sequences, we have found 99% of similarity between the Rio de Janeiro sequence and three other C. sativa rbcL genes. These findings suggest that the fragment utilized at this study is efficient in identifying C. sativa samples, therefore, useful in genetic discrimination of samples seized in forensic cases.

First record of a large-scale bloom-causing species Nannochloropsis granulata (Monodopsidaceae, Eustigmatophyceae) in China Sea waters.

Nannochloropsis is an ubiquitous genus, found in diverse aquatic environments including open ocean as well as fresh and brackish water. Recently, large-scale blooms occurred frequently along eutrophic coastal zone from the Bohai Sea to the northern Yellow Sea in China. The cell density reached 10(9) to 10(10)cells per liter during a bloom near Qinhuangdao, Hebei Province. The bloom forming species, a yellow-green microalgae was successfully isolated and cultivated in the laboratory. Microscopic observation indicated that the cells contained simple morphological characteristics with a diameter about 2 µm. Pigment analyses confirmed that the pigment composition of the newly isolated strain BDH02 was similar to that of Nannochloropsis granulata. Phylogenetic analyses of 18S rRNA gene, ITS, and rbcL gene indicated that the strain was closely related to N. granulata. This is the first record of a bloom caused by N. granulata in China.

Variation of phytoplankton community structure from the Pearl River estuary to South China Sea.

The Pearl River is located in the northern part of South China Sea. The environment of the Pearl River estuary (PRE) is significantly impacted by nutrients from anthropogenic activities. Along the anthropogenic pollution gradient from the PRE to South China Sea, the phylogenetic diversity and biomass of phytoplankton was examined in relation to physic-chemical variables. The richness of rbcL gene was higher in the open sea than the estuary, while the concentration of chlorophyll a (Chl a) was higher in the estuary than in the open sea. The cluster analysis of the sequences data resulted in seven phytoplankton community types and the dominant species of phytoplankton changed from Cryptophytes and Diatoms to Prymnesiophytes and Diatoms along the gradient. The community structure of phytoplankton was shaped by nutrients and salinity. The phytoplankton biomass was significantly positively affected by phosphorus, nitrite and ammonium (P < 0.01) but negatively by salinity (P < 0.05); the phytoplankton diversity was highly positively affected by salinity (P < 0.05) but negatively by silicate and nitrate (P < 0.01; P < 0.05, respectively). Anthropogenic activities played a critical role in the phytoplankton distribution and biomass of the study area. Further research is necessary to reveal the influence mechanism of environmental factors on the phytoplankton.

Spatial variation of phytoplankton community structure in Daya Bay, China.

Daya Bay is one of the largest and most important gulfs in the southern coast of China, in the northern part of the South China Sea. The phylogenetic diversity and spatial distribution of phytoplankton from the Daya Bay surface water and the relationship with the in situ water environment were investigated by the clone library of the large subunit of ribulose-1, 5-bisphosphate carboxylase (rbcL) gene. The dominant species of phytoplankton were diatoms and eustigmatophytes, which accounted for 81.9 % of all the clones of the rbcL genes. Prymnesiophytes were widely spread and wide varieties lived in Daya Bay, whereas the quantity was limited. The community structure of phytoplankton was shaped by pH and salinity and the concentration of silicate, phosphorus and nitrite. The phytoplankton biomass was significantly positively affected by phosphorus and nitrite but negatively by salinity and pH. Therefore, the phytoplankton distribution and biomass from Daya Bay were doubly affected by anthropic activities and natural factors.

Intra-specific genetic diversity, phylogenetic analysis and ecological preferences of Pentaclethra macrophylla Benth., across Nigeria based on rbcL dataset.

Pentaclethra macrophylla Benth., commonly referred to as "African oil bean"; is a leguminous tree species that belongs to the subfamily Caesalpinioideae of the family Fabaceae and it is native to the dry tropical rainforest forest of West to Central Africa. It is widely used as a resource for food, medicine, firewood, construction, arts, and craft and particularly of socio-economic and cultural value to indigenous people of southern, Nigeria. Despite its significant potential, it is considered underutilized in the aspect of research attention and global trade. The dataset highlights the distribution pattern, genetic diversity, phylogenetic relationship, and ecological preferences of P. macrophylla accessions collected across the various agro-ecological zones in Nigeria where it is distributed, using the Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase (rbcL) gene.

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.

rbcL gene dataset on intra-specific genetic variability and phylogenetic relationship of Crassocephalum crepidioides (Benth) S. Moore. (Asteraceae) in Nigeria.

Crassocephalum crepidioides (Benth) S. Moore (Asteraceae) commonly called "thickhead" is underutilised, indigenous to the rainforest of West and Central Africa but has also been introduced and naturalised throughout tropical and sub-tropical Asia, Australia, Tonga and Samoa. The species is an important medicinal and leafy vegetable endemic to the South-western region of Nigeria. Its cultivation, utilisation and local knowledge base could be stronger than the mainstream vegetables. Genetic diversity is uninvestigated for breeding and conservation purposes. The dataset consists of partial rbcL gene sequences, amino acid profiles and nucleotide compositions for 22 accessions of C. crepidioides. The dataset provides information on the species distribution (Nigeria), genetic diversity and evolution. The sequence information is integral for developing specific DNA markers for breeding and conservation purposes.

Spatial and temporal changes in the assembly mechanism and co-occurrence network of the chromophytic phytoplankton communities in coastal ecosystems under anthropogenic influences.

As a typical semiclosed coastal sea area in China, the ecological environment of Bohai Bay has been significantly disturbed by human activities. As primary producers, the chromophytic phytoplankton are the basis of ecosystems, especially in coastal ecosystems, and changes in the chromophytic phytoplankton community can affect the stability of the entire ecosystem. In this study, we investigated the effects of the human activity-induced spatial and temporal environmental heterogeneity on the community composition, diversity, assembly mechanisms, and co-occurrence networks of chromophytic phytoplankton in Bohai Bay during the wet season and the dry season. The results showed that in both seasons, there was obvious environmental heterogeneity between the nearshore area and the offshore area, and the nearshore areas were more affected by human disturbance. Although higher diversity was supported by the abundance of nutrients in nearshore areas, co-occurrence network analysis revealed that the chromophytic phytoplankton were less closely connected to each other in nearshore areas than in offshore areas due to chemical oxygen demand (COD), eutrophication index (EI), and dissolved inorganic nitrogen (DIN). The nearshore network was less stable than the offshore co-occurrence network in both seasons, which was related to the concentration of dissolved oxygen and COD. Both stochastic and deterministic processes dominated the assembly of the chromophytic phytoplankton communities, with different importance rankings of stochastic and deterministic processes in the nearshore and offshore areas. Drift dominated the assembly of the communities in nearshore areas, while variable selection dominated the assembly of the communities in offshore areas. DIN, EI, and COD, rather than geographic distance, were the main environmental factors affecting the phylogenetic turnover of the chromophytic phytoplankton. Our study showed that environmental heterogeneity caused by human disturbance had a greater impact on the chromophytic phytoplankton communities in Bohai Bay than natural factors such as temperature and salinity.

rbcL-based dataset on intra-specific diversity and conservation of Adansonia digitata L. (Malvaceae) in the savannah belt of Nigeria.

The African baobab species belong to the family Malvaceae and the genus Adansonia. The disjointed tree thrives in arid or semi-arid regions, is native to the thorn woodlands of Africa, along tracks, and is associated with human-populated forest areas. It is considered indigenous to Central and West Africa and has been introduced to the Arabian Peninsula, South-East Asia, the Indian sub-continent, and the Caribbeans. Adansonia digitata is a multifunctional tree with a long lifespan of over 1000 years old. The leaves, roots, flowers, fruit pulp, seeds and barks are used for food, medicine, or other ethnic-practices. The utilisation level and distribution are significantly undermined by climate change and poor use practices. The data set offers insight into the distribution pattern and genetic diversity of Adansonia digitata across the savannah belt of Nigeria using the rbcL gene.

Luticola tenera sp. nov. (Diadesmidaceae, Naviculales)-A New Diatom from the Soil of the State Nature Reserve "Bastak" (Jewish Autonomous Region, Russia).

Diatoms inhabit different aquatic and non-aquatic environments, including soils. The naviculoid genus Luticola is widespread in various habitats and accounts for 264 species that are only based on morphological and morphometric characteristics. These parameters can greatly vary during the life cycle, making the species very similar to each other and complicating their unambiguous identification. During a study on soil algal diversity in the Russian Far East (Jewish Autonomous Region), we isolated a strain of naviculoid diatom and examined it using an integrative approach (phylogenetic, morphological, ultrastructural data, and life cycle). Phylogenetic analyses, based on chloroplast rbcL gene data, showed affinity of the new strain with the genus Luticola. Our alga shares morphological features typical of the genus members but differs from them by having valves with a larger width and hook-shaped external proximal raphe ends deflected to the side opposite the stigma. It was revealed that the strain reproduces via two types of sexual reproduction-isogamy and cis-anisogamy. Based on these phenotypic traits, we described the new isolate as Luticola tenera sp. nov.

Dataset on estimate of intra-specific genetic variability of African yam bean (Sphenostylis stenocarpa (Hochst. ex A. Rich.) Harms.) based on rbcL gene marker.

African yam bean (Sphenostylis stenocarpa (Hochst. ex A. Rich.) Harms.) (Fabaceae) is a versatile crop of nutritional, nutraceutical, and pharmacological value widely grown for its edible seeds and underground tubers. Its high-quality protein, rich mineral elements, and low cholesterol make it a suitable source of food for age groups. However, the crop is still under-exploited and constrained by factors such as intra-specific incompatibility, low yields, indeterminate growth pattern and long gestation period, hard-to-cook (HTC) seeds, and the presence of antinutritional factors (ANFs). To efficiently utilize its genetic resources for improvement and utilization, it is necessary to understand the crop's sequence information and select promising accessions for molecular hybridization trials and conservation purposes. A total of 24 accessions of AYB were collected from the Genetic Resources center of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria, and subjected to PCR amplification and Sanger sequencing. The dataset determines genetic relatedness among the twenty-four accessions of AYB. The data consist of partial rbcL gene sequences (24), estimates of intra-specific genetic diversity, the maximum likelihood of transition/transversion bias, and evolutionary relationships based on the UPMGA clustering method. The data identified 13 variables (segregating sites) as SNPs, 5 haplotypes, and codon usage of the species that can be explored further to advance the genetic utilization of AYB.

Dataset on rbcL-based intra-specific diversity of Gongronema latifolium Benth: (Apocynaceae) in South-East Nigeria.

Gongronema latifolium (Apocynaceae) is a versatile plant of nutritional and medicinal value and is widely distributed and endemic to the South-Eastern region of Nigeria. The plant is relatively wild and its natural habitat is threatened by deforestation, excessive exploitation and constant expansion of the urban areas into its endemic space. Hence, there is a need to understand its genetic diversity for breeding and conservation. The data consist of fourteen partial rbcL gene sequences, nucleotide compositions and amino acid profiles of G. latifolium. The data set provides insight on the species genetic diversity and evolution that is important for scientist and breeders alike as well as for conservation efforts of the species.

rbcL gene in global molecular data repository.

The ribulose-bisphosphate carboxylase (rbcL) gene sequence data in the molecular data repository has been increasing significantly, over the years with contributions from different parts of the world. The abundance of the gene has enhanced its applications in several ways. Bulk records were obtained from National Center for Biotechnology Information (NCBI) GenBank database using the entrez efetch utility as implemented in the Biopython package version 1.77. Records corresponding to the following keywords "rbcL AND plants [filter] AND biomol_genomic [PROP] AND is _nuccore [filter]" were created. Generated records were cleaned and then further analysed using the code file in the supplementary materials. Country information was obtained by searching reference information for matches to countries present in the pycountry package. Where no match was found, null was returned. This data article contains information about the plant family and species whose rbcL gene sequence has been deposited on the NCBI and regions of the world that has contributed to the rbcL repository growth. This data can be used to analyse the intra and inter family relatedness of plant and compare with existing relationships the molecular characterization of plants, evolutionary relationship studies, inferring biogeography origin of plant.

Ecological stoichiometry influences phytoplankton alpha and beta diversity rather than the community stability in subtropical bay.

Numerous studies have shown that changes in environmental factors can significantly impact and shift the structure of phytoplankton communities in marine ecosystems. However, little is known about the association between the ecological stoichiometry of seawater nutrients and phytoplankton community diversity and stability in subtropical bays. Therefore, we investigated the relationship between the phytoplankton community assemblage and seasonal variation in the Beibu Gulf, South China Sea. In this study, we found that the abundance of Bacillariophyceae in spring was relatively greater than in other seasons, whereas the abundance of Coscinodiscophyceae was relatively low in spring and winter but greatly increased in summer and autumn. Values of the alpha diversity indices gradually increased from spring to winter, revealing that seasonal variations shifted the phytoplankton community structure. The regression lines between the average variation degree and the Shannon index and Bray-Curtis dissimilarity values showed significantly positive correlations, indicating that high diversity was beneficial to maintaining community stability. In addition, the ecological stoichiometry of nutrients exhibited significantly positive associations with Shannon index and Bray-Curtis dissimilarity, demonstrating that ecological stoichiometry can significantly influence the alpha and beta diversity of phytoplankton communities. The C:N:P ratio was not statistically significantly correlated with average variation degree, suggesting that ecological stoichiometry rarely impacted the community stability. Temperature, nitrate, dissolved inorganic phosphorous, and total dissolved phosphorus were the main drivers of the phytoplankton community assemblage. The results of this study provide new perspectives about what influences phytoplankton community structure and the association between ecological stoichiometry, community diversity, and stability in response to environmental changes.

Deciphering the diversity and distribution of chromophytic phytoplankton in the Bohai Sea and the Yellow Sea via RuBisCO genes (rbcL).

Present study investigated composition and distribution of chromophytic phytoplankton in the Bohai Sea (BS) and the Yellow Sea (YS) by using rbcL genes. Bacillariophyceae, Haptophyceae and Pelagophyceae were the most abundant phytoplankton groups. Distinct phytoplankton communities were observed in the BS and the YS: offshore stations were dominated by bloom forming genera Thalassiosira and Skeletonema, while brown tide-forming species including Chrysochromulina spp. and Aureococcus anophagefferens were commonly found in the nearshore areas. Redundancy analysis showed that phosphate, temperature and silicic acid play key roles in structuring chromophytic phytoplankton, such as phytoplankton at nearshore stations were affected by nutrient runoff from adjacent rivers (Yellow River). Anthropogenic activities in the Bohai Sea and seasonal circulation of ocean currents may also contribute to shaping chromophytic phytoplankton communities. This study provides data support and foundational observations of chromophytic phytoplankton in the BS and the YS, and their responses to environmental gradients and human activities.