Assembly and comparative analysis of the first complete mitochondrial genome of Acer truncatum Bunge: a woody oil-tree species producing nervonic acid

Background Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). The species is admired as a landscape plant with high developmental prospects and scientific research value. The A. truncatum chloroplast genome has recently been reported; however, the mitochondrial genome (mitogenome) is still unexplored. Results We characterized the A. truncatum mitogenome, which was assembled using reads from PacBio and Illumina sequencing platforms, performed a comparative analysis against different species of Acer. The circular mitogenome of A. truncatum has a length of 791,052 bp, with a base composition of 27.11% A, 27.21% T, 22.79% G, and 22.89% C. The A. truncatum mitogenome contains 62 genes, including 35 protein-coding genes, 23 tRNA genes and 4 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the A. truncatum mitogenome. To determine the evolutionary and taxonomic status of A. truncatum, we conducted a phylogenetic analysis based on the mitogenomes of A. truncatum and 25 other taxa. In addition, the gene migration from chloroplast and nuclear genomes to the mitogenome were analyzed. Finally, we developed a novel NAD1 intron indel marker for distinguishing several Acer species. Conclusions In this study, we assembled and annotated the mitogenome of A. truncatum, a woody oil-tree species producing nervonic acid. The results of our analyses provide comprehensive information on the A. truncatum mitogenome, which would facilitate evolutionary research and molecular barcoding in Acer.

Diversity of tropical macroalgae in the New Zealand marine aquarium trade

<p>Exotic species often slip through international borders undetected. Many perish but for some species introduction to a foreign land or sea brings release from natural enemies and a chance to establish a population. Increased global trade has increased the frequency of species introductions through stowaways and lapses in biosecurity. Once an invader is established there is the opportunity for explosive population growth at the detriment of native species and humans. The marine aquarium trade is a significant vector of species introductions, including algal introductions. The most publicized introduction from aquaria was the release of the green alga Caulerpa taxifolia from the Oceanographic Museum in Monaco. C. taxifolia introduction had large negative impacts on the invaded ecosystem. Molecular barcoding of tropical macroalgae entering the New Zealand aquarium trade was implemented using various molecular markers (cox1, cox3, rbcL tufA, LSU). Both NCBI Blast searches and maximum-likelihood phylogenies were used to identify the isolates. A total of 62 species of tropical macroalgae were identified from coral rocks imported into New Zealand, plus samples from reef hobbyists. Some species found are known as invasive elsewhere, for example, Caulerpa cylindracea, C. racemosa, C. sertularioides, Ulva ohnoi and Chaetomorpha vieillardii. All three major groups of algae were well represented in my findings with 26 species of red algae, 24 species of green algae and 12 species of brown algae. Temperature tolerance limits are the largest determinant in survival in algae, while salinity and pH are less significant. Temperature tolerance of tropical algae to the minimum Sea Surface Temperature in Auckland (14°C) and Wellington (11°C) was tested. My results show that one species Chaetomorpha vieillardii can survive at Auckland minimum winter sea surface temperatures. Our findings have important implications for New Zealand biosecurity, as not only are a large diversity of exotic macroalgae entering the New Zealand marine aquarium trade unregulated, but there is also the potential for them to survive in New Zealand waters. </p>

Diversity of tropical macroalgae in the New Zealand marine aquarium trade

<p>Exotic species often slip through international borders undetected. Many perish but for some species introduction to a foreign land or sea brings release from natural enemies and a chance to establish a population. Increased global trade has increased the frequency of species introductions through stowaways and lapses in biosecurity. Once an invader is established there is the opportunity for explosive population growth at the detriment of native species and humans. The marine aquarium trade is a significant vector of species introductions, including algal introductions. The most publicized introduction from aquaria was the release of the green alga Caulerpa taxifolia from the Oceanographic Museum in Monaco. C. taxifolia introduction had large negative impacts on the invaded ecosystem. Molecular barcoding of tropical macroalgae entering the New Zealand aquarium trade was implemented using various molecular markers (cox1, cox3, rbcL tufA, LSU). Both NCBI Blast searches and maximum-likelihood phylogenies were used to identify the isolates. A total of 62 species of tropical macroalgae were identified from coral rocks imported into New Zealand, plus samples from reef hobbyists. Some species found are known as invasive elsewhere, for example, Caulerpa cylindracea, C. racemosa, C. sertularioides, Ulva ohnoi and Chaetomorpha vieillardii. All three major groups of algae were well represented in my findings with 26 species of red algae, 24 species of green algae and 12 species of brown algae. Temperature tolerance limits are the largest determinant in survival in algae, while salinity and pH are less significant. Temperature tolerance of tropical algae to the minimum Sea Surface Temperature in Auckland (14°C) and Wellington (11°C) was tested. My results show that one species Chaetomorpha vieillardii can survive at Auckland minimum winter sea surface temperatures. Our findings have important implications for New Zealand biosecurity, as not only are a large diversity of exotic macroalgae entering the New Zealand marine aquarium trade unregulated, but there is also the potential for them to survive in New Zealand waters. </p>

Subclonal heterogeneity and evolution in breast cancer

Subclonal heterogeneity and evolution are characteristics of breast cancer that play a fundamental role in tumour development, progression and resistance to current therapies. In this review, we focus on the recent advances in understanding the epigenetic and transcriptomic changes that occur within breast cancer and their importance in terms of cancer development, progression and therapy resistance with a particular focus on alterations at the single-cell level. Furthermore, we highlight the utility of using single-cell tracing and molecular barcoding methodologies in preclinical models to assess disease evolution and response to therapy. We discuss how the integration of single-cell profiling from patient samples can be used in conjunction with results from preclinical models to untangle the complexities of this disease and identify biomarkers of disease progression, including measures of intra-tumour heterogeneity themselves, and how enhancing this understanding has the potential to uncover new targetable vulnerabilities in breast cancer.

Phylogenetic relationship of coffee leaf rust in the central jungle of Peru

Coffee leaf rust is the main disease that causes significant losses in Coffea arabica. In Peru, this disease caused epidemics between 2008 and 2013 with production losses of 35 %. The objective was to identify H. vastatrix using a morphological and molecular approach based on a phylogenetic species concept. Coffee leaf samples with symptoms of chlorotic lesions with the presence of yellow uredospores at different severity stages of different cultivars were collected from 11 locations in the departments of Pasco and Junin during 2017-2018. DNA was purified as proposed by Cristancho and coworkers. The major subunit of ribosomal DNA was amplified with universal primers LR0R and LR5, and sequenced by Macrogen and deposited in GenBank. Sequences from the genera Achrotelium, Blastospora, Cystopsora, Hemileia, and Mikronegeria were included for phylogenetic analysis. The results showed that the rust was distributed in coffee growing regions of Pasco: Villa Rica (Catimor, Caturra, and Gran Colombia); Oxapampa (Yellow Caturra), and Junín: San Luis de Shuaro (Catimor), Chanchamayo (Catimor), San Ramón (Catimor), Vitoc (Caturra), Pichanaki (Caturra), Río Negro (Caturra), Pangoa (Yellow Caturra, Gran Colombia, Limani). It was also grouped into a single clade with isolated H. vastatrix from Mexico and Australia, suggesting that they come from a common ancestor. This is the first confirmed report using molecular barcoding of H. vastatrix in the central jungle of Peru.

The first record of the invasive mosquito species Aedes albopictus in Chişinӑu, Republic of Moldova, 2020

Background In Europe, Aedes albopictus is an important vector of chikungunya virus and Dirofilaria nematodes and has been involved in local autochthonous circulation of dengue and Zika viruses. Due to the ongoing spread, targeted field surveillance at potential points of entry of invasive Aedes mosquitoes was initiated by the Republic of Moldova in 2020 as part of the transboundary “Invasive Aedes Mosquitoes COST-Action project.” Methods In 2020, ovitraps were positioned at each of three locations: the border crossing to Romania in Leuşeni (Hancesti region), Chişinӑu International Airport and Chişinӑu Botanical Garden. Results A total of 188 Aedes spp. eggs were collected at the Chişinӑu International Airport between August and September 2020. Twenty-three adults reared in the laboratory were identified morphologically as Ae. albopictus (Skuse, 1895), and 12 selected specimens were confirmed by molecular barcoding of the cytochrome oxidase subunit I gene region. In addition, one adult Ae. albopictus female at the same site was caught with a manual aspirator. Conclusions This is the first documented report of Ae. albopictus in the Republic of Moldova. The presence of immature and adult stages indicates the local reproduction of the species in the country. Therefore, it is crucial to extend and strengthen surveillance of the invasive Aedes mosquitoes to prevent Ae. albopictus and other exotic mosquito species from becoming established in the Republic of Moldova. Graphical abstract

Single-Cell Approaches to Deconvolute the Development of HSCs

Hematopoietic stem cells (HSCs) play a core role in blood development. The ability to efficiently produce HSCs from various pluripotent stem cell sources is the Holy Grail in the hematology field. However, in vitro or in vivo HSC production remains low, which may be attributable to the lack of understanding of hematopoiesis. Here, we review the recent progress in this area and introduce advanced technologies, such as single-cell RNA-seq, spatial transcriptomics, and molecular barcoding, which may help to acquire missing information about HSC generation. We finally discuss unresolved questions, the answers to which may be conducive to HSC production, providing a promising path toward HSC-based immunotherapies.

Molecular Barcoding of Melissa Officinalis L. (Badranjboye) in Iran and Identification of Adulteration in Its Medicinal Services

Medication plants are an important source of disease treatment in many countries. Today, quality control of the products of medicinal plants is a major task. Customer health may be at risk due to fraud and misconduct in the sales associates ' sales centres. Melissa officinalis (Badranjboye) is an important medicinal plant in Iran used for several diseases. In Iran, the species of Dracocephalum, Hymencrater, Nepeta and Stachys are mistakenly sold under the name of badranjboye in the selling centers of medicinal plants that have different pharmaceuticals properties. To avoid this mistake, we will follow the following goals in this research: 1 - Check the cheating and identification of badranjboye in the Iran market of medicinal plants and 2 - Provision of molecular barcode for the medicinal species of Melissa officinalis. We compared the plant samples sold (leaf) and reference species with morphological properties, odor, and molecular sequences and performed various molecular analyzes, such as sequencing, genetic distance determination, and phylogenetic tree construction. The reports indicated that internal transcribed spacer (ITS) and psbA–trnH intergenic spacer (psbA–trnH) sequences are an efficient molecular marker to produce barcode gap and differentiating Melissa officinalis from other species.

SunCatcher: Clonal Barcoding with qPCR-Based Detection Enables Functional Analysis of Live Cells and Generation of Custom Combinations of Cells for Research and Discovery

Over recent decades, cell lineage tracing, clonal analyses, molecular barcoding, and single cell-omic analysis methods have proven to be valuable tools for research and discovery. Here, we report a clonal molecular barcoding method, which we term SunCatcher, that enables longitudinal tracking and retrieval of live barcoded cells for further analysis. Briefly, single cell-derived clonal populations are generated from any complex cell population and each is infected with a unique, heritable molecular barcode. One can combine the barcoded clones to recreate the original parental cell population or generate custom pools of select clones, while also retaining stocks of each individual barcoded clone. We developed two different barcode deconvolution methods: a Next-Generation Sequencing method and a highly sensitive, accurate, rapid, and inexpensive quantitative PCR-based method for identifying and quantifying barcoded cells in vitro and in vivo. Because stocks of each individual clone are retained, one can analyze not only the positively selected clones but also the negatively selected clones result from any given experiment. We used SunCatcher to barcode individual clones from mouse and human breast cancer cell lines. Heterogeneous pools of barcoded cells reliably reproduced the original proliferation rates, tumor-forming capacity, and disease progression as the original parental cell lines. The SunCatcher PCR-based approach also proved highly effective for detecting and quantifying early spontaneous metastases from orthotopic sites that otherwise would not have been detected by conventional methods. We envision that SunCatcher can be applied to any cell-based studies and hope it proves a useful tool for the research community.