REFMAKER: Make your own reference to target nuclear loci in low coverage genome skimming libraries. Phylogenomic application in Sapotaceae.

Genome skimming approach is widely used in plant systematics to infer phylogenies mostly from organelle genomes. However, organelles represent only 10 % of the produced libraries, and the low coverage associated with these libraries (<3X) prevents the capture of nuclear sequences, which are not always available in non-model organisms or limited to the ribosomal regions. We developed REFMAKER, a user-friendly pipeline, to create specific sets of nuclear loci that can be extracted directly from the genome skimming libraries. For this, a catalogue is built from the meta-assembly of each library contigs, and cleaned by selecting the nuclear regions and removing duplicates from clustering steps. Libraries are next mapped onto this catalogue and consensus sequences are generated to produce a ready-to-use phylogenetic matrix following different filtering parameters aiming at removing putative errors and paralogous sequences. REFMAKER allowed us to infer a well resolved phylogeny in Capurodendron (Sapotaceae) on 67 nuclear loci from low-coverage libraries (<1X). The resulting phylogeny is concomitant with one previously inferred on 638 nuclear genes from target enrichment libraries. While it remains preliminary because of this low sequencing depth, REFMAKER therefore opens perspectives in phylogenomics by allowing nuclear phylogeny reconstructions with genome skimming datasets.

Species Delimitation and Conservation in Taxonomically Challenging Lineages: The Case of Two Clades of Capurodendron (Sapotaceae) in Madagascar.

Capurodendron is the largest endemic genus of plants from Madagascar, with around 76% of its species threatened by deforestation and illegal logging. However, some species are not well circumscribed and many of them remain undescribed, impeding a confident evaluation of their conservation status. Here we focus on taxa delimitation and conservation of two species complexes within Capurodendron: the Arid and Western complexes, each containing undescribed morphologies as well as intermediate specimens alongside well-delimited taxa. To solve these taxonomic issues, we studied 381 specimens morphologically and selected 85 of them to obtain intergenic, intronic, and exonic protein-coding sequences of 794 nuclear genes and 227 microsatellite loci. These data were used to test species limits and putative hybrid patterns using different approaches such as phylogenies, PCA, structure analyses, heterozygosity level, FST, and ABBA-BABA tests. The potential distributions were furthermore estimated for each inferred species. The results show that the Capurodendron Western Complex contains three well-delimited species, C. oblongifolium, C. perrieri, and C. pervillei, the first two hybridizing sporadically with the last and producing morphologies similar to, but genetically distinct from C. pervillei. The Arid Complex shows a more intricate situation, as it contains three species morphologically well-delimited but genetically intermixed. Capurodendron mikeorum nom. prov. is shown to be an undescribed species with a restricted distribution, while C. androyense and C. mandrarense have wider and mostly sympatric distributions. Each of the latter two species contains two major genetic pools, one showing interspecific admixture in areas where both taxa coexist, and the other being less admixed and comprising allopatric populations having fewer contacts with the other species. Only two specimens out of 172 showed clear genetic and morphological signals of recent hybridization, while all the others were morphologically well-delimited, independent of their degree of genetic admixture. Hybridization between Capurodendron androyense and C. microphyllum, the sister species of the Arid Complex, was additionally detected in areas where both species coexist, producing intermediate morphologies. Among the two complexes, species are well-defined morphologically with the exception of seven specimens (1.8%) displaying intermediate patterns and genetic signals compatible with a F1 hybridization. A provisional conservation assessment for each species is provided.

Phylogeographic reconstructions can be biased by ancestral shared alleles: The case of the polymorphic lichen Bryoria fuscescens in Europe and North Africa.

Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them with 14 microsatellites. We studied population structure and genetic diversity at the local and continental scales, discussed the post-glacial phylogeography, and compared dispersal capacities of phenotypes with and without soralia. Our main hypothesis is that the estimated phylogeography, migration routes, and dispersal capacities may be strongly biased by ancestral shared alleles. Scandinavia is genetically the richest area, followed by the Iberian Peninsula, the Carpathians, and the Alps. Three gene pools were detected: two partially linked to phenotypic characteristics, and the third one genetically related to the American sister species B. pseudofuscescens. The comparison of one gene pool producing soredia and one not, suggested both as panmictic, with similar levels of isolation by distance (IBD). The migration routes were estimated to span from north to south, in disagreement with the assessed glacial refugia. The presence of ancestral shared alleles in distant populations can explain the similar IBD levels found in both gene pools while producing a false signal of panmixia, and also biasing the phylogeographic reconstruction. The incomplete lineage sorting recorded for DNA sequence loci also supports this hypothesis. Consequently, the high diversity in Scandinavia may rather come from recent immigration into northern populations than from an in situ diversification. Similar patterns of ancestral shared polymorphism may bias the phylogeographical reconstruction of other lichen species.

New genetic markers for Sapotaceae phylogenomics: More than 600 nuclear genes applicable from family to population levels.

Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from Capurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. Altogether, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.

SARS-CoV-2 en aguas residuales y superficiales: ¿cómo lidiar con el problema? / Sars-cov-2 in wastewater and surface water: how to deal with the problem?

Introducción: hoy la humanidad sufre uno de los peores episodios debido a la pandemia causada por el SARS-CoV-2. Su alta infectividad, rápida propagación y persistencia en ciertas superficies dificultan el combate de este virus. Su presencia en aguas residuales y posible transmisión fecal-oral podría ser una nueva amenaza para la salud pública. Objetivo: alertar a la comunidad científica internacional y a los gobiernos sobre la presencia de SARS-CoV-2 en las aguas residuales y sobre qué hacer para evitar su propagación por este medio. Métodos: se realizó una revisión de artículos referenciados en SCOPUS y Web of Science desde el año 2019 relacionados con la presencia del virus en aguas residuales y superficiales. Resultados y discusión: es necesario establecer sistemas de monitoreo, utilizar métodos analíticos sensibles y rápidos para la detección del virus en las aguas residuales y superficiales. Asimismo, implantar protocolos de inactivación del virus en las unidades de salud y en las plantas de tratamiento de aguas. Se recomiendan procesos con oxidantes químicos, radiación ultravioleta, fotocatálisis, foto-Fenton, ozono o filtración por membrana. Además, se debe alertar a la población sobre la importancia del lavado y de la desinfección de productos agrícolas, así como del cuidado en su manejo por parte de los trabajadores agrícolas

Introduction: Today, humanity suffers one of the worst episodes due to a pandemic caused by the SARS-CoV-2. Its high infectivity and rapid spread combined with its persistence on certain surfaces difficult to fight this virus. Its presence in wastewater and possible fecal-oral transmission could be a new public health threat. Objective: To alert the international scientific community and governments about the presence of SARS-CoV-2 in wastewater, and what to do to prevent its spread by this means. Methods: A review of articles referenced in SCOPUS and Web of Science since 2019 related to the presence of the virus in wastewater and surface water was performed. Results and discussion: It is necessary to establish monitoring systems with the use of sensitive and rapid analytical methods for the on-site detection of viruses in wastewaters and surface waters. It should be established virus inactivation protocols at the health units, and water treatment plants, where are recommended processes with chemical oxidants, ultraviolet radiation, photocatalysis, photo-Fenton, ozone, or membrane filtration. It is necessary to alert the population about the importance of washing and disinfecting agricultural products, mainly vegetables and fruits, as well as the care in its handling by agricultural workers

Evolutionary Trends in the Mitochondrial Genome of Archaeplastida: How Does the GC Bias Affect the Transition from Water to Land?

Among the most intriguing mysteries in the evolutionary biology of photosynthetic organisms are the genesis and consequences of the dramatic increase in the mitochondrial and nuclear genome sizes, together with the concomitant evolution of the three genetic compartments, particularly during the transition from water to land. To clarify the evolutionary trends in the mitochondrial genome of Archaeplastida, we analyzed the sequences from 37 complete genomes. Therefore, we utilized mitochondrial, plastidial and nuclear ribosomal DNA molecular markers on 100 species of Streptophyta for each subunit. Hierarchical models of sequence evolution were fitted to test the heterogeneity in the base composition. The best resulting phylogenies were used for reconstructing the ancestral Guanine-Cytosine (GC) content and equilibrium GC frequency (GC*) using non-homogeneous and non-stationary models fitted with a maximum likelihood approach. The mitochondrial genome length was strongly related to repetitive sequences across Archaeplastida evolution; however, the length seemed not to be linked to the other studied variables, as different lineages showed diverse evolutionary patterns. In contrast, Streptophyta exhibited a powerful positive relationship between the GC content, non-coding DNA, and repetitive sequences, while the evolution of Chlorophyta reflected a strong positive linear relationship between the genome length and the number of genes.

Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi.

We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.

Characterization of microsatellite loci in lichen-forming fungi of Bryoria section Implexae (Parmeliaceae).

PREMISE OF THE STUDY: The locally rare, haploid, lichen-forming fungi Bryoria capillaris, B. fuscescens, and B. implexa are associated with boreal forests and belong to Bryoria sect. Implexae. Recent phylogenetic studies consider them to be conspecific. Microsatellite loci were developed to study population structure in Bryoria sect. Implexae and its response to ecosystem disturbances. • METHODS AND RESULTS: We developed 18 polymorphic microsatellite markers using 454 pyrosequencing data assessed in 82 individuals. The number of alleles per locus ranged from two to 13 with an average of 4.6. Nei's unbiased gene diversity, averaged over loci, ranged from 0.38 to 0.52. The markers amplified with all three species, except for markers Bi05, Bi15, and Bi18. • CONCLUSIONS: The new markers will allow the study of population subdivision, levels of gene introgression, and levels of clonal spread of Bryoria sect. Implexae. They will also facilitate an understanding of the effects of forest disturbance on genetic diversity of these lichen species.

Iridoides y secoiridoides (1): clasificación, biosíntesis, importancia ecológica, estrategias evolutivas y modificaciones semisintéticas / Iridoids and secoiridoids (1): classification, biosynthesis, ecological interest, evolutionary strategies and semisynthetic modifications

Los iridoides y secoiridoides incluyen un grupo diverso de monoterpenos presentes en plantas e insectos, que poseen propiedades beneficiosas para la salud. La biosíntesis de estos compuestos transcurre en los distintos organismos mediante rutas similares, siendo su principal función la defensiva o, en el caso de insectos, también la de servir como feromonas sexuales. Estos compuestos han demostrado tener una amplia variedad de accciones biológicas y farmacológicas entre las que destaca la actividad hepatoprotectora, colerética, antimicrobiana, antiviral, antitumoral y antinflamatoria. Dada la relevancia de sus actividades farmacológicas, la obtención de nuevos derivados por semisíntesis resulta interesante. En este sentido, el empleo de enzimas en medios orgánicos se ha revelado como una metodología especialmente valiosa (AU)

Iridoids and secoiridoids include a broad group of monoterpenes present in plants and insects, which have beneficial health properties. The biosynthesis of these compounds takes place in the different organisms by similar pathways, being the defense its main role, or in the case of insects, used in addition as sex pheromones. These compounds have been shown to have a wide variety of biological and pharmacological activities, among them, hepatoprotective, choleretic, antimicrobial, antiviral, antitumor and anti-inflammatory. Given the relevance of their pharmacological activities, it is interesting to obtain new semisynthetic derivatives. In this regard, the use of enzymes in organic media has proved to be an especially valuable methodology (AU)

Regioselective enzymatic acylation and deacetylation of secoiridoid glucosides.

Candida antarctica lipase (CAL) catalyses the regioselective cinnamoylation and benzoylation of the aglycone moiety of 10-hydroxyoleoside dimethyl ester a secoiridoid glucoside. This enzyme catalyses as well regioselective deacetylation of the aglycone moiety of 10,2',3',4',6'-pentaacetoxyoleoside dimethyl ester. Further action of the enzyme results in deacetylation at C-6' and C-4' of the glucoside moiety.

Semisynthesis of justicidone and a 1,2-quinone lignan. Cytotoxic activity of some natural and synthetic lignans.

The dioxo-lignans of the arylnaphthalene-type named justicidone (2) and elenodione (3) were obtained from elenoside (1) through a short and efficient semisynthetic process. Justicidone (2), one of its synthetic precursors, 4-(benzo[d][1,3]dioxol-5-yl)-5,6,8-trimethoxy-3a,4-dihydronaphtho[2,3-c]furan-1(3H)-one (9), and the aglycone of elenoside (5) showed cytotoxic activity towards the HL-60 cell line (IC50 = 7.25 miroM, 5.41 microM and 2.06 miroM, respectively).

Lignanos (3): enterolignanos y actividad estrogénica / No disponible

Los lignanos ingeridos con los alimentos de origen vegetal pueden ser biotransformados por las bacterias del tracto intestinal de los mamíferos y posteriormente absorbidos, dando compuestos detectables en suero, saliva, orina, bilis y fluidos seminales. Estos compuestos son conocidos como enterolignanos o lignanos de mamíferos y, al igual que otros fitoestrógenos, imitan algunos de los efectos de los estrógenos. En la actualidad se cree que pueden ejercer un efecto quimioprotector contra cánceres hormonodependientes como son el cáncer de mama y de próstata

Lignans ingested with food of plant origin are biotransformated by intestinal bacteria of the mammals and then absorbed, giving compounds detectable in serum, saliva, urine, bile and seminal fluids. These compounds are known as enterolignans or mammalian lignans and, like other phytoestrogens, can have some estrogen-like effects. Nowadays it is believed that they could exert a chemoprotective effect against hormone-dependent cancer, such as breast and prostate cancer

Lignanos (2): actividad farmacológica / No disponible

En lo que a actividad farmacológica se refiere, los lignanos son principalmente conocidos por su actividad citotóxica, que es particularmente importante en el grupo de los ciclolignanos. No obstante, estos productos naturales también son inhibidores de la fosfodiesterasa del AMPc, confieren protección frente a hepatotoxinas, actúan sobre el tracto gastrointestinal, sistema cardiovascular y sistema nervioso central. También han demostrado tener actividad antiinflamatoria, antivírica y sobre el factor activador de plaquetas (PAF). Finalmente, tienen propiedades fitoestrogénicas, que serán tratadas en la tercera parte de esta serie de artículos sobre lignanos

Regarding the pharmacological activities, lignans are mainly known by their cytotoxic activity that is very important in cyclolignans. Nevertheless, these natural products are also inhibitors of AMPc phosphodiesterase, protectors against hepatotoxins and they act on the gastrointestinal tract, cardiovascular system and central nervous system. They have al so shown antiinflammatory and antiviral activities, as well as on the platelet activating factor (PAF). Finally, they also have phytoestrogenic properties, that will be described in the third part of these series of papers on lignans

First total synthesis of justicidone, a p-quinone-lignan derivative from Justicia hyssopifolia.

The first synthesis of justicidone (4-(1',3'-Benzodioxol-5'-yl)-6-methoxynaphtho[2,3-c]furan-1,5,8(3H)-trione) was carried out from piperonal, as a starting compound, through a lineal process using well known reactions.

Lignanos (1): estructura y funciones en las plantas / No disponible

Los lignanos constituyen un grupo de productos naturales ampliamente distribuido en el reino vegetal, cuyas unidades estructurales son biosintetizadas a través de la ruta del ácido sikímico. Pese a la elevada diversidad de estructuras que presentan, poseen la característica común de estar formados por dos unidades de fenilpropano enlazadas por el átomo central de sus cadenas laterales. Estos compuestos están presentes en desde briófitos y helechos hasta plantas superiores, donde desempeñan importantes funciones fisiológicas, principalmente de tipo defensivo

Lignans are a group of natural products widely distributed within the plant kingdom. The structural units of these compounds are biosynthesized via shikimic acid pathway. Although their structures can be very different, they have in common two units of phenylpropane bound by the central atom of their side chains. These compounds can be found in Bryophytes, ferns as well as in superior plants, in which they are responsible for important physiological functions, mostly of defensive kind

Regioselective enzymatic acetylation of the aglycone moiety of a secoiridoid glucoside. Two new secoiridoid glucoside acetates.

Candida antarctica lipase (CAL) catalyses the regioselective acetylation of the 10-hydroxyl group of 10-hydroxyoleoside dimethyl ester, a secoiridoid glucoside, using THF as a solvent and ethyl acetate or vinyl acetate as acetyl group suppliers. Two acetyl derivatives at 3'- and 6'-sites of the glucosidic ring of 10-acetoxyoleoside dimethylester, not previously described, were obtained by acetylation in the same conditions.

Justicidone, a novel p-quinone-lignan derivative from Justicia hyssopifolia.

An uncommon, previously unreported p-quinone-lignan compound called justicidone (4-(1,3-benzodioxol-5-yl)-6-methoxynaphtho[2,3-c]furan-1,5,8(3H)-trione) (2), along with the known savinin (1) were isolated from Justicia hyssopifolia (Acanthaceae). Their structures were determined by spectroscopic methods.