Integrative taxonomy and molecular phylogeny of genus Aplysina (Demospongiae: Verongida) from Mexican Pacific

José Antonio Cruz-Barraza (2012, [Artículo])

Integrative taxonomy provides a major approximation to species delimitation based on integration of different perspectives (e.g. morphology, biochemistry and DNA sequences). The aim of this study was to assess the relationships and boundaries among Eastern Pacific Aplysina species using morphological, biochemical and molecular data. For this, a collection of sponges of the genus Aplysina from the Mexican Pacific was studied on the basis of their morphological, chemical (chitin composition), and molecular markers (mitochondrial COI and nuclear ribosomal rDNA: ITS1-5.8-ITS2). Three morphological species were identified, two of which are new to science. A. clathrata sp. nov. is a yellow to yellow-reddish or -brownish sponge, characterized by external clathrate-like morphology; A. revillagigedi sp. nov. is a lemon yellow to green, cushion-shaped sometimes lobate sponge, characterized by conspicuous oscules, which are slightly elevated and usually linearly distributed on rims; and A. gerardogreeni a known species distributed along the Mexican Pacific coast. Chitin was identified as the main structural component within skeletons of the three species using FTIR, confirming that it is shared among Verongida sponges. Morphological differences were confirmed by DNA sequences from nuclear ITS1-5.8-ITS2. Mitochondrial COI sequences showed extremely low but diagnostic variability for Aplysina revillagigedi sp. nov., thus our results corroborate that COI has limited power for DNA-barcoding of sponges and should be complemented with other markers (e.g. rDNA). Phylogenetic analyses of Aplysina sequences from the Eastern Pacific and Caribbean, resolved two allopatric and reciprocally monophyletic groups for each region. Eastern Pacific species were grouped in general accordance with the taxonomic hypothesis based on morphological characters. An identification key of Eastern Pacific Aplysina species is presented. Our results constitute one of the first approximations to integrative taxonomy, phylogeny and evolutionary biogeography of Eastern Pacific marine sponges; an approach that will significantly contribute to our better understanding of their diversity and evolutionary history. © 2012 Cruz et al.

chitin, genomic DNA, mitochondrial DNA, molecular marker, ribosome DNA, allopatry, Aplysina clatharata, Aplysina gerardogreeni, Aplysina revillagigedi, article, DNA barcoding, DNA sequence, genetic polymorphism, genetic variability, infrared spectros CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Comprehending the evolution of gene editing platforms for crop trait improvement

deepmala sehgal Apekshita Singh SoomNath Raina (2022, [Artículo])

Cas9 Base Editing Prime Editing Epigenome Editing CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CRISPR ABIOTIC STRESS ARABIDOPSIS CROP IMPROVEMENT DNA ELECTROPORATION GENE EDITING RICE WHEAT

Molecular characterization of divergent isolates of Citrus bent leaf viroid (CBLVd) from citrus cultivars of Punjab, Pakistan

Abdelfattah DABABAT Yong Suk Chung (2023, [Artículo])

Biological Indexing Sequencing Analysis Citrus Orchards CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA PHYLOGENETIC ANALYSIS CITRUS RNA DNA

Influence of conservation agriculture-based production systems on bacterial diversity and soil quality in rice-wheat-greengram cropping system in eastern Indo-Gangetic Plains of India

Anup Das virender kumar Peter Craufurd Andrew Mcdonald Sonam Sherpa (2023, [Artículo])

Introduction: Conservation agriculture (CA) is gaining attention in the South Asia as an environmentally benign and sustainable food production system. The knowledge of the soil bacterial community composition along with other soil properties is essential for evaluating the CA-based management practices for achieving the soil environment sustainability and climate resilience in the rice-wheat-greengram system. The long-term effects of CA-based tillage-cum-crop establishment (TCE) methods on earthworm population, soil parameters as well as microbial diversity have not been well studied. Methods: Seven treatments (or scenarios) were laid down with the various tillage (wet, dry, or zero-tillage), establishment method (direct-or drill-seeding or transplantation) and residue management practices (mixed with the soil or kept on the soil surface). The soil samples were collected after 7 years of experimentation and analyzed for the soil quality and bacterial diversity to examine the effect of tillage-cum-crop establishment methods. Results and Discussion: Earthworm population (3.6 times), soil organic carbon (11.94%), macro (NPK) (14.50–23.57%) and micronutrients (Mn, and Cu) (13.25 and 29.57%) contents were appreciably higher under CA-based TCE methods than tillage-intensive farming practices. Significantly higher number of OTUs (1,192 ± 50) and Chao1 (1415.65 ± 14.34) values were observed in partial CA-based production system (p ≤ 0.05). Forty-two (42) bacterial phyla were identified across the scenarios, and Proteobacteria, Actinobacteria, and Firmicutes were the most dominant in all the scenarios. The CA-based scenarios harbor a high abundance of Proteobacteria (2–13%), whereas the conventional tillage-based scenarios were dominated by the bacterial phyla Acidobacteria and Chloroflexi and found statistically differed among the scenarios (p ≤ 0.05). Composition of the major phyla, i.e., Proteobacteria, Actinobacteria, and Firmicutes were associated differently with either CA or farmers-based tillage management practices. Overall, the present study indicates the importance of CA-based tillage-cum-crop establishment methods in shaping the bacterial diversity, earthworms population, soil organic carbon, and plant nutrient availability, which are crucial for sustainable agricultural production and resilience in agro-ecosystem.

Metagenomics Bacterial Diversity Rice-Wheat-Greengram CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CONSERVATION AGRICULTURE DNA SEQUENCES EARTHWORMS METAGENOMICS SOIL QUALITY AGROECOSYSTEMS

Molecular markers help with breeding for agronomic traits of spring wheat in Kazakhstan and Siberia

Alexey Morgounov Cecile Ben Susanne Dreisigacker Laurent Gentzbittel awais rasheed Timur Savin Sergey Shepelev Vladimir Shamanin (2024, [Artículo])

DNA Markers Grain Yield CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CEREALS DNA GENOTYPE ENVIRONMENT INTERACTION GRAIN YIELDS SPRING WHEAT

Corrigendum: The sole DNA ligase in Entamoeba histolytica is a high-fidelity DNA ligase involved in DNA damage repair

ELISA IRENE AZUARA LICEAGA Abigail Betanzos CESAR SALVADOR CARDONA FELIX ELIZABETH JACQUELINE CASTAÑEDA ORTIZ HELIOS CARDENAS HERNANDEZ ROSA ELENA CARDENAS GUERRA GUILLERMO PASTOR PALACIOS GUILLERMINA GARCIA RIVERA DAVID HERNANDEZ ALVAREZ CARLOS HUMBERTO TRASVIÑA ARENAS Corina Diaz Quezada Esther Orozco Luis Gabriel Brieba de Castro (2022, [Artículo])

"A Corrigendum on

The soleDNA ligase in Entamoeba histolytica is a high-fidelity DNA ligase involved in DNA damage repair

By Azuara-Liceaga E, Betanzos A, Cardona-Felix CS, Castañeda-Ortiz EJ, Cárdenas H, Cárdenas-Guerra RE, Pastor-Palacios G, García-Rivera G, Hernández-Álvarez D, Trasviña-Arenas CH, Diaz-Quezada C, Orozco E and Brieba LG (2018) Front. Cell. Infect. Microbiol. 8:214. doi: 10.3389/fcimb.2018.00214"

EhDNAlig Protozoan DNA insults Ligation Repairing 8-oxoG adduct NER and BER pathways BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA MICROBIOLOGÍA MICROBIOLOGÍA

Maize ZmBES1/BZR1-3 and-9 transcription factors negatively regulate drought tolerance in transgenic arabidopsis

Fuai Sun XUECAI ZHANG Haoqiang Yu (2022, [Artículo])

BZR1s CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA ARABIDOPSIS DNA BINDING PROTEINS PLANT PROTEIN TRANSCRIPTION FACTORS DROUGHT GENE EXPRESSION REGULATION GENETICS MAIZE METABOLISM TRANSGENIC PLANTS ABIOTIC STRESS

Editorial: Functional genomic approaches in molecular breeding for crop improvement

Philomin Juliana (2023, [Artículo])

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA DNA MARKER-ASSISTED SELECTION QUANTITATIVE TRAIT LOCI CROP IMPROVEMENT

A new species of Encelia (Compositae, Heliantheae, Enceliinae) from the southern Baja California Peninsula

JOSE LUIS LEON DE LA LUZ Isaac Lichter-Marck (2022, [Artículo])

"Se ilustra y describe a una nueva especie de Asteraceae, Encelia balandra. Se conoce solo de las laderas rocosas de los cerros próximos a puerto Balandra y Pichilingue, dentro de la bahía de La Paz, en Baja California Sur, México. Encontramos que esta nueva especie tiene ciertas semejanzas con otras de Encelia por su hábito semiarbustivo, las flores radiales neutras y cipselas comprimidas con ápice hendido. Confirmamos tal condición con datos de secuencia para las regiones ITS y ETS del genoma. También presentamos fotografías detalladas, un evaluación de conservación, y un clave dichotomus para los Encelia de Baja California sur. Se discute la semejanza con las especies peninsulares más cercanas de Encelia, se presenta una clave dicotómica para los taxonesaustrales de la península de Baja California, y finalmente se muestran imágenes detalladas de esta nueva especie."

"Here, we describe and illustrate Encelia balandra sp. nov., a new species of Compositae from the Baja Cal- ifornia Peninsula. It is rare and known only from the rocky hills around Puerto Balandra and Pichilingüe, inside the bay of La Paz, in the State of Baja California Sur, Mexico. We determine that this new species has affinities with Encelia, based on its suffruticose woody habit, neuter ray florets and compressed disc cypselae with a cleft apex. The taxonomic placement within Encelia is supported by nuclear ribosomal sequence data from two regions, ITS and ETS. We also present detailed photographs, a conservation assessment and a dichotomous key to the Encelia of the southern Baja California Peninsula. Finally, we discuss the uniqueness of Encelia balandra amongst peninsular Encelia and its potential significance for understanding the enigmatic biogeography of this ecologically important genus."

Asteraceae, Cape region, DNA barcoding, narrow endemism, synantherology, taxonomy Código de barras ADN, Micro-endemismo, Región de Los Cabos, Sinanterología, Taxonomía BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) ECOLOGÍA VEGETAL ECOLOGÍA VEGETAL

The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences

ARLETTE MARIMAR PACHECO SANDOVAL (2019, [Artículo])

Diet is a primary driver of the composition of gut microbiota and is considered one of the main routes of microbial colonization. Prey identification is fundamental for correlating the diet with the presence of particular microbial groups. The present study examined how diet influenced the composition and function of the gut microbiota of the Pacific harbor seal (Phoca vitulina richardii) in order to better understand the role of prey consumption in shaping its microbiota. This species is a good indicator of the quality of the local environment due to both its foraging and haul-out site fidelity. DNA was extracted from 20 fecal samples collected from five harbor seal colonies located in Baja California, Mexico. The V4 region of 16S rRNA gene was amplified and sequenced using the Illumina technology. Results showed that the gut microbiota of the harbor seals was dominated by the phyla Firmicutes (37%), Bacteroidetes (26%) and Fusobacteria (26%) and revealed significant differences in its composition among the colonies. Funtional analysis using the PICRUSt software suggests a high number of pathways involved in the basal metabolism, such as those for carbohydrates (22%) and amino acids (20%), and those related to the degradation of persistent environmental pollutants. In addition, a DNA metabarcoding analysis of the same samples, via the amplification and sequencing of the mtRNA 16S and rRNA 18S genes, was used to identify the prey consumed by harbor seals revealing the consumption of prey with mainly demersal habits. Functional redundancy in the seal gut microbiota was observed, irrespective of diet or location. Our results indicate that the frequency of occurrence of specific prey in the harbor seal diet plays an important role in shaping the composition of the gut microbiota of harbor seals by influencing the relative abundance of specific groups of gut microorganisms. A significant relationship was found among diet, gut microbiota composition and OTUs assigned to a particular metabolic pathway. © 2019 Pacheco-Sandoval et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

RNA 16S, RNA 18S, amino acid analysis, animal food, Article, bacterium colony, Bacteroidetes, basal metabolic rate, biodegradation, controlled study, DNA barcoding, feces analysis, Firmicutes, Fusobacteria, intestine flora, metabolism, Mexico, microb BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) BIOLOGÍA ANIMAL (ZOOLOGÍA)