Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

Spurthi Nayak Polavarapu Kavi Kishor Rajeev Varshney (2010, [Artículo])

Simple Sequence Repeats Mapping Population Translational Studies CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA ANCHORS CHICKPEAS CICER ARIETINUM GENETIC MAPS GENETIC MARKERS MEDICAGO MEDICAGO TRUNCATULA MICROSATELLITES SINGLE NUCLEOTIDE POLYMORPHISM GENES

Taxonomic versus ecological prey traits among arthropodophagous bats: implications for surveying trophic partitioning patterns

CINTYA ARACELI SEGURA TRUJILLO SERGIO TICUL ALVAREZ CASTAÑEDA SUSETTE SAMI CASTAÑEDA RICO Jesus Maldonado (2022, [Artículo])

"Species can coexist spatially and temporally by partitioning the niche space and forming complex assemblages made up of different species that share the prey resource. Chiroptera is the second most species-rich mammalian order and about 75% of bat species feed on arthropods, which makes these bats a good model group for studying complex trophic interactions. Next-generation parallel sequencing techniques allow a detailed analysis of arthropod resource partitioning patterns in bats. However, previous studies have not reached a consensus on the concordance between diet composition, habitat use, and segregation of trophic resources in bats. We analyzed diet composition in terms of taxonomy of the insect prey, and the prey characteristics. Feces of 16 bat species were examined in the Mexican Neotropics. We carried out a SIMPER (similarity percentage) test, nonmetric multidimensional scaling, and principal component analyses to identify general segregation patterns of trophic resources in relation to the habitat-use guild of bats and computed Pianka’s niche overlap index between species and Levin’s index to estimate the niche width of each species. Bats from the same locality tend to partition their diet, with a niche overlap ranging between 0.5 and 0.8. The highest values were found between species with different foraging behaviors. We suggest that future bat diet studies should incorporate the ecological and taxonomic information of arthropod prey to better understand the trophic interactions with bats."

"Aproximadamente el 75% de las especies de murciélagos se alimentan de artrópodos, algunas de estas especies pueden coexistir espacial y temporalmente al particionar el espacio del nicho. Los murciélagos forman ensamblajes complejos compuestos por diferentes especies que comparten su recurso trófico. Por tanto, los murciélagos pueden utilizarse como grupo modelo para estudiar interacciones tróficas complejas. Las técnicas de secuenciación masiva paralela del ADN permiten un análisis detallado de sus patrones de partición de recursos tróficos. Sin embargo, los estudios no han llegado a un consenso sobre la concordancia entre la composición de la dieta, el uso del hábitat y la partición de los recursos tróficos en los murciélagos. Analizamos la composición de la dieta en términos de taxonomía de los artrópodos presa y sus características ecológicas. Examinamos las heces de 16 especies de murciélagos a lo largo del Neotrópico Mexicano. Se utilizaron análisis de similitud porcentual (SIMPER), escalamiento multidimensional no métrico y análisis de componentes principales para identificar patrones generales de partición de recursos tróficos en relación con el gremio de uso de hábitat de los murciélagos. Calculamos el índice de superposición de nicho de Pianka entre especies y el índice de Levin para estimar la amplitud del nicho de cada especie. Encontramos que los murciélagos de la misma localidad tienden a diferenciar su dieta, con una superposición de nicho que varía entre 0.5 y 0.8. Los valores más altos se encontraron entre especies con diferentes hábitos de alimentación. Sugerimos que, en el futuro, los estudios de dieta de murciélagos consideren las características ecológicas de sus presas y utilicen la información taxonómica como clave para recuperar información sobre la biología de las presas y comprender la ecología de estas interacciones tróficas."

arthropods, bats, foraging ecology, next-generation sequencing, prey traits, resource partitioning, trophic ecology artrópodos, ecología trófca, murciélagos, partición de recursos, rasgos de presa, secuenciación de nueva generación BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) ECOLOGÍA ANIMAL ECOLOGÍA ANIMAL

Whole-genome comparison between reference sequences and oyster Vibrio vulnificus C-genotype strains

CARLOS ABRAHAM GUERRERO RUIZ (2019, [Artículo])

Whole-genome sequences of Vibrio vulnificus clinical genotype (C-genotype) from the CICESE Culture Collection, isolated from oysters, were compared with reference sequences of CMCP6 and YJ016 V. vulnificus C-genotype strains of clinical origin. The RAST web server estimated the whole genome to be ~4.8 Mb in CICESE strain 316 and ~4.7 Mb in CICESE strain 325. No plasmids were detected in the CICESE strains. Based on a phylogenetic tree that was constructed with the whole-genome results, we observed high similarity between the reference sequences and oyster C-genotype isolates and a sharp contrast with environmental genotype (E-genotype) reference sequences, indicating that the differences between the C- and E-genotypes do not necessarily correspond to their isolation origin. The CICESE strains share 3488 genes (63.2%) with the YJ016 strain and 3500 genes (63.9%) with the CMCP6 strain. A total of 237 pathogenicity associated genes were selected from reference clinical strains, where—92 genes were from CMCP6, 126 genes from YJ016, and 19 from MO6-24/ O; the presence or absence of these genes was recorded for the CICESE strains. Of the 92 genes that were selected for CMCP6, 67 were present in both CICESE strains, as were as 86 of the 126 YJ016 genes and 13 of the 19 MO6-24/O genes. The detection of elements that are related to virulence in CICESE strains—such as the RTX gene cluster, vvhA and vvpE, the type IV pili cluster, the XII genomic island, and the viuB genes, suggests that environmental isolates with the C-genotype, have significant potential for infection. © 2019 Guerrero 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.

Article, bacterial gene, bacterial strain, bacterial virulence, comparative study, controlled study, gene cluster, gene identification, genomic island, genotype, nonhuman, phylogenetic tree, sequence analysis, strain identification, Vibrio vulnificus BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA

Genetic analysis of Vibrio parahaemolyticus O3:K6 strains that have been isolated in Mexico since 1998

CARLOS ABRAHAM GUERRERO RUIZ (2017, [Artículo])

Vibrio parahaemolyticus is an important human pathogen that has been isolated worldwide from clinical cases, most of which have been associated with seafood consumption. Environmental and clinical toxigenic strains of V. parahaemolyticus that were isolated in Mexico from 1998 to 2012, including those from the only outbreak that has been reported in this country, were characterized genetically to assess the presence of the O3:K6 pandemic clone, and their genetic relationship to strains that are related to the pandemic clonal complex (CC3). Pathogenic tdh+ and tdh+/trh+ strains were analyzed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Also, the entire genome of a Mexican O3:K6 strain was sequenced. Most of the strains were tdh/ORF8-positive and corresponded to the O3:K6 serotype. By PFGE and MLST, there was very close genetic relationship between ORF8/O3:K6 strains, and very high genetic diversities from non-pandemic strains. The genetic relationship is very close among O3:K6 strains that were isolated in Mexico and sequences that were available for strains in the CC3, based on the PubMLST database. The whole-genome sequence of CICESE-170 strain had high similarity with that of the reference RIMD 2210633 strain, and harbored 7 pathogenicity islands, including the 4 that denote O3:K6 pandemic strains. These results indicate that pandemic strains that have been isolated in Mexico show very close genetic relationship among them and with those isolated worldwide. © 2017 Guerrero 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.

Article, bacterial strain, biofouling, controlled study, Crassostrea, food intake, gene sequence, genetic analysis, genetic variability, Japan, Mexican, Mexico, molecular phylogeny, nonhuman, pandemic, pathogenicity island, sea food, serotyping, toxi BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA

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