Development of functional ectopic compound eyes in scarabaeid beetles by knockdown of orthodenticle

Complex traits like limbs, brains, or eyes form through coordinated integration of diverse cell fates across developmental space and time, yet understanding how complexity and integration emerge from uniform, undifferentiated precursor tissues remains limited. Here, we use ectopic eye formation as a paradigm to investigate the emergence and integration of novel complex structures following massive ontogenetic perturbation. We show that down-regulation via RNAi of a single head patterning gene—orthodenticle—induces ectopic structures externally resembling compound eyes at the middorsal adult head of both basal and derived scarabaeid beetle species (Onthophagini and Oniticellini). Scanning electron microscopy documents ommatidial organization of these induced structures, while immunohistochemistry reveals the presence of rudimentary ommatidial lenses, crystalline cones, and associated neural-like tissue within them. Further, RNA-sequencing experiments show that after orthodenticle down-regulation, the transcriptional signature of the middorsal head—the location of ectopic eye induction—converges onto that of regular compound eyes, including up-regulation of several retina-specific genes. Finally, a light-aversion behavioral assay to assess functionality reveals that ectopic compound eyes can rescue the ability to respond to visual stimuli when wild-type eyes are surgically removed. Combined, our results show that knockdown of a single gene is sufficient for the middorsal head to acquire the competence to ectopically generate a functional compound eye-like structure. These findings highlight the buffering capacity of developmental systems, allowing massive genetic perturbations to be channeled toward orderly and functional developmental outcomes, and render ectopic eye formation a widely accessible paradigm to study the evolution of complex systems.Fil: Zattara, Eduardo Enrique. Indiana University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Macagno, Anna L. M.. Indiana University; Estados UnidosFil: Busey, Hannah A.. Indiana University; Estados UnidosFil: Moczek, Armin P.. Indiana University; Estados Unido

Inbreeding ratio and genetic relationships among strains of the Western clawed frog, Xenopus tropicalis

The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts

Dissecting the genome-wide evolution and function of R2R3-MYB transcription factor family in Rosa chinensis

Rosa chinensis, an important ancestor species of Rosa hybrida, the most popular ornamental plant species worldwide, produces flowers with diverse colors and fragrances. The R2R3-MYB transcription factor family controls a wide variety of plant-specific metabolic processes, especially phenylpropanoid metabolism. Despite their importance for the ornamental value of flowers, the evolution of R2R3-MYB genes in plants has not been comprehensively characterized. In this study, 121 predicted R2R3-MYB gene sequences were identified in the rose genome. Additionally, a phylogenomic synteny network (synnet) was applied for the R2R3-MYB gene families in 35 complete plant genomes. We also analyzed the R2R3-MYB genes regarding their genomic locations, Ka/Ks ratio, encoded conserved motifs, and spatiotemporal expression. Our results indicated that R2R3-MYBs have multiple synteny clusters. The RcMYB114a gene was included in the Rosaceae-specific Cluster 54, with independent evolutionary patterns. On the basis of these results and an analysis of RcMYB114a-overexpressing tobacco leaf samples, we predicted that RcMYB114a functions in the phenylpropanoid pathway. We clarified the relationship between R2R3-MYB gene evolution and function from a new perspective. Our study data may be relevant for elucidating the regulation of floral metabolism in roses at the transcript level

Chickens First\ud \ud Speciation by “Hopeful Monsters” in Fraternal Supertwins\ud

The idea of “hopeful monster” was proposed by Goldschmidt who envisioned that speciation could occur instantaneously via major chromosomal rearrangement in a one-step process; but he could not unravel how similar individual in the opposite sex to appear on the same time and location to generate next generation. This paper provides the answer for the challenge. \ud In this paper, a model of speciation in animals is discussed in detail. Only four steps are needed to generate a new species in sexual animals: fraternal twin zygotes, similar gross mutation on the zygotes, self-splitting of mutated zygotes into two groups of identical zygotes of both sexes, development of zygotes with birth of babies, and inbreeding when they mature. The outcome of these steps is generation of new species with chromosomal homozygosity. Viviparous animals (living young not eggs are produced) are used to explain the model. With slight modifications, other asexual organisms could be accommodated. \ud As the model provides the simplest explanation for speciation in all sexual animals, which plausibly explains many puzzles in biology; such as chicken egg, Cambrian explosion, appearance of new organs, etc. The author presents a few predictions that can be falsified. \ud This model needs only one assumption and it is consistent with many well-known observations. \u

Frequent Episode Mining to support Pattern Analysis in Developmental Biology

Computer Systems, Imagery and Medi

Implementation of Bayesian inference MCMC algorithm in phylogenetic analysis of Dipterocarpaceae family

Dipterocarpaceae is one of the most prominent plant families, with more than 500 members of species. This family mostly used timber plants for housing, making ships, decking, and primary materials for making furniture. In Indonesia, many Dipterocarpaceae species have morphological similarities and are challenging to recognize in the field. As a result, the classification process becomes difficult and even results are inconsistent when viewed only from the morphology. This research will analyze the phylogenetic tree of Dipterocarpaceae based on the chloroplast matK gene. The aim of the research is to classify the phylogenetics tree of Dipterocarpaceae family using Bayesian inference algorithm. This research used the chloroplast gene instead of morphological characters which has more accurate. The analysis steps are collecting data, modifying the structure sequence name, sequence alignment, constructing tree by using Markov Chain Monte Carlo (MCMC) from Bayesian Inference, and evaluating and analyzing the phylogenetic tree. The results showed that the tree constructed based on the gene is different from the tree based on morphology. Based on the morphological, Dipterocarpus should be in the Dipterocarpeae tribe but based on the similarity of its genes, Dipterocarpus is more similar to the Shoreae tribe.  

Implementation of Bayesian inference MCMC algorithm in phylogenetic analysis of Dipterocarpaceae family

Dipterocarpaceae is one of the most prominent plant families, with more than 500 members of species. This family mostly used timber plants for housing, making ships, decking, and primary materials for making furniture. In Indonesia, many Dipterocarpaceae species have morphological similarities and are challenging to recognize in the field. As a result, the classification process becomes difficult and even results are inconsistent when viewed only from the morphology. This research will analyze the phylogenetic tree of Dipterocarpaceae based on the chloroplast matK gene. The aim of the research is to classify the phylogenetics tree of Dipterocarpaceae family using Bayesian inference algorithm. This research used the chloroplast gene instead of morphological characters which has more accurate. The analysis steps are collecting data, modifying the structure sequence name, sequence alignment, constructing tree by using Markov Chain Monte Carlo (MCMC) from Bayesian Inference, and evaluating and analyzing the phylogenetic tree. The results showed that the tree constructed based on the gene is different from the tree based on morphology. Based on the morphological, Dipterocarpus should be in the Dipterocarpeae tribe but based on the similarity of its genes, Dipterocarpus is more similar to the Shoreae tribe.