Principal component regression analysis demonstrates the collinearity-free effect of sub estimated climatic variables on tree growth in the central Amazon / El análisis de regresión por componentes principales muestra el efecto libre de colinealidad de variables climáticas subestimadas sobre el crecimiento de los árboles en la Amazonía central

Abstract Introduction: Climatic variables show a seasonal pattern in the central Amazon, but the intra-annual variability effect on tree growth is still unclear. For variables such as relative humidity (RH) and air vapor pressure deficit (VPD), whose individual effects on tree growth can be underestimated, we hypothesize that such influences can be detected by removing the effect of collinearity between regressors. Objective: This study aimed to determine the collinearity-free effect of climatic variability on tree growth in the central Amazon. Methods: Monthly radial growth was measured in 325 trees from January 2013 to December 2017. Irradiance, air temperature, rainfall, RH, and VPD data were also recorded. Principal Component Regression was used to assess the effect of micrometeorological variability on tree growth over time. For comparison, standard Multiple Linear Regression (MLR) was also used for data analysis. Results: Tree growth increased with increasing rainfall and relative humidity, but it decreased with rising maximum VPD, irradiance, and maximum temperature. Therefore, trees grew more slowly during the dry season, when irradiance, temperature and VPD were higher. Micrometeorological variability did not affect tree growth when MLR was applied. These findings indicate that ignoring the correlation between climatic variables can lead to imprecise results. Conclusions: A novelty of this study is to demonstrate the orthogonal effect of maximum VPD and minimum relative humidity on tree growth.

Resumen Introducción: Las variables climáticas muestran un patrón estacional en la Amazonía central, pero el efecto de la variabilidad intra-anual en el crecimiento de los árboles aún no está claro. Para variables como la humedad relativa (HR) y el déficit de presión de vapor (VPD), cuyo efecto individual en el crecimiento de los árboles puede ser subestimada, planteamos la hipótesis de que tales influencias pueden detectarse eliminando el efecto de colinealidad entre regresores. Objetivo: Este estudio tuvo como objetivo determinar el efecto libre de colinealidad de la variabilidad climática sobre el crecimiento de los árboles en la Amazonía central. Métodos: Se midió el crecimiento radial mensual en 325 árboles desde enero 2013 hasta diciembre 2017. También se registraron datos de irradiancia (PAR), temperatura del aire, lluvia, humedad relativa (RH) y déficit de presión de vapor de aire (VPD). Se utilizó la regresión de componentes principales para evaluar el efecto de la variabilidad micrometeorológica a lo largo del tiempo sobre el crecimiento de los árboles. Para comparación, también se utilizó la regresión lineal múltiple (MLR) estándar para el análisis de datos. Resultados: El crecimiento de los árboles incrementó con el aumento de las precipitaciones y la humedad relativa, y disminuyó con el aumento de la VPD máxima, la irradiancia y la temperatura máxima. Por lo tanto, los árboles crecieron más lentamente durante la estación seca, cuando la irradiancia, la temperatura y la VPD eran más altas. La variabilidad micrometeorológica no afectó el crecimiento de los árboles cuando se aplicó MLR. Estos hallazgos indican que ignorar la correlación entre las variables climáticas puede conducir a resultados imprecisos. Conclusiones: Una novedad de este estudio es demostrar el efecto ortogonal del VPD máximo y la humedad relativa mínima sobre el crecimiento de los árboles.

misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny

As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.

A possible role of Drosophila CTCF in mitotic bookmarking and maintaining chromatin domains during the cell cycle

BACKGROUND: The CCCTC-binding factor (CTCF) is a highly conserved insulator protein that plays various roles in many cellular processes. CTCF is one of the main architecture proteins in higher eukaryotes, and in combination with other architecture proteins and regulators, also shapes the three-dimensional organization of a genome. Experiments show CTCF partially remains associated with chromatin during mitosis. However, the role of CTCF in the maintenance and propagation of genome architectures throughout the cell cycle remains elusive. RESULTS: We performed a comprehensive bioinformatics analysis on public datasets of Drosophila CTCF (dCTCF). We characterized dCTCF-binding sites according to their occupancy status during the cell cycle, and identified three classes: interphase-mitosis-common (IM), interphase-only (IO) and mitosis-only (MO) sites. Integrated function analysis showed dCTCF-binding sites of different classes might be involved in different biological processes, and IM sites were more conserved and more intensely bound. dCTCF-binding sites of the same class preferentially localized closer to each other, and were highly enriched at chromatin syntenic and topologically associating domains boundaries. CONCLUSIONS: Our results revealed different functions of dCTCF during the cell cycle and suggested that dCTCF might contribute to the establishment of the three-dimensional architecture of the Drosophila genome by maintaining local chromatin compartments throughout the whole cell cycle.

Epidemiologia genômica de Bordetella pertussis no Brasil / Genomic epidemiology of bordetella pertussis in Brazil

A coqueluche, ou pertússis, é uma doença do trato respiratório causada principalmente pela bactéria Bordetella pertussis. Após 50 anos de vacinação, pertussis reemergiu, passando a ser a doença imunoprevinível mais frequente mesmo em países desenvolvidos. Várias são as hipóteses para a reemergência de pertússis, uma delas é a adaptação do patógeno frente à vacinação. Linhagens contemporâneas de B. pertussis diferem de linhagens do período pré-vacinal, especialmente em genes codificadores de proteínas usadas na produção de vacinas acelular. Esta re-emergência também tem sido observada no Brasil, assim, realizamos a caracterização genética por MLST baseado nesses genes, de 26 isolados B. pertussis de surtos de três regiões brasileiras (Norte, Sul e Nordeste). Foram identificados dois perfis alélicos, em 24 isolados: prn2-ptxS1A-fim3B-ptxP3, de surtos (2008-2013) de Alagoas, Pernambuco e Rio Grande do Sul - e o perfil prn2-ptxS1A-fim3A-ptxP3 , em dois isolados de Pará/2004. Análises filogenéticas agruparam esses perfis com isolados do período pós vacinal de outras partes do globo. Deste conjunto, três do perfil mais frequente e um do perfil menos frequente, tiveram seus genomas sequenciados na plataforma GS 454 Junior. A comparação desses genomas com outros genomas de B. pertussis disponíveis em dados públicos não identificou SNPs ou genes únicos que caracterizassem os isolados do Brasil. Este estudo desenvolveu uma metodologia que permitiu definir a posição da IS481 nos genomas, e uma delas corresponde a um gene relacionado a regulação da transcrição da família MarR, Análise filogenômica, baseada em 826 SNPs, demonstrou que os isolados recentes do Brasil da linhagem pandêmica que presente em todos os continentes, exceto a África...

Pertussis more commonly referred as whooping cough is respiratory tract diseasemainly caused by the bacteria B. pertussis. After 50 years of vaccination pertussisremerged, becoming the most frequent vaccine preventable disease in developedcountries. Many hypotheses have been proposed for the re-emergence of pertussis,one being the pathogen adaptation in a vaccinated environment. Current pertussisstrains are different than those from the prevaccination era, especially in genes thatcode for proteins used in acelluar pertussis vaccines. This re-emergence is alsoobserved in Brazil, therefore we characterized 26 isolates from 3 regions of Brazil(North,South,Northeast) using an MLST approach based on these genes. We identifiedtwo allelic profiles, 24 isolates from the states of Rio Grande do Sul (2008-2009),Alagoas (2008-2009), Pernambuco (2013) and Pará (2004) presented the prn2-ptxS1A-fim3B-ptxP3 allelic profile, while 2 isolates from Pará (2004) presented theprn2-ptxS1A-fim3A-ptxP3 allelic profile. Phylogenetic analysis branch these two allelicprofiles along with other post vaccination isolates around the globe. Four isolates, threefrom the dominant profile and one from the less frequent profile, had their genomescompleted sequenced on the GS 454 Junior Platform. We compared these genomeswith others available in public databases and no SNP or unique genes were identifiedin the Brazilian genomes. This study also developed a methodology that identifies thelocation of the repetitive region IS481, and what genes it interrupted. One of them wasthe MarR transcriptional regulator gene. Phylogenomic analysis based on 826 SNPsrevealed that Brazilian B. pertussis lineages are part of the current pandemic linagepresent in all continents, except Africa...

Non-Synteny Regions in the Human Genome

Closely related species share large genomic segments called syntenic regions, where the genomic elements such as genes are arranged co-linearly among the species. While synteny is an important criteria in establishing orthologous regions between species, non-syntenic regions may display species-specific features. As the first step in cataloging human- or primate-specific genomic elements, we surveyed human genomic regions that are not syntenic with any other non-primate mammalian genomes sequenced so far. Based on the data compiled in Ensembl databases, we were able to identify 10 such regions located in eight different human chromosomes. Interestingly, most of these highly human- or primate-specific loci are concentrated in subtelomeric or pericentromeric regions. It has been reported that subtelomeric regions in human chromosomes are highly plastic and filled with recently shuffled genomic elements. Pericentromeric regions also show a great deal of segmental duplications. Such genomic rearrangements may have caused these large human- or primate-specific genome segments.

GATA family of transcription factors of vertebrates: phylogenetics and chromosomal synteny.

GATA genes are an evolutionarily conserved family, which encode a group of important transcription factors involved in the regulation of diverse processes including the development of the heart, haematopoietic system and sex gonads. However, the evolutionary history of the GATA family has not been completely understood. We constructed a complete phylogenetic tree with functional domain information of the GATA genes of both vertebrates and several invertebrates,and mapped the GATA genes onto relevant chromosomes. Conserved synteny was observed around the GATA loci on the chromosomes. GATAs have a tendency to segregate onto different chromosomes during evolution. The phylogenetic tree is consistent with the relevant functions of GATA members. Analysis of the zinc finger domain showed that the domain tends to be duplicated during evolution from invertebrates to vertebrates. We propose that the balance between duplications of zinc finger domains and GATA members should be maintained to exert their physiological roles in each evolutionary stage. Therefore,evolutionary pressure on the GATAs must exist to maintain the balance during evolution from invertebrates to vertebrates. These results reveal the evolutionary characteristics of the GATA family and contribute to a better understanding of the relationship between evolution and biological functions of the gene family, which will help to uncover the GATAs' biological roles,evolution and their relationship with associated diseases.

Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis.

Nuclear hormone receptors (NRs) form a large superfamily of ligand-activated transcription factors, which regulate genes underlying a wide range of (patho) physiological phenomena. Availability of the full genome sequence of Tetraodon nigroviridis facilitated a genome wide analysis of the NRs in fish genome. Seventy one NRs were found in Tetraodon and were compared with mammalian and fish NR family members. In general, there is a higher representation of NRs in fish genomes compared to mammalian ones. They showed high diversity across classes as observed by phylogenetic analysis. Nucleotide substitution rates show strong negative selection among fish NRs except for pregnane x receptor (PxR), estrogen receptor (ER) and liver x receptor (LxR). This may be attributed to crucial role played by them in metabolism and detoxification of xenobiotic and endobiotic compounds and might have resulted in slight positive selection. Chromosomal mapping and pairwise comparisons of NR distribution in Tetraodon and humans led to the identification of nine syntenic NR regions, of which three are common among fully sequenced vertebrate genomes. Gene structure analysis shows strong conservation of exon structures among orthologoues. Whereas paralogous members show different splicing patterns with intron gain or loss and addition or substitution of exons played a major role in evolution of NR superfamily.

Homology of polytene elements between Drosophila and Zaprionus determined by in situ hybridization in Zaprionus indianus

The drosophilid Zaprionus indianus due to its economical importance as an insect pest in Brazil deserves more investigation into its genetics. Its mitotic karyotype and a line-drawing map of its polytene chromosomes are already available. This paper presents a photomap of Z. indianus polytene chromosomes, which was used as the reference map for identification of sections marked by in situ hybridization with gene probes. Hybridization signals for Hsp70 and Hsr-omega were detected, respectively, in sections 34B and 32C of chromosome V of Z. indianus, which indicates its homology to the chromosomal arm 3R of Drosophila melanogaster and, therefore, to Muller's element E. The main signal for Hsp83 gene probe hybridization was in section 17C of Z. indianus chromosome III, suggesting its homology to arm 3L of D. melanogaster and to element D of Muller. The Ubi probe hybridized in sections 10C of chromosome II and 17A of chromosome III. Probably the 17A is the polyubiquitin locus, with homology to arm 3L of D. melanogaster and to the mullerian D element, as suggested also by Hsp83 gene location. The Br-C gene was mapped in section 1D, near the tip of the X chromosome, indicating its homology to the X chromosome of D. melanogaster and to mullerian element A. The Dpp gene probe hybridized mainly in the section 32A of chromosome V and, at lower frequencies to other sections, although no signal was observed as expected in the correspondent mullerian B element. This result led to the suggestion of a rearrangement including the Dpp locus in Z. indianus, the secondary signals possibly pointing to related genes of the TGF-beta family. In conclusion, the results indicate that chromosomes X, III, V of Z. indianus are respectively correspondents to elements A, D, and E of Muller. At least chromosome V of Z. indianus seems to share synteny with the 3R arm of D. melanogaster, as indicated by the relative positions of Hsp70 and Hsr-omega, although the Dpp gene indicates a disruption of synteny in its distal region.