An overview of bibliometric indicators about endangered Brazilian Cerrado plant species

The Cerrado is an important Brazilian biome due to the high levels of endemism and species diversity. Due to anthropic actions and natural causes, the Cerrado also includes some species of plants threatened with extinction.  We perform a bibliometric survey of scientific information regarding a set of endangered Cerrado plant species to answer two main questions: i) How much is known about Brazilian endemic plant species in the Cerrado threatened with extinction?; and ii) When, by whom and where were scientific articles on endemic endangered Cerrado plants published? We identified and mapped science to a list of 117 endemic endangered species of Cerrado flora from 35 different families. A total of 151 articles were published with these species and indexed on the Scopus database. We found that even after more than twenty years of the publication of the normative instruction, little is known about these species from a scientific point of view

Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae

Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys — rps16, ndhC – tRNA-Val, petA – psbJ, ndhF, rpl32 – ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family’s evolutionary history

The complete mitochondrial genome of the aquatic coralsnake Micrurus surinamensis (Reptilia, Serpentes, Elapidae)

In this study, we report the first complete mitochondrial genome sequence of the Aquatic Coralsnake Micrurus surinamensis. The mitochondrial genome lengthis 17,375 bp, comprising 13 protein-coding genes, 2 rRNA (12S and 16S) and 22 tRNA, as well as two typical control regions. Phylogenetic analysis based upon 13 protein-coding genes showed clusters based on terrestrial and marine species

Identification and characterization of SNPs in the genome of Eugenia dysenterica DC. (Myrtaceae)

Submitted by Luciana Ferreira ([email protected]) on 2016-09-01T13:42:46Z No. of bitstreams: 2 Dissertação - Rhewter Nunes - 2015.pdf: 16056651 bytes, checksum: e2b26d20076c285e8944154d20506e8f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)Approved for entry into archive by Luciana Ferreira ([email protected]) on 2016-09-01T13:43:15Z (GMT) No. of bitstreams: 2 Dissertação - Rhewter Nunes - 2015.pdf: 16056651 bytes, checksum: e2b26d20076c285e8944154d20506e8f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)Made available in DSpace on 2016-09-01T13:43:15Z (GMT). No. of bitstreams: 2 Dissertação - Rhewter Nunes - 2015.pdf: 16056651 bytes, checksum: e2b26d20076c285e8944154d20506e8f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2015-12-18Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESThe cagaiteira (Eugenia dysenterica DC), belonging to the Myrtaceae family, is a neotropical fruit tree species and native Brazilian Cerrado. As for the vast majority of neotropical species, very little is known about the genome of cagaiteira and genetic studies conducted so far are based on the use of a small number of molecular markers. In order to facilitate the development of genetic analysis studies in genomic scale for the species, this study aimed to identify and characterize variants of a single nucleotide (SNPs) in the genome of E. dysenterica using next-generation sequencing data. Genomic DNA libraries extracted from leaf tissue of five individuals of E. dysenterica, descendants of five distinct natural populations were subjected to sequencing on Illumina MiSeq platform, using the paired-end strategy (2x300). The sequences obtained were submitted to quality control examination to remove adapters and low quality regions. An assembly for the draft genome of E. dysenterica was produced by use of dipSPAdes program. To identify SNPs, after controlling for data quality, we performed the alignment of the assembly reads the draft with the BWA program and variants were identified using the platform of GATK tools. After three stages of filtration were identified 999,016 SNPs, with a Ts / Tv ratio equal to 1.86. We observed a density of one SNP every ~ 251 bases and most SNPs occurs in the context gene (59.79%). Most effects of putative SNPs identified are missense mutations (57.70%), but which have a low impact (0.74%). This work provides subsidies for the development of molecular markers for application in genomic studies of populations of E. dysenterica.A cagaiteira (Eugenia dysenterica DC), pertencente à família Myrtaceae, é uma espécie vegetal neotropical, arbórea, frutífera e nativa do Cerrado brasileiro. Como ocorre para a grande maioria das espécies neotropicais, muito pouco se sabe sobre o genoma da cagaiteira e os estudos genéticos realizados até agora se fundamentam na utilização de um pequeno número de marcadores moleculares. A fim de viabilizar o desenvolvimento de estudos de análise genética em escala genômica para a espécie, esse trabalho teve como objetivo identificar e caracterizar variantes de um único nucleotídeo (SNPs) no genoma de E. dysenterica, utilizando dados de sequenciamento de nova geração. Bibliotecas de DNA genômico extraído de tecidos foliares de cinco indivíduos de E. dysenterica, descendentes de cinco populações naturais distintas, foram submetidas ao sequenciamento na plataforma Illumina MiSeq, utilizando a estratégia de paired-end (2x300). As sequências obtidas foram submetidas à análise de controle de qualidade para remoção de adaptadores e de regiões de baixa qualidade. Um draft assembly para o genoma de E. dysenterica foi produzido pela utilização do programa dipSPAdes. Para a identificação de SNPs, após o controle de qualidade dos dados, foi realizado o alinhamento dos reads ao draft assembly com o programa BWA e as variantes foram identificadas utilizando-se as ferramentas da plataforma GATK. Após três etapas de filtragem foram identificados 999.016 SNPs, apresentando uma relação Ts/Tv igual a 1,86. Observou-se uma densidade de um SNP a cada ~251 bases e que a maior parte dos SNPs ocorre em contexto gênico (59,79%). A maior parte dos efeitos putativos dos SNPs identificados são de mutações do tipo missense (57,70%), mas que apresentam um baixo impacto (0,74%). Esse trabalho fornece subsídios para o desenvolvimento de marcadores moleculares para aplicação em estudos de genômica de populações de E. dysenterica

Research and partnership in studies of sugarcane using molecular markers : a scientometric approach

In this study, we applied scientometric methods and performed a science mapping analysis to investigate and describe the application of molecular markers in genetic studies for sugarcane. We analyzed 344 papers retrieved from Web of Science Thomson Reuters database, considering the time frame from 1974 to 2017, allowing the analysis of the produced scientific knowledge, temporal trends and research partnership in the subject. To our knowledge, a scientometric evaluation of the use of molecular markers for genetic studies in sugarcane has not yet been reported. Our main finding shows that dominant markers are more commonly used than co-dominant markers, and that when co-dominant markers are applied, most of the retrieved information is underexploited, due to lack of knowledge for the use of dosage information. Our results also show that despite the development of high-throughput sequencing technologies, for sugarcane only 13.33% of the studies reported the use of more than 1000 markers. We also found connectivity among researchers and institutions publishing worldwide, but only few authors represented a bridge between different research groups. Thus, the international research partnership is still low. Our findings show dominance in country publication. Six countries (India, Brazil, USA, Australia, China, and France) were responsible for 80% of the published papers and received most citations. We suggest special reinforcement in building international partnership, since collaborations occur mostly within countries. International collaboration can improve research performance and eventually lead to a better exploitation and more development of knowledge for sugarcane1191335355CAPES - Coordenação de Aperfeiçoamento de Pessoal e Nível SuperiorCNPQ - Conselho Nacional de Desenvolvimento Científico e Tecnológico88881.131685/2016-01Não tem2017-09817-0; 2015/23789-4465610/2014-5INCT - Instituto Nacional de Ciência e Tecnologi

Environmental DNA and biodiversity patterns: a call for a community phylogenetics approach

Environmental DNA (eDNA) metabarcoding is a relatively new technology allowing effective non-invasive analyses and monitoring of biodiversity patterns. Studies on eDNA metabarcoding focus on using sequence data to delimit basic units (i.e., such as Molecular Operational Taxonomic Units – MOTUS – or Amplicon Sequence Variation – ASVs), and after this definition standard analytical approaches from community ecology are applied. However, there is more information inherent to eDNA data and it is now straightforward to use more general approaches in which analyses are based directly on phylogenies or genetic distances between MOTUs or ASVs, rather than in discrete units without any accounting for hierarchical structure, providing a more continuum understanding of biodiversity patterns. Here we briefly review the concepts and methods to incorporate phylogenetic patterns into eDNA metabarcoding analyses, illustrating some of the main issues with eukaryote diversity data along the Araguaia River Basin. Hopefully this perspective stimulates researchers obtaining eDNA metabarcoding data to perform their data under the community phylogenetics framework instead of (or in addition to) the more standard community ecology approach

Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily

Abstract Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group

RECEPÇÃO “CALOUROSA”: CONHECIMENTOS, EXPECTATIVAS E OPINIÕES DE INGRESSANTES DO CURSO DE LICENCIATURA EM CIÊNCIAS BIOLÓGICAS

Este estudo objetivou relatar de forma crítica e reflexiva a atividade de recepção dos ingressantes do curso de Licenciatura em Ciências Biológicas e avaliar seus conhecimentos, expectativas e opiniões. A recepção foi realizada no primeiro semestre letivo de 2012, por alunos do Programa de Educação Tutorial (PET), envolvendo alunos do curso de Licenciatura em Ciências Biológicas do IF Goiano – Câmpus Urutaí e ofereceu atividades diversas de caráter informativo, integrativo e de estímulo à permanência no curso. Após a atividade de recepção foi aplicado um questionário para um feedback e planejamento de ações futuras. A atividade foi avaliada por 46% dos calouros como “excelente” e 46%, como “boa”. Para 71% dos ingressantes, a atividade contribuiu para a interação com outros discentes, 76,9% disseram que foi uma motivação para ingressar no PET. De modo geral, conclui-se que a recepção foi importante para a adaptação dos ingressantes à vida acadêmica e para minimizar as possíveis dificuldades encontradas pelos calouros