scholarly journals Gene discovery in Atlantic Forest plant species using GR-RSC simplified genomes

2016 ◽  
Author(s):  
Marcella A A Detoni ◽  
Raony G C C L Cardenas ◽  
Marcela Uliano-Silva ◽  
Mauro de Freitas Rebelo
Keyword(s):  
Plant Species ◽  
Atlantic Forest ◽  
Restriction Site ◽  
Gene Discovery ◽  
Data Bank ◽  
Biological Processes ◽  
A Genome ◽  
Short Period ◽  
Metabolite Synthesis ◽  
Forest Plant Species

The Atlantic Forest is one of the most import biodiversity hotspots in the world, nevertheless, its 20,000 plant species are poorly characterized genetically, what could undermine conservational efforts and bioprospection of natural products. We used a genome reduction using restriction site conservation (GR-RSC) technique to minimize sequencing effort and build in a short period a data bank of gene sequences from 35 plant species from the Atlantic Forest in a private natural protected area in Southwest Brazil. After Illumina sequencing and standard bioinformatics, we produced more than 66 million super reads, of which 11 million (17\%) were annotated using Diamond and UNIREF90 database and 55 million were 'No hit'. We picked 17 enzymes from 2 secondary metabolite synthesis pathways that are both important representatives of biological processes for plants and also of industrial interest, to test the usefulness of the databank we created for gene discovery. All 17 genes were detected in at least one of the 35 species and all species exhibited at least one of the genes. Eight of the 35 species exhibited all 17 genes. These results shows that genome simplification by restriction enzyme can be applied to preliminary screen thousands of species in tropical forests, generating useful databanks for scientific and entreprenurial activities both in conservational biology and bioprospection.

scholarly journals Gene discovery in Atlantic Forest plant species using GR-RSC simplified genomes

2016 ◽  
Author(s):  
Marcella A A Detoni ◽  
Raony G C C L Cardenas ◽  
Marcela Uliano-Silva ◽  
Mauro de Freitas Rebelo
Keyword(s):  
Plant Species ◽  
Atlantic Forest ◽  
Restriction Site ◽  
Gene Discovery ◽  
Data Bank ◽  
Biological Processes ◽  
A Genome ◽  
Short Period ◽  
Metabolite Synthesis ◽  
Forest Plant Species

The Atlantic Forest is one of the most import biodiversity hotspots in the world, nevertheless, its 20,000 plant species are poorly characterized genetically, what could undermine conservational efforts and bioprospection of natural products. We used a genome reduction using restriction site conservation (GR-RSC) technique to minimize sequencing effort and build in a short period a data bank of gene sequences from 35 plant species from the Atlantic Forest in a private natural protected area in Southwest Brazil. After Illumina sequencing and standard bioinformatics, we produced more than 66 million super reads, of which 11 million (17\%) were annotated using Diamond and UNIREF90 database and 55 million were 'No hit'. We picked 17 enzymes from 2 secondary metabolite synthesis pathways that are both important representatives of biological processes for plants and also of industrial interest, to test the usefulness of the databank we created for gene discovery. All 17 genes were detected in at least one of the 35 species and all species exhibited at least one of the genes. Eight of the 35 species exhibited all 17 genes. These results shows that genome simplification by restriction enzyme can be applied to preliminary screen thousands of species in tropical forests, generating useful databanks for scientific and entreprenurial activities both in conservational biology and bioprospection.

Do vegetal communities dominated by invasive exotic plant species affect the structure of bird communities in an Atlantic Forest area?

2020 ◽  
Vol 28 (4) ◽  
pp. 241-249
Author(s):  
Cleverton da Silva ◽  
Arleu Barbosa Viana-Junior ◽  
Cristiano Schetini de Azevedo ◽  
Juliano Ricardo Fabricante
Keyword(s):  
Plant Species ◽  
Atlantic Forest ◽  
Bird Communities ◽  
Forest Area ◽  
Exotic Plant ◽  
Exotic Plant Species ◽  
Invasive Exotic

scholarly journals Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice

2021 ◽  
Author(s):  
Xiaoping Huang ◽  
Hongyu Zhang ◽  
Qiang Wang ◽  
Rong Guo ◽  
Lingxia Wei ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Leaf Senescence ◽  
Flag Leaf ◽  
Reduction Process ◽  
Sequencing Analysis ◽  
Biological Processes ◽  
Genome Wide ◽  
A Genome ◽  
Non Coding Rnas ◽  
Systematic Identification

Abstract Key message This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. Abstract LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation–reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.

Accumulation Parameters and Seasonal Trends for PCBs in Temperate and Boreal Forest Plant Species

2008 ◽  
Vol 42 (16) ◽  
pp. 5911-5916 ◽  
Author(s):  
Luca Nizzetto ◽  
Cristina Pastore ◽  
Xiang Liu ◽  
Paolo Camporini ◽  
Daniela Stroppiana ◽  
...  
Keyword(s):  
Boreal Forest ◽  
Plant Species ◽  
Seasonal Trends ◽  
Forest Plant Species

Boreal forest plant species responses to pH: ecological interpretation and application to reclamation

2017 ◽  
Vol 420 (1-2) ◽  
pp. 195-208 ◽  
Author(s):  
Monica Calvo-Polanco ◽  
Wenqing Zhang ◽  
S. Ellen Macdonald ◽  
Jorge Señorans ◽  
Janusz J. Zwiazek
Keyword(s):  
Boreal Forest ◽  
Plant Species ◽  
Species Responses ◽  
Forest Plant Species

Plant Species from the Atlantic Forest Biome and Their Bioactive Constituents

2019 ◽  
pp. 217-256
Author(s):  
Rebeca Previate Medina ◽  
Carolina Rabal Biasetto ◽  
Lidiane Gaspareto Felippe ◽  
Lilian Cherubin Correia ◽  
Marília Valli ◽  
...  
Keyword(s):  
Plant Species ◽  
Atlantic Forest ◽  
Bioactive Constituents ◽  
Forest Biome

scholarly journals Cecidomyiidae (Diptera, Insecta): richness of species and distribution in Brazil

2021 ◽  
Vol 21 (2) ◽  
Author(s):  
Valéria Cid Maia
Keyword(s):  
Plant Species ◽  
Atlantic Forest ◽  
Gall Midge ◽  
The Other ◽  
Amazon Forest ◽  
Gall Midges ◽  
Species Origin ◽  
Neotropical Species ◽  
Fauna Composition ◽  
Almost All

Abstract: Most Neotropical species of Cecidomyiidae (Diptera) have been described from Brazil, but a list of species with occurrence in the country has never been published. Little is known about their distribution and richness in the Brazilian phytogeographic domains. Additionally, a list of host plant species has never been gathered. The present study aims to fill these knowledge gaps and provides an overview of this family in Brazil. For this, data were obtained mainly from the literature, but also from the Cecidomyiidae collection of Museu Nacional and two herbaria (RB and R). Based on the site "Flora do Brasil 2020", botanical names were updated and plant species origin and distribution were verified. A total of 265 gall midge species have been recorded in Brazil, most from the Atlantic Forest (183), followed by Cerrado (60), and Amazon Forest (29). The other phytogeographic domains shelter from five to ten species. Phytophagous gall midges occur on 128 plant species of 52 families, almost all native, being 43 endemic to Brazil (21 endemic to Atlantic Forest, five to Cerrado, and one to Amazon). Although, the taxonomical knowledge is focused on the Atlantic Forest, each domain has its own fauna composition and these informations can be useful for environmental conservational purposes. About 58% of the Brazilian fauna are known only from the type-locality. In order to fill these gaps, it is necessary and important to collect in uninvestigated areas.

scholarly journals Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 270 ◽  
Author(s):  
Yun Gyeong Lee ◽  
Sang Chul Choi ◽  
Yuna Kang ◽  
Kyeong Min Kim ◽  
Chon-Sik Kang ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Genome Structure ◽  
Plant Genome ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

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