Analysis of the Rhizophora mangle's transcriptome: adaptations to extremophilic trees within a scenario of climate changes

Author(s)

Stephanie Karenina Bajay

• Document type: Master's Dissertation
• Press: Campinas, SP.
• Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia
• Defense date: 2017-06-05

Examining board members

Anete Pereira de Souza; Renato Vicentini; André Fujita

• Advisor: Anete Pereira de Souza; Marcelo Mendes Brandão

Abstract

Mangroves are extremely important ecosystems in terms of aquatic and terrestrial biodiversity, with peculiarities in terms of the characteristics and composition of their habitats, being considered an extreme environment for the survival of vascular plants. In the Brazilian littoral, the arboreal composition of the mangroves is restricted to only six species evolutionarily adapted to the functional complexity of these ecosystems. Rhizophora mangle is one of the most abundant species of this ecosystem on the Atlantic coast of the American coast. Studies with neutral microsatellite markers in the species pointed to a strong population structure that divides the species into two large groups in Brazil: one to the north and one to the south of Rio Grande do Norte. The genomic study of R. mangle can provide an addition to existing information on mechanisms that influence the distribution of diversity and the adaptive responses of this plant to the environment it occupies. Although the importance of mangroves in the geomorphic stability of the coastline, the preservation of biodiversity and the maintenance of their ecosystem services are well known, these ecosystems are constantly threatened by anthropic actions and global climate change (GCM). The adaptability and regeneration capacity of the true mangrove species in the face of disturbances and changes in environmental conditions is dependent, in addition to the physical and environmental characteristics of each mangrove environment, of phenotypic and genotypic adaptations in response to environmental conditions. This project proposes the sequencing of the transcriptome and elaboration of the gene expression profile of individuals that characterize natural populations of R. mangle in the extreme south and north of its occurrence in the Brazilian coast. This study aims to understand how different selective pressures associated to MCGs can affect the patterns and levels of gene expression in natural populations of R. mangle, allowing the elaboration of better strategies for conservation and management of R. mangle genetic resources and their habitats. Using the sequencing data by the R. mangle RNA-seq technique, new assemblies were tested with three assembly software, CLC, Trinity and Mira. The final assembly of the transcriptome was generated from the union between the assembly generated by Mira and Trinity, keeping the common transcripts and hybridizing the unique transcripts of each assembly. In this way, it was possible to obtain better assembly metrics. A total of 50,379,733 paired-end reads were used for reassembly of R. mangle in 72,054 unigenes with a N50 of 1350 bp. A total of 34% of contigs / unigenes were annotated in the Swiss-Prot database and 43.86% of contigs / unigenes annotated in the National Center for Biotechnology Information (NCBI) Non-Redundant Protein Database (NR). A total of 22,669 ORFs were identified in R. mangle transcripts and a total of 18,888 contigs provided information on domains and families of protein sequences identified by the InterProScan tool. We also identified 11,751 single sequence repeats (SSRs) and 46,508 SNPs in the alignment of the reads of the Santa Catarina samples and 87,813 SNPs in the reads of the Pará samples. Among the SNP variants detected, 20,741 were common between both populations. Through the functional annotation by terms of gene ontology (GO), we identified 159 terms in "response to stress", which may be associated with the osteous environment that R. mangle inhabits. For the validation of sequencing results and bioinformatics analyzes, 11 differentially expressed genes were selected for validation in RT-PCR (real-time PCR), confirming the results of analysis of abundance of RSEM reads (AU)

• FAPESP's process: 14/11426-1 - Analysis of the Rhizophora mangle' s transcriptome: adaptations to extremophilic trees within a scenario of climate changes
• Grantee: Stephanie Karenina Bajay
• Support Opportunities: Scholarships in Brazil - Master