Caracterização parcial e tamanho do genoma de Stryphnodendron adstringens (Leguminosae)
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2019-01-25
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Universidade Federal de Goiás
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Using the massively parallel sequencing data generate from two individuals of the
Stryphnodendron adstringens, it was possible to structure this thesis in two chapters. The first
describes the assembly and annotation of the S. adstringens chloroplast genome and their
comparison between species belonging to the mimosoid clade from Caesalpinoideae-Leguminosae
subfamily. The second chapter describes the estimate genome size, assembly and annotation of
repetitive elements and genes in the nuclear genome of the S. adstringens. Genomic libraries were
sequenced using the Illumina HiSeq 2500 platform. Approximately 10 million reads were filtered
and used to assemble the chloroplast genome using a combination of de novo and reference-guided
strategies. The complete chloroplast genome of S. adstringens was assembled in a single circular
molecule containing 162,169 base pairs, contained 111 different genes, with 77 protein-coding
genes, 30 transfer tRNA and 4 ribosomal rRNA. A total of 137 microsatellites and 42 repeats
structures were identified, with the highest proportion in the LSC (Large Single Copy) region. The
average nucleotide variability among the five chloroplast genomes of Mimosoid species was
estimated to be 0.01771. The Ka/Ks ratio indicated positive selection for three genes analyzed,
rps16, psbH and clpP. The comparison of the structural characteristics in chloroplast genome
among Mimosoid species demonstrated that gene coding regions are highly conserved. The
phylogenetic reconstruction based on 73 protein-coding genes indicated that the Leguminosae-
Caesalpinoideae subfamily was paraphyletic. The size of the nuclear genome of S. adstringens was
estimated as 1C = 0.684 pg, which corresponds to a haploid genome of 669 Mpb. The nuclear
genome was made of 63.320 contigs with a total size of approximately 495 Mbp. A total of 20.124
microsatellite regions were identified in the nuclear genome, with AT/TA repeats being the most
frequent (44.16%). It was possible to identify that 44.58% of the nuclear genome of S. adstringens
is composed of transposable elements. The most common class were retroelements, among these,
the long terminal repeats (LTR) the most abundant family. 31,636 genes and 95,811 transcripts
were predicted with an average of 3.03 per gene. From the total number of predicted transcripts,
60,798 were classified functionally, according to Gene Ontology. Around 1,521 transcripts
(1.58%) were similar with protein sequences involved in the tannin biosynthesis pathways. This
work represents a great advance in the knowledge on the structure and organization of the nuclear
and chloroplast genomes of S. adstringens. In addition, the results obtained provide genomic
resources for future genetic and biotechnological investigations on the species.
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SOUZA, Ueric José Borges de. Caracterização parcial e tamanho do genoma de Stryphnodendron adstringens (Leguminosae). 2019. 117 f. Tese (Doutorado em Genética e Melhoramento de Plantas) - Universidade Federal de Goiás, Goiânia, 2019.