Genômica de organelas de cana-de-açúcar (Saccharum spp. cultivar RB867515)
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2017-09-29
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Universidade Federal de Goiás
Resumo
Sugarcane (Saccharum spp.) is one of the most important crops in tropical and subtropical
regions of the world. It is cultivated in more than 100 countries, where it is used as raw
material to obtain sugar and bioethanol. Given its importance, many efforts have been carried
out to characterize the genome of sugarcane cultivars. The eukaryotic genomes are confined
in different cellular compartments that present different inheritance patterns. Plastids and
mitochondria have their own genetic system, comprising DNA, RNA and all the demanded
components for replication, transcription and protein synthesis, that occur inside these
organelles. The primary function of chloroplasts and mitochondria is energy transduction.
Chloroplasts are responsible to convert light into chemical energy during photosynthesis,
while mitochondria provides energy to the cell in form of ATP molecules during respiration. In
this work, the chloroplast and mitochondrial genomes of sugarcane cultivar RB867515 are
assembled and characterized, using data from two next generation sequencing technologies –
Illumina and PacBio. In chloroplasts, we sought to identify evidences of heteroplasmy, by
using long reads from PacBio technology in the assembly process. In mitochondria, we
investigated the occurrence of genetic and structural genomic variations. The assemblies were
carried out using screened reads for the organellar genomes. These reads were selected by
mapping whole genome shotgun reads to reference genome sequences of chloroplast and
mitochondria, that are publicly available. The organellar reads were assembled using SPAdes
and Organelle_PBA. Gene annotation was obtained using DOGMA, GeSeq and Mitofy tools.
Two chloroplast haplotypes (isoforms) were identified in the cultivar RB867515. These
isoforms are different from each other because they present a distinct orientation of the SSC
(small single copy) region, confirming the hypothesis of chloroplast heteroplasmy in
sugarcane. The genome of each chloroplast isoform comprises 141,181 bp, and shows a typic
quadripartite structure, that includes a long single copy region (LSC) of 83,047 bp, which is
flanked by two inverted repeat regions (IRs) of 22,795 bp and a small-single copy region
(SSC), between IRs, of 12,544 bp. The assembled mitochondrial genome comprised two
chromosomes of 300,765 bp and 194,383 bp. The estimates of GC (~44%) and AT (~56%)
contents were similar to those obtained for other angiosperms. A total of 39 CDSs, 5hypothetical conserved genes, 5 rRNAs, 18 tRNAs and 9 gene fragments transferred from
chloroplast were annotated. The RB867515 mitochondrial chromosomes showed differences
when compared to those from S. officinarum, including single nucleotide polymorphisms
(SNPs), genetic duplications and genomic expansions.
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FEITOSA, M. S. S. M. Genômica de organelas de cana-de-açúcar (Saccharum spp. cultivar RB867515). 2017. 65 f. Dissertação (Mestrado em Genética e Melhoramento de Plantas) - Universidade Federal de Goiás, Goiânia,
2017.