Banca de DEFESA: PAULO EDUARDO TOSCANO SOARES

Uma banca de DEFESA de DOUTORADO foi cadastrada pelo programa.
STUDENT : PAULO EDUARDO TOSCANO SOARES
DATE: 01/12/2023
TIME: 08:00
LOCAL: Videoconferencia
TITLE:

Application of Next Generation Sequencing in Penaeus vannamei shrimp cultives from Rio Grande do Norte

KEY WORDS:

Short Reads Sequencing, Quasispecies, Heteroplasmy, Penaeus vannamei,
Genotyping

PAGES: 127
BIG AREA: Ciências Biológicas
AREA: Bioquímica
SUMMARY:

 

Over the last two decades, short-read sequencing has become a central tool in genomic
studies allowing the rapid and accurate discovery of high-quantity DNA sequences. This
made it possible to apply sequencing in activities of economic interest such as shrimp
farming, allowing, for example, the identification of pathogens and genotyping of hundreds to
thousands of shrimps simultaneously and the detection of genetic variants of these pathogens.
This sequencing can also help in the discovery of genetic markers, such as microsatellites and
SNPs, which can be brought together in a genotyping panel, making it scalable and reducing
the cost per sample of its application.
Specifically in shrimp farming, this technology has proven to be extremely valuable,
especially for studying the shrimp genome. Nuclear and mitochondrial genome analyzes
provide crucial information about origin, adaptability and other evolutionary aspects that are
vital for optimizing shrimp farming. Due to the high depth of coverage of these sequences, it
is possible to capture genetic diversity in the samples, allowing the discovery of genetic
variations in mitochondrial populations (heteroplasmy) occurring in shrimp and in pathogens,
such as viruses that affect them. This presents a unique opportunity to study the impacts of
this genetic diversity on the use of mitochondrial markers and the discovery of viral variants
and quasispecies. This translates into more informed management practices, minimizing
outbreaks and optimizing shrimp health. The implementation of panels based on SNPs is a
clear example of the impact of genotyping, demonstrating how the technology can be used to
improve genetic selection practices in shrimp farming.
In this work, the impact of mitochondrial genetic diversity was evaluated in a virus
that affects shrimp farming and shrimp using bioinformatics approaches. First, the occurrence
of heteroplasmy was assessed by analyzing muscle sequencing data from a single shrimp,
detecting patterns of variability and conservation in the mitogenomes of that individual, in
addition to comparing this internal variability with that observed among other mitogenomes
and observing the impact on markers in the control region, widely used in population studies.
Second, the genetic variability of the shrimp infectious myonecrosis virus obtained from tanks
in a viral outbreak situation was evaluated, obtaining the genotype of the most prevalent
variant for phylogenetic analyses, revealing its possible origin and relationship with other
existing lineages, and secondary variants, evaluating the occurrence of viral quasispecies.
Finally, based on previously existing data, a panel of 25 SNP markers (15 genomic and 10
mitochondrial) was developed aiming at low-cost genotyping of the shrimp Penaeus
vannamei by multiplex PCR amplification followed by silico parentage analysis. This last
project is currently ongoing, and the primers have already been evaluated, and now it remains
to continue with sequencing and bioinformatics analyses. In short, this work showed that
short-read sequencing is capable of capturing genetic diversity, bringing new insights to
shrimp farming by exposing the impact on markers, viral variability and, in the future, the
impact of this variability on genotyping panels.

 

COMMITTEE MEMBERS:
Presidente - 1880243 - DANIEL CARLOS FERREIRA LANZA
Externo à Instituição - JOSÉ MIGUEL ORTEGA - UFMG
Interno - 1507794 - RODRIGO JULIANI SIQUEIRA DALMOLIN
Externo à Instituição - SÁVIO TORRES DE FARIAS - UFPB
Externo ao Programa - 3063244 - TETSU SAKAMOTO - null