SEKALI, JASIEL JUNIOR KARO (2022) KEANEKARAGAMAN GENETIK UDANG PUTIH YANG DITANGKAP DI PERAIRAN MENCO DAN GEJOYO, DEMAK (22ik384). Undergraduate thesis, Universitas Diponegoro.

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Abstract

RINGKASAN
Jasiel Junior Karo Sekali. 26040118120024. Keanekaragaman Genetik Udang
Putih yang Ditangkap di Perairan Menco dan Gejoyo, Demak. (Diah Permata
Wijayanti dan Subagiyo).
Udang Putih merupakan jenis udang yang tergolong dalam kelas
Craustacea, ordo Decapoda dan Famili Penaeidae. Udang Putih merupakan salah
satu komoditas perikanan tangkap terbesar di wilayah Demak. Sehingga identifikasi
spesies Udang Putih dan keanekaragaman genetiknya perlu dilakukan sebagai
acuan pengelolaan penangkapan demi menjaga berkelanjutan populasi. Penentuan
spesies dilakukan menggunakan penanda genetik gen COI mtDNA. Selanjutnya
dilakukan analisis filogenetik dan analisis keanekaragaman genetik Udang Putih di
perairan Menco dan Gejoyo.
Penelitian ini bertujuan untuk mengidentifikasi spesies Udang Putih dan
keanekaragaman genetiknya di perairan Menco dan Gejoyo, Demak berdasarkan
gen COI mtDNA. Sebanyak 40 individu Udang Putih diambil dan disimpan dalam
ethanol 96% sebagai preservasi sampel. Selanjutnya dilakukan analisis
laboratorium yang meliputi proses ekstraksi DNA, amplifikasi DNA dan visualisasi
DNA. Proses sekuensing dilakukan menggunakan metode Sanger Dideoxy
Sequencing di PT. Genetika Science Indoneisa. Selanjutnya hasil sekuens dianalisis
menggunakan aplikasi MEGA11 untuk mengedit sekuen, membuat pohon
filogenetik dan jarak genetik. Penelusuran spesies menggunakan BLAST untuk
menyocokkan sekuen dengan database GenBank. Aplikasi DNAsp digunakan untuk
analisis keanekaragaman haplotype dan nucleotide, serta Genetic Differentiation
Estimate. Analysis Molecular Variance (AMOVA) dilakukan dengan Arlequin 3.1.
Berdasarkan hasil penelitian menggunakan gen mtDNA COI sampel Udang
Putih diperoleh 3 spesies dari total 37 sampel yang berhasil disekuens, yaitu
Penaeus merguiensis (32 sampel) dengan persentase kemiripan 98,56% - 100%;
Fenneropenaeus penicillatus (4 sampel) dengan persentase kemiripan 98,83% -98,98% ; dan Penaeus vannamei (1 sampel) dengan persentase kemiripan 99,85%.
Hasil pohon filogenetik menunjukkan adanya 3 clade yang mengelompok
berdasarkan spesies. Jarak genetik terdekat adalah 5,07% yaitu jarak antara P.
merguiensis dan F. penicillattus. Sedangkan jarak genetik terjauh adalah 19,15%
yaitu jarak antara F. penicillattus dan P. vannamei. Hasil analisa keanekaragaman
genetik 32 sekuen Penaeus merguiensis menunjukkan adanya 4 sharing haplotype
dari total 9 haplotype yang diperoleh. Nilai rata-rata keanekaragaman haplotype
(Hd) 0,6734; dimana Gejoyo (n=18) memiliki nilai Hd 0,808, sedangkan Menco
(n=19) memiliki nilai Hd 0,533. Nilai π wilayah Gejoyo yaitu 0,00210, sedangkan
nilai π wilayah Menco yaitu 0,00089. Hasil AMOVA menujukkan nilai FST
0,00513 (P < 0,05), yang menunjukkan keanekaragaman genetik rendah dan masih
berasal dari satu populasi yang sama.
Kata kunci: Keanekaragaman Genetik, Udang Putih, MtDNA dan COI.

SUMMARY
Jasiel Junior Karo Sekali. 26040118120024. Genetic Diversity of White Shrimp
Caught in Menco and Gejoyo Waters, Demak. (Diah Permata Wijayanti and
Subagiyo).
White Shrimp is a type of shrimp belongs to the Craustacea class, the
Decapoda order and the Penaeidae Family. White Shrimp is one of the largest
capture fisheries commodities in the Demak area. So that the species identification
of White Shrimp and their genetic diversity needs to be done as a reference for
capture management in order to maintain a sustainable population. Species
determination was carried out using the genetic marker of the COI mtDNA gene.
In addition, phylogenetic and genetic diversity analyses of White Shrimp in Menco
and Gejoyo waters were carried out.
The purpose of this study is to identify the White Shrimp species and their
genetic diversity caught in the waters of Menco and Gejoyo, Demak based on the
COI mtDNA gene. A total of 40 individuals of White Shrimp were taken and stored
in 96% ethanol as sample preservation. Subsequently, laboratory analysis was
carried out which included DNA extraction, DNA amplification and DNA
visualization. The sequencing process was carried out using the Sanger Dideoxy
Sequencing method at PT. Genetics Science Indonesia. Furthermore, the sequence
results were analyzed using the MEGA11 application to edit the sequence, create a
phylogenetic tree and genetic distance. Species tracing used BLAST to match
sequences against the GenBank database. DNAsp application is used for haplotype
and nucleotide diversity analysis, as well as Genetic Differentiation Estimate.
Molecular Variance Analysis (AMOVA) was performed with Arlequin 3.1.
Based on the results of research using the mtDNA COI gene for White
Shrimp samples, 3 species from a total of 37 samples were successfully sequenced,
namely Penaeus merguiensis (32 samples) with a similarity percentage of 98.56%
- 100%; Fenneropenaeus penicillatus (4 samples) with a similarity percentage of
98.83% - 98.98% ; and Penaeus vannamei (1 sample) with a similarity percentage
of 99.85%. The results of the phylogenetic tree showed that there were 3 clades
grouped by species. The closest genetic distance was 5.07%, namely the distance
between P. merguiensis and F. penicillatus. While the farthest genetic distance was
19.15%, namely the distance between F. penicillattus and P. vannamei. The results
of the analysis of the genetic diversity of 32 Penaeus merguiensis sequences showed
that there were 4 sharing haplotypes out of a total of 9 haplotypes obtained. The
average value of haplotype diversity (Hd) 0.6734; where Gejoyo (n=18) has an Hd
value of 0.808, while Menco (n=19) has an Hd value of 0.533. The value for the
Gejoyo area is 0.00210, while the value for the Menco area is 0.00089. The AMOVA
results show an FST value of 0.00513 (P < 0.05), which indicates low genetic
diversity and still comes from the same population.
Keywords: Genetic Diversity, White Shrimp, MtDNA, and COI.

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