The genetic relationships and Indo-Pacific connectivity of whale sharks (Rhincodon typus) with particular reference to mitochondrial COI gene sequences from Cendrawasih Bay, Papua, Indonesia

Toha, Abdul Hamid A.; Dailami, Muhammad; Anwar, Saiful; Setiawan, Juswono B.; Jentewo, Yusup; Lapadi, Ida; Sutanto, Sanny; Aryasari, Ratih; Ambariyanto, Ambariyanto; Runtuboi, Ferawati; Madduppa, Hawis

doi:10.13057/biodiv/d210544

Cited by 10 publications

(20 citation statements)

References 38 publications

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“…Teluk Cenderawasih merupakan salah satu teluk terbesar di Indonesia (Huffard et al, 2010;Toha et al, 2019). Wilayah ini menjadi habitat alami bagi hiu paus (R. typus) (Saleky et al, 2016;Toha et al, 2020) yang dapat ditemui hampir sepanjang tahun (Maruanaya, Noor, & Tania, 2019;Ranintyari, et al, 2018). Teluk Cenderawasih menjadi habitat berbagai populasi biota, seperti dugong dan buaya, tempat endemisitas lokal tinggi (Allen & Erdmann, 2009) dan banyak haplotipe unik dari berbagai invertebrata laut (Allen & Erdmann, 2012;Crandall, Taffel, & Barber, 2009;DeBoer et al, 2008).…”

Section: Pendahuluanunclassified

“…Isolasi DNA dilakukan dengan menggunakan DNAeasy mini Kit, GeneAid sesuai dengan metode yang digunakan oleh Toha et al, (2020) dan Lutfi, et al, (2019. Secara singkat, sebanyak 30 mg sampel daging ikan teri diambil dan dimasukkan dalam buffer lisis (200 µL).…”

Section: Isolasi Dnaunclassified

“…Reaksi PCR berlangsung dalam larutan dengan volume 50 µL yang terdiri dari 5 µL isolat DNA, 1 µL DMSO, 1 µL BSA (bovine serum albumin), 25 µL Go Taq Green Mastermix, 2.5 µL primer jg-LCO, 2.5 µL primer jg-HCO dan 13 µL ddH2O. Adapun suhu pada mesin thermocyler sesuai dengan profil suhu yang digunakan oleh Toha et al, (2020).…”

Section: Pcr Gen Coi Dan Elektroforesisunclassified

“…Gel elektroforesis dari produk PCR fragmen gen COI ikan teri Ukuran pita DNA yang diperoleh memiliki ukuran yang sama dengan yang ditemukan pada ikan Cirhilabruss cf. ryukyuensis (Dailami et al, 2018), Rhincodon typus (Toha et al, 2020), bahkan pada kelompok gastropoda (Leatemia et al, 2018;Saleky et al, 2016). Hal ini menunjukkan bahwa daerah yang diamplifikasi untuk fragmen gen COI untuk analisis DNA barcoding memiliki posisi dan ukuran yang sama.…”

Section: Hasil Dan Pembahasan Amplikon Fragmen Gen Coiunclassified

“…Beberapa penelitian terdahulu yang juga berhasil menggunakan fragmen gen COI untuk identifikasi spesies ikan diantaranya yaitu ikan genus Mystus (Pramono et al, 2017), ikan Cirrhilabruss cf. ryukyuensis (Dailami et al, 2018), hiu paus Rhincodon typus (Toha et al, 2020) dan ikan teri famili Engraulidae (Afrand et al, 2020).…”

Section: Urutan Sekuens Dnaunclassified

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Genetic Identification of Anchovy from Cenderawasih Bay using DNA Barcoding Approach

Dailami

Widyawati

Toha

2021

Mus.Fish.Mar.Journal

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The Cenderawasih Bay is a marine habitat for whale sharks (R. typus) which appear almost all year round. The appearance of this whale shark is triggered by various factors, including the food. Anchovy is one of the attractions for the emergence of whale sharks, so it is necessary to conduct genetic, biological and ecological studies. Anchovy has a small in size, making it difficult to identify morphologically. The purpose of this study was to genetically identify anchovy samples obtained from Cenderawasih Bay and compare the sequences with the GenBank database. The COI gene fragments were amplified by PCR method, using primer jg-LCO and jg-HCO. Sequencing is carried out from two directions, forward and reverse with the sanger termination dideoxy method. The resulting DNA sequence has a length of 669 base pairs encoding 223 amino acids. The results of homological comparisons with the NCBI and BOLD System databases show that this sample has similarities to the COI sequence of Spratelloides gracilis with a similarity number up to 99%. The results of the phylogenetic tree analysis showed that the anchovy samples from Cenderawasih Bay were in one clade with S. gracilis from Japan and separated from the clade of S. gracilis from the Red Sea, with a distance between clades is 0.104. This result is in line with the identification by homological comparison in the NCBI and BOLD System.

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Section: Pendahuluanunclassified

Section: Isolasi Dnaunclassified

Section: Pcr Gen Coi Dan Elektroforesisunclassified

Section: Hasil Dan Pembahasan Amplikon Fragmen Gen Coiunclassified

Section: Urutan Sekuens Dnaunclassified

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Genetic Identification of Anchovy from Cenderawasih Bay using DNA Barcoding Approach

Dailami

Widyawati

Toha

2021

Mus.Fish.Mar.Journal

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Shark shuffle: segregated co-occurrence of multiple dusky and sandbar lineages at a human-altered habitat in the eastern Mediterranean Sea

Bigal,

Livne,

Zemah-Shamir

et al. 2024

Sci Rep

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Molecular phylogeny of anchovy (Clupeiformes: Clupeidae) from southern waters of Lombok using mitochondrial DNA CO1 gene sequences

2022

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Abstract. Mahrus H, Idrus AA, Zulkifli L. 2022. Molecular phylogeny of anchovy (Clupeiformes: Clupeidae) from southern waters of Lombok using mitochondrial DNA CO1 gene sequences. Biodiversitas 23: 2433-2443. This study aimed to identify anchovy samples genetically and evaluate their phylogenetic relationship to anchovies using the CO1 genetics markers. Fragment amplification of COI gene anchovy used a pair of COI commercially available primer with a length amplicon of about 693 base pairs (bp), coding for 231 amino acids successfully. The reconstruction of the phylogenetic tree with the neighbor-joining (NJ) method using Kimura 2 Parameters (K2P) by employing a bootstrap of 1000 replications. The genetic distance analysis between 19 fishes species in different families and 13 species in the genera Spartelloides acceded from NCBI indicated the closest distance between anchovy samples from the southern waters of Lombok and Spratelloides delicatulus from Australia is 0.02. The comparisons results of homology with the NCBI and the BOLD database show the anchovy sample has similarities to the CO1 sequences of S. delicatulus with a similar of 99%. The results of the phylogenetic tree analysis showed that the anchovy samples from the southern waters of Lombok were in the same clade as S. delicatulus from Australia. The study concluded a fish sample of anchovy from the southerly waters of Lombok was a closed related species to S. delicatulus.

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The genetic relationships and Indo-Pacific connectivity of whale sharks (Rhincodon typus) with particular reference to mitochondrial COI gene sequences from Cendrawasih Bay, Papua, Indonesia

Cited by 10 publications

References 38 publications

Genetic Identification of Anchovy from Cenderawasih Bay using DNA Barcoding Approach

Genetic Identification of Anchovy from Cenderawasih Bay using DNA Barcoding Approach

Shark shuffle: segregated co-occurrence of multiple dusky and sandbar lineages at a human-altered habitat in the eastern Mediterranean Sea

Molecular phylogeny of anchovy (Clupeiformes: Clupeidae) from southern waters of Lombok using mitochondrial DNA CO1 gene sequences

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