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  • 1
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    Online Resource
    High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergenic Spacer atpB-rbcL
    Universitas Negeri Semarang ; 2018
    In:  Biosaintifika: Journal of Biology & Biology Education Vol. 10, No. 1 ( 2018-04-02), p. 41-47
    Details
    In: Biosaintifika: Journal of Biology & Biology Education, Universitas Negeri Semarang, Vol. 10, No. 1 ( 2018-04-02), p. 41-47
    Abstract: Synedrella nodiflora (L.) Gaertn has taxonomically been the only species of genus Synedrella, which spreads over many tropical countries. In spite of its wide range of distribution, the genus remains monospecific. This leads to assumption of the very low genetic diversity among S. nodiflora populations worldwide. It may also be the case in Java Island, though rapid changes in ecosystem condition occurs. Here we report our study on S. nodiflora population genetics in Java Island using intergenic spacer (IGS) atpB –  rbcL as a molecular marker, since it has been well known as one of the most variable chloroplast genome regions in a wide range of plant species so far. As many as 58 individuals were collected randomly from ten different locations in the island. Based on IGS atpB – rbcL sequences of 860 bp length, only two haplotypes were observed. Both show only one polymorphic site (0.12%) and one transversion, where T is substituted by G at position 790, indicating that high connectivity among populations of S. nodiflora in Java Island is observed. This results in a low genetic differences among the populations, which at the same time provides a fact of nearly no variation among the IGS atpB – rbcL sequences.
    Type of Medium: Online Resource
    ISSN: 2338-7610 , 2085-191X
    URL: Issue
    URL: Article
    DOI: 10.15294/biosaintifika.v10i1
    DOI: 10.15294/biosaintifika.v10i1.12038
    Language: Unknown
    Publisher: Universitas Negeri Semarang
    Publication Date: 2018
    detail.hit.zdb_id: 3069992-7
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  • 2
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    Genetic diversity assessment of Hemibagrus nemurus from rivers in Java Island, Indonesia using COI gene
    UNS Solo ; 2019
    In:  Biodiversitas Journal of Biological Diversity Vol. 20, No. 9 ( 2019-08-28)
    Details
    In: Biodiversitas Journal of Biological Diversity, UNS Solo, Vol. 20, No. 9 ( 2019-08-28)
    Abstract: Abstract. Nuryanto A, Komalawati N, Sugiharto. 2019. Genetic diversity assessment of Hemibagrus nemurus from rivers in Java Island, Indonesia using COI gene. Biodiversitas 20: 2707-2717. Green catfish (Hemibagrus nemurus) is a popular freshwater fish that highly exploited in almost all the rivers in Java Island. The exploited population tends to have low genetic diversity. Meanwhile, separated populations might lead to a genetic difference among the river populations. This study aims to investigate the genetic diversity and population variation of H. nemurus collected at eleven rivers across Java Island. The analysis based on 465 bp fragment of the cytochrome c oxidase 1 gene from 140 individuals. Analysis of overall populations proved that H. nemurus had a high gene diversity (h= 0.935±0.016) and nucleotide diversity (π = 0.073±0.036). Within population analysis also showed that H. nemurus populations showed high levels of gene diversity (h= 0.338±0.128 to 1.000±0.022) and nucleotide diversity (π =0.001±0.001 to 0.071±0.038). Those diversity values indicated that H. nemurus had high level of genetic diversity, except for the Citanduy population. Population comparison showed that significant genetic differences observed among populations (p= 0.000 for both variance component and Fst-value). However, pairwise comparison analysis indicated complex pattern of population differentiation. The high genetic diversity and complex pattern of population differentiation have important implication for H. nemurus conservation in Java Island.
    Type of Medium: Online Resource
    ISSN: 2085-4722 , 1412-033X
    URL: Article
    DOI: 10.13057/biodiv/d200936
    Language: Unknown
    Publisher: UNS Solo
    Publication Date: 2019
    detail.hit.zdb_id: 2660049-3
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  • 3
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    Molecular Identification of Fish Larvae from East Plawangan of Segara Anakan, Cilacap, Central Java, Indonesia
    Universitas Negeri Semarang ; 2017
    In:  Biosaintifika: Journal of Biology & Biology Education Vol. 9, No. 1 ( 2017-03-12), p. 33-
    Details
    In: Biosaintifika: Journal of Biology & Biology Education, Universitas Negeri Semarang, Vol. 9, No. 1 ( 2017-03-12), p. 33-
    Abstract: 〈 p 〉 Correct identification of fish larvae from East Plawangan is very difficult to be done due to undefined of their morphology, while correct name is an important information for management of that area as spawning and nersery ground. Therefore, so far no scientific report on what species that utilize East Plawangan as their spawning and nursery ground. Cytochrome c oxidase 1 gene provide a precise tool for correct larvae identification. This study aims to test the accuracy of the cytochrome c oxidase 1 gene on fish larvae identification. The COI gene were amplified and sequenced. The homology of sequences were checked using 〈 em 〉 Basic Local Alignment Search Tool 〈 /em 〉 (BLAST). Genetic distances were calculated with the help of MEGA 6 software. Taxonomic tree was reconstructed using neighbor-joining and maximum parsimony methods with 1000 bootstraps repeats. A sum of 24 morphotypes were identified, indicating high diversity of fish that utilize East Plawangan as their spawning and nursery ground. BLAST result showed that seven morphotypes were convincingly identified into species level, while three remaining morphotypes could only be identified at generic level. Taxonomic tree shows clear discrimination among morphotypes. This proved that cytochrome c oxidase 1 gene showed high accuracy on larval species discrimination. 〈 /p 〉
    Type of Medium: Online Resource
    ISSN: 2338-7610 , 2085-191X
    URL: Issue
    URL: Article
    DOI: 10.15294/biosaintifika.v9i1
    DOI: 10.15294/biosaintifika.v9i1.9191
    Language: Unknown
    Publisher: Universitas Negeri Semarang
    Publication Date: 2017
    detail.hit.zdb_id: 3069992-7
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  • 4
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    Karakterisasi Molekuler Ikan Gurami Soang (Osphronemus gouramy Lac.) yang Mati pada Rentang Waktu Berbeda Menggunakan PCR-RFLP Gen Major Histocompatibility Complex Kelas II B
    Universitas Jenderal Soedirman ; 2017
    In:  Biosfera Vol. 33, No. 2 ( 2017-08-24), p. 92-
    Details
    In: Biosfera, Universitas Jenderal Soedirman, Vol. 33, No. 2 ( 2017-08-24), p. 92-
    Abstract: Gurami (Osphronemus gouramy Lac.) is a popular fish species among Indonesian people. Several Gurami strains have been cultivated by fish farmer, one of which is Gurami Soang. This strain is belived to have a faster growth rate compared to other strains. However, like other strains, the fingerling of Soang strain have also a low survival and suceptible to disease, especially that caused by Aeromonas hydrophila infection. It has been proved that seeds from a single spawning event show varibale disease resistance. The difference in resistance among individuals is suggested related to the difference in their genetic component. One of the genes responsible for resistance is Major Histocompatibility Complex (MHC) class II B gene. Variability in resistance can be analyzed by using PCR - RFLP technique. PCR-RFLP is a technique that can produce a specific DNA fragments by PCR, followed by cutting the PCR product using restriction enzymes to describe the presence or absence of restriction sites in DNA fragments. This research aims to determine genetic marker to differiantiate between resitant and irresistant individual of Gurami Soang infected by A. hydrophila which die at a different time priod based on PCR-RFLP MHC class IIB gene. The study used survey method with purposive random sampling. The Data of PCR-RFLP band patterns were analyzed descriptively. The result indicated that cutting of the MHC class II B gene using HinfI produce two RFLP bands with 300 bp and 100 bp length in all samples. Meanwhile, the MHC IIB gene was not cuted by PstI, HindIII, BamHI and EcoRI enzymes forall samples. These mean that MHC II gene in all individuals were monomorphic. Therefore,it can be concluded that there is no specific genetic marker to differentiate gurami soang individulas which was dying in different time periods.
    Type of Medium: Online Resource
    ISSN: 2528-2050 , 0853-1625
    URL: Article
    DOI: 10.20884/1.mib.2016.33.2.373
    Language: Unknown
    Publisher: Universitas Jenderal Soedirman
    Publication Date: 2017
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  • 5
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    Genetic Homogenity of Commerson’s Anchovy (Stolephorus commersonnii) in Segara Anakan Cilacap Central Java Inferred from PCR-RFLP Markers
    Universitas Islam Negeri Alauddin Makassar ; 2019
    In:  Biogenesis: Jurnal Ilmiah Biologi Vol. 7, No. 1 ( 2019-06-30), p. 14-
    Details
    In: Biogenesis: Jurnal Ilmiah Biologi, Universitas Islam Negeri Alauddin Makassar, Vol. 7, No. 1 ( 2019-06-30), p. 14-
    Abstract: Commerson’s anchovy (Stolephorus commersonnii) is a small pelagic fish that live in a group and its existence is very abundant in Segara Anakan Cilacap. This anchovy is widely consumed by communities live around Segara Anakan. This leads to a high exploitation rate. Exploited populations generally have low genetic diversity. This study aims to evaluate genetic diversity of commerson’s anchovy population in Segara Anakan Cilacap inferred from PCR-RFLP of the cytochrome c oxidase 1 (CO1) gene. This study was conducted from January to April 2018 and used survey method by applying random sampling. As many as 30 samples of anchovy were taken. Genomic mtDNA was isolated using modified Chelex method. Partial sequences of the COI gene were amplified using a pair forward commercially available primer. The lengths of 650 base pair of the PCR products were digested with four restriction enzymes. The HindIII enzyme produces PCR-RFLP fragment with the size of 416 bp and 234 bp lengths, VspI produces 435 bp and 214 bp, CO1-TaqI produces 556 bp and 94 bp and RsaI produces 319 bp, 183 bp, and 148 bp fragments, respectively. The PCR-RFLP fragments were obtained from all samples but they produced uniform band pattern for all 30 anchovy individuals. These results indicated that the anchovy population in Segara Anakan Cilacap has monomorphic allele for all PCR-RFLP markers. Hence, it can be concluded that genetic homogenity was observed on anchovy population in Segara Anakan Cilacap as inferred from PCR-RFLP COI gene.
    Type of Medium: Online Resource
    ISSN: 2580-2909 , 2302-1616
    URL: Article
    DOI: 10.24252/bio.v7i1.6352
    Language: Unknown
    Publisher: Universitas Islam Negeri Alauddin Makassar
    Publication Date: 2019
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  • 6
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    Concordance of microsatellite and mitochondrial DNA markers in detecting genetic population structure in the boring giant clam Tridacna crocea across the Indo‐Malay Archipelago
    Wiley ; 2017
    In:  Marine Ecology Vol. 38, No. 1 ( 2017-02)
    Details
    In: Marine Ecology, Wiley, Vol. 38, No. 1 ( 2017-02)
    Abstract: Mitochondrial DNA (mt DNA ) is a single, usually non‐recombining locus, and often uniparentally inherited. Therefore, its ability to reveal recent gene flow among populations is usually questioned. In this study, the genetic population structure of 16 populations of Tridacna crocea (n = 366) from the Indo‐Malay Archipelago ( IMA ) was examined with 10 microsatellite markers and compared to previous studies using mt DNA , in order to test if the revealed population structure was congruent between the two marker systems. The results showed that the genetic population structure revealed by the two marker systems was mostly congruent, with a high correlation between cytochrome c oxidase subunit I ( COI ) and microsatellites. The studied populations could be divided by both marker systems as follows: (i) Eastern Indian Ocean, (ii) Central IMA , and (iii) Western Pacific. Populations in the Central IMA showed high gene flow. However, populations in the Java Sea (Karimunjava, Pulau Seribu) were grouped into a separate cluster by mt DNA analysis, while this grouping was not detected by microsatellites. It was also noteworthy that there is obvious heterozygosity deficiency in most of the populations, which may be caused by null alleles, inbreeding or population expansion. Overall, these results indicate that the mitochondrial COI gene is applicable for population genetic analysis and precise recovery of connectivity patterns of giant clams. Therefore, the combination of mt DNA and nuclear DNA markers can lead to a more complete understanding of population genetics. Moreover, this study is expected to facilitate fully displaying the population genetic structure of giant clams combining with other researchers' results.
    Type of Medium: Online Resource
    ISSN: 0173-9565 , 1439-0485
    URL: Issue
    URL: Article
    DOI: 10.1111/maec.2017.38.issue-1
    DOI: 10.1111/maec.12389
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2020745-1
    detail.hit.zdb_id: 225578-9
    SSG: 12
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  • 7
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    Resistensi dan karakter molekuler benih gurami sowang Osphronemus goramy Lacepede, 1801 asal induk berbeda
    Institute of Postgraduate Studies, Syiah Kuala University ; 2017
    In:  Depik Vol. 6, No. 3 ( 2017-11-19), p. 242-251
    Details
    In: Depik, Institute of Postgraduate Studies, Syiah Kuala University, Vol. 6, No. 3 ( 2017-11-19), p. 242-251
    Abstract: The cultivation of giant gourami is constrained by its high mortality due to low resistance to diseases. Resistance is an inherited character from the parental to their seeds. High resistance seeds can be selected using molecular marker, such as Major Histocompatibility complex (MHC) gene. Resistance character is assumed to be different among individual from different broodstocks and is suggested related to their genetic constituent.  This research aims to analyze the resistance of sowang gouramy seeds from different broodstocks and describe genetic character of seeds from different broodstocks. An explorative survey was perfomed. One hundred individuals were taken purposively from Balai Benih Ikan Sikamaju Ciamis West Java and hundred individuals were bought from fish farmer in Ciamis West Java. Sampling was performed in 2015 for the first seed group and in 2016 for the second seed group. Samples were subjected to Aeromonas hydrophila and Pseudomonas aeruginosa infection. The fragments of MHC gene were amplified using PCR technique from eight individual of first group and six individuals of second group. The resistance characteristic was analyzed using simple mathematics based on the number of living seeds compared total infected seeds and molecular characteristics was analyzed descriptively based on DNA band pattern. Different resistance to A. hydrophila was observed between seed groups from different broodstocks. The seeds group from the first broodstocks showed lower resistance level with the value of 29% than that from the second broodstocks with the resistance value reached of 100%. Both seed groups also showed resistance differences to P.aeruginosa, although  not as high as A.hydrophila infection. The differencies were also reflected in their MHC gene between seed groups from two different broodstocks. The amplication of MHC gene of the seeds from the first broodstacks resulted of 585 bp and 400 bp length fragments, while from those second broodstocks was only resulted of 400 bp frament. The differences on DNA band pattern between seed groups indicate a different molecular characteristics among seeds from different broodstocks.Usaha budidaya ikan gurami terhambat oleh tingginya mortalitas benih karena rendahnya resistensi terhadap penyakit. Resistensi merupakan sifat yang diwariskan dari tetua ke anakan. Benih yang resisten dapat diseleksimenggunakan marka molekuler seperti gen Major Histocompatibility complex (MHC). Sifat resisten diduga berbeda diantara benih yang beraasal dari induk berbeda dan diduga terkait dengan kompenen genetik yang dimiliki. Tujuan penelitian ini adalah untuk mengetahui sifat reisten dan karakter molekuler benih gurami sowang asal induk berbeda. Fragmen gen MHC diamplifikasimenggunakan teknik PCR. Sifat resistensi dianalisis menggunakan perhitungan matematika sederhana berdasarkan jumlah benih hidup dibagi jumlah total benih yang diinfeksi, sedangkan karakter molekuler dianalisis secara deskritif berdasakan pola pita yang dihasilkan. Kedua kelompok benih memiliki sifat resistensi berbeda terhadap Aeromonas hydrophila. Benih dari induk pertama memiliki sifat resistensi lebih rendah dengan nilai kelangsungan hidup sebesar 29% daripada kelompok benih dari induk kedua yang memiliki kelangsungan hidup mencapai 100%. Kedua kelompok benih juga memperlihatkan perbedaan sifat resisten terhadap P. aeruginosa, meskipun perbedaannya tidak sebesar terhadap A.hydrophila. Perbedaan tersebut juga tercermin pada gen MHC kedua kelompok benih. Pada kelompok benih pertama dihasilkan dua fragmen gen MHC dengan ukuran 585 pb dan 400 pb, sedangkan dari kelompok benih kedua hanya dihasilkan fragmen berukeuran 400 pb. Perbedaan pola pita diantara kedua kelompok benih tersebut merupakan idikasi adanya perbedaan karakter molekuler pada benih yang berasal dari dua induk berbeda
    Type of Medium: Online Resource
    ISSN: 2502-6194 , 2089-7790
    URL: Article
    DOI: 10.13170/depik.6.3.6539
    Language: Unknown
    Publisher: Institute of Postgraduate Studies, Syiah Kuala University
    Publication Date: 2017
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  • 8
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    Molecular Characterization Reveals Genetic Differences Between Wild and Captive Populations of Mandiangin Giant Gourami (Osphronemus goramy)
    Sunan Gunung Djati State Islamic University of Bandung ; 2019
    In:  Jurnal Biodjati Vol. 4, No. 1 ( 2019-05-28), p. 1-10
    Details
    In: Jurnal Biodjati, Sunan Gunung Djati State Islamic University of Bandung, Vol. 4, No. 1 ( 2019-05-28), p. 1-10
    Abstract:   Captive population of Mandiangin giant gourami (Osphronemus goramy Lac.) is a new strain developed from wild pop-ulations in Riam Kanan Dam. No much is known about the genetic constituent of this strain compared to the parental population. This re-search was done to obtain information whether genetic alteration has occurred in captive population compared to their wild parental pop-ulation. Wild population was caught from Riam Kanan Dam, while captive population was collected from Balai Perikanan Budidaya Air Tawar (BPBAT) “Freshwater Aquaculture Centre” Mandiangin, South Kalimantan. The captive population of Batanghari strain from BPBAT Sungai Gelam, Jambi was also analyzed. Molecular assess-ment was done using CO1 PCR-RFLP which was developed by digest-ing the amplicon of the CO1 gene from all populations using two re-striction enzymes, namely HindIII and TaqI and resulted CO1-HindIII and CO1-TaqI RFLP markers. All tested populations showed uniform patterns of those CO1-RFLP markers but with different fragment sizes among populations. This means all resulted RFLP markers were mono-morphic in each populations but polymorphic among giant gourami populations. In other words, no genetic diversity within population but substantial genetic differences was observed between wild and cap-tive Mandiangin populations. This proved that genetic alteration has occurred in Mandiangin captive populations compared to the wild pa-rental giant gourami population. In conclusion, captive and wild pop-ulations of Mandiangin giant gourami were genetically different. This result is vital as scientific base for future development of inland fish-eries, especially for breeding strategy of Mandiangin giant gourami. 
    Type of Medium: Online Resource
    ISSN: 2548-1606 , 2541-4208
    URL: Article
    DOI: 10.15575/biodjati.v4i1.3942
    Language: Unknown
    Publisher: Sunan Gunung Djati State Islamic University of Bandung
    Publication Date: 2019
    detail.hit.zdb_id: 2978114-0
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  • 9
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    Phylogeny of Marine Ornamental Fish Members of Labridae from the South Coast of West Java
    Universitas Islam Negeri Alauddin Makassar ; 2019
    In:  Biogenesis: Jurnal Ilmiah Biologi Vol. 7, No. 2 ( 2019-12-29)
    Details
    In: Biogenesis: Jurnal Ilmiah Biologi, Universitas Islam Negeri Alauddin Makassar, Vol. 7, No. 2 ( 2019-12-29)
    Abstract: Labridae is a large and diverse fish family. Many species under Labridae inhabits Indonesian coral reefs. However, limited scientific data are available on ornamental fish diversity in Labridae from the South Coast of West Java. The purpose of the research is to give information about species diversity and phylogenetic relationships among species of Labridae fish family in the South Coast of West Java. This research will be conducted using a survey method with a purposive sampling technique. The observed parameters include morphometric and meristic characters and evolutionary relationships among species within  Labridae family species collected from the South Coast of Sukabumi and Garut, West Java. Morphological data will be analyzed descriptively based on morphometric and meristic data. Species-level identification performed by referring to the available identification guide book. Phylogenetic relationships will be analyzed statistically using cladistics method as implemented in PAUP 4.0 applying maximum parsimony algorithm.  The cladogram has a consistency index of 0.563, indicating low homoplasy and proved that the tree was the most parsimonious. Labridae formed monophyletic clade compared to Acanthurus maculiceps, and Cheilio inermis was basal species while the others derived species.
    Type of Medium: Online Resource
    ISSN: 2580-2909 , 2302-1616
    URL: Article
    DOI: 10.24252/bio.v7i2.10205
    Language: Unknown
    Publisher: Universitas Islam Negeri Alauddin Makassar
    Publication Date: 2019
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  • 10
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    Historical divergences associated with intermittent land bridges overshadow isolation by larval dispersal in co‐distributed species of Tridacna giant clams
    Wiley ; 2018
    In:  Journal of Biogeography Vol. 45, No. 4 ( 2018-04), p. 848-858
    Details
    In: Journal of Biogeography, Wiley, Vol. 45, No. 4 ( 2018-04), p. 848-858
    Abstract: The aim of this study was to test historical and contemporary influences on population structure in the giant clams, Tridacna maxima (Röding, 1798) and T. crocea (Lamarck, 1819). To refine the location of clade boundaries within a newly resurrected species, Tridacna noae (Röding, 1798). Location Indo‐Australian archipelago, including Indonesia, the Philippines, Australia, Papua New Guinea, the Solomon Islands, Republic of Kiribati, the Line Islands and Taiwan. Methods We used isolation‐migration ( IM a) coalescent models and distance‐based redundancy analyses (db RDA ) to test the relative influence of barriers and continuous distances on historical divergence, gene flow and population structure of T. maxima and T. crocea . Continuous metrics of distance included present‐day and Last Glacial Maximum overwater distances along with probability of larval dispersal (LD) among sampling sites. We combined new mitochondrial cytochrome oxidase subunit I (mt DNA COI ) sequences with existing data to compile the largest data set of these species yet analysed. Results The Pleistocene land barriers of the Sunda Shelf and Torres Strait were associated with old ( 〉 0.5 Myr) divergence times. The western and eastern boundaries of the Halmahera Eddy were also locations of significant, but more recent, divergence. No gene flow was detected across any of the four barriers tested. Larval dispersal distances between sampling sites were significant predictors of T. crocea population structure, accounting for differentiation above and beyond the contribution of barriers. We further delineated the species range of T. noae and showed that its two known clades are sympatric in central Indonesia. Main conclusions The strong signature of historical barriers on genetic differentiation argues against the assumption that Indo‐Pacific Tridacna are open meta‐populations. Despite similar life histories, T. maxima and T. crocea differ in their mt DNA population structure. The widespread species ( T. maxima ) exhibits population structure linked solely with historical factors, whereas T. crocea's population structure reflects both historical factors and LD distances.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    URL: Article
    DOI: 10.1111/jbi.2018.45.issue-4
    DOI: 10.1111/jbi.13163
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 188963-1
    detail.hit.zdb_id: 2020428-0
    SSG: 12
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