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Biodiversitas Journal of Biological Diversity
Published by Universitas Sebelas Maret
ISSN : 1412033X     EISSN : 20854722     DOI : https://doi.org/10.13057/biodiv/d230231
Core Subject : Science, Agriculture,
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology
The Biodiversitas Journal was first published in 2000 by the Department of Biology, FMNS, Universitas Sebelas Maret, Surakarta, Indonesia, then in 2006 it was co-published by the Society for Indonesian Biodiversity and that department; since 2017 it was also hosted by Smujo. From 2003-2012 it was accredited by DGHE, Ministry of Education, R.I., since 2014 was indexed by Scopus, where DOAJ and Google Scholar was indexed first.
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Biokimia, Genetika dan Biologi Molekuler (Lain-Lain)
Articles 6,269 Documents
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Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene Sri Riani; ROMANUS EDY PRABOWO; Agus Nuryanto
Biodiversitas Journal of Biological Diversity Vol. 22 No. 3 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220349

Abstract

Abstract. Riani S, Prabowo RE, Nuryanto A. 2021. Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene. Biodiversitas 22: 1456-1466. Amphibalanus variegatus and A. reticulatus have similar external morphology. Morphological similarities can be a severe problem for direct species-level identification. The problem can be overcome through anatomy-based identification and validated through molecular barcoding. Molecular characterization using the cytochrome c oxidase 1 (COI) gene provides a useful tool for precise species identification. This study attempted to assess the molecular characteristics of morphologically similar barnacle (Amphibalanus) specimens collected at five localities in Indonesia to validate their taxonomic status. Forty-five barnacle specimens were collected during the field trips in Lampung, Jakarta, Semarang, Bali, and Lombok. The COI gene was amplified using LCO1490 and HCO2198 primers. The gene was sequenced using bidirectional sequencing at 1st base Asia. The specimens' taxonomic status was determined based on sequence identity, genetic distance, monophyly, nucleotide compositions, and nucleotides in a particular position. Shell shapes-based identification placed barnacle specimens into A. reticulatus. However, anatomical-based identification placed barnacle samples into two different anatomic groups, which was further validated by molecular data that two anatomic groups of Amphibalanus samples have significant differences in their COI gene. Based on the molecular characteristics, 43 samples were identified as A. reticulatus, while the two remaining samples were identified as A. variegatus.
Genetic diversity and relationship of husk tomato (Physalis spp.) from East Java Province revealed by SSR markers halimatus sadiyah; Sumeru Ashari; Budi Waluyo; andy Soegianto
Biodiversitas Journal of Biological Diversity Vol. 22 No. 1 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220124

Abstract

Abstract. Sadiyah H, Ashari S, Waluyo B, Soegianto A. 2021. Genetic diversity and relationship of husk tomato (Physalis spp.) from East Java Province revealed by SSR markers. Biodiversitas 22: 184-192. This study aimed to investigate the genetic diversity and relationship of Physalis spp. from East Java province, Indonesia. A total of the 33 Physalis accessions was analyzed employing 16 SSR markers. AMOVA, UPGMA clustering, and non-parametric ANOVA analyses were applied. The results showed Genetic diversity in this sample showed lower levels (He =0.171), as compared to other studies of Physalis that used different molecular markers. The dendrogram revealed the presence of five groups, the different species belong to different small groups. The two major groups consist of accessions originated from eastern Java and Madura Island, indicating that there is no significant difference between accessions from both areas although there is geographic isolation in the form of the strait. It is consistent with the low population differentiation and high genetic drift. The AMOVA revealed that 96% of the total variation came from the within-population (among accession), reflect that the accessions used in this study have high variation and valuable for plant improvement through breeding programs. It is recommended that future evaluation studies include more accession from minor accessions detected in the sample of this study to better represent the genetic diversity available in this crop.
Classical and molecular cytogenetics of Belontia hasselti (Perciformes: Osphronemidae): Insights into the ZZ/ZW sex chromosome system PATCHARAPORN CHAIYASAN; BOONYADA MINGKWAN; SITTHISAK JANTARAT; CHATMONGKON SUWANNAPOOM; MARCELO CIOFFI; THOMAS LIEHR; SUCHEELA TALUMPHAI; ALONGKLOD TANOMTONG; Weerayuth Supiwong
Biodiversitas Journal of Biological Diversity Vol. 22 No. 2 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220205

Abstract

Abstract. Chaiyasan P, Mingkwan B, Jantarat S, Suwannapoom C, Cioffi MDB, Liehr T, Talumphai S, Tanomtong A, Supiwong W. 2021. Classical and molecular cytogenetics of Belontia hasselti (Perciformes: Osphronemidae): Insights into the ZZ/ZW sex chromosome system. Biodiversitas 22: 546-554. Karyotype of Java combtail fish, Belontia hasselti, from To Daeng peat swamp forest, Narathiwat Province, southern Thailand, was studied for the first time. Mitotic chromosome preparations were prepared directly from kidney cells from ten male and ten female fish. Conventional staining, NOR banding, and molecular cytogenetics with ?uorescence in situ hybridization (FISH) using 5S and 18S rDNAs, as well as microsatellites d(CA)15 and d(CAC)10 as probes were applied. The diploid chromosome number (2n) was 48 and a female heterogametic sex chromosome system (ZZ/ZW) is suggested. The fundamental numbers (NF) were 48 and 49 in males and females, respectively. The karyotype of males comprised 48 telocentric chromosomes while the female ones were composed of one metacentric and 47 telocentric chromosomes. A single Ag-NOR-bearing chromosomal pair was identified. The NOR positions were characterized at the interstitial sub-centromeric region of pair 13, which coincided with signals of 18S rDNA and d(CAC)10 probes. The 5S rDNA signals were located at interstitial sites of the largest telocentric pair. Microsatellite d(CA)15 repeats were highly distributed throughout almost all entire chromosomes except for centromeric regions on some chromosome pairs, including sex chromosomes. The present study is a novel report for a ZZ/ZW sex chromosome system of this fish family in Thailand.
Short Communication: Presence of the vulnerable freshwater goby Sicyopus auxilimentus (Gobiidae, Sicydiinae) on Sangihe Island, Indonesia: Sicyopus auxilimentus from Sangihe Island VERYL HASAN; FITRI SIL VALEN; R. ADHARYAN ISLAMY; Maheno Widodo; ADITYA MIRZAPAHLEVI SAPTADJAJA; IZZUL ISLAM
Biodiversitas Journal of Biological Diversity Vol. 22 No. 2 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220208

Abstract

Abstract. Hasan V, Valen FS, Islamy RA, Widodo MS, Saptadjaja AM, Islam I. 2021. Short Communication: Presence of the vulnerable freshwater goby Sicyopus auxilimentus (Gobiidae, Sicydiinae) on Sangihe Island, Indonesia. Biodiversitas 22: 571-579. A single specimen of freshwater goby Sicyopus auxilimentus was photographed and collected using fish traps between 8 and 15 September 2019 in the Laine waterfall, Sangihe island district, North Sulawesi Province, Indonesia. S. auxilimentus is amphidromous that live in both freshwater and marine environments. This species is currently listed as Vulnerable (VU) within the IUCN Red List Status. The specimen was identified as male S. auxilimentus based on the coloration of the preserved specimen: background yellowish; scale edges brown; posterior flanks and caudal peduncle orange; first dorsal fin black, second dorsal fin dusky black; pectoral fin slightly brown; ventral fin slightly dusky; anal fin blackish; caudal fin dusky brown. Specific morphological features were as follows: the base of the first dorsal fin was not connected to the second dorsal fin base; distance between the base of first and second dorsal fin was generally less than half of eye diameter; ventral fin rays were fused to belly only between fifth rays; posterior margin of caudal fins rays was rounded; scales were all ctenoid; scales appeared on the caudal peduncle, and between anal and second dorsal fins; anterior to which, scales became widely spaced and did not imbricate. Meristic characters were as follows: first dorsal fin rays VI; second dorsal fin rays I+9; ventral fin rays I+5; pectoral-fin rays 14; anal-fin rays I+9; caudal-fin rays 13; scales in lateral series 13; scales in zigzag series 7; scales in transverse series backward 7; scales in transerves series forward 4. This finding is considered the first record in Sulawesi and the fifth from Indonesian waters after findings in Halmahera, Java, Bali and Lombok. This record enhances the understanding of the distribution of S. auxilimentus in Indonesian waters. Monitoring is needed to assess the possibility of Sangihe Island being a growth ground, spawning ground, and/or on the migration route of S. auxilimentus. In the Laine waterfall, Sangihe island, freshwater conditions were as follows: salinity 3.5 psu, temperature 23-25°C, and dissolved oxygen 7.7-9.2 mg/l, which were ideal habitat for S. auxilimentus. S. auxilimentus from Sangihe Island, had 0.000 genetic distance than from S. auxilimentus from Bali, while the next closest genetic distance was S. zosterophorus at genetic distance of 0.090. In addition to onsite conservation, domestication programs are needed to increase commercial availability without depending on natural catches.
Review: Winged bean (Psophocarpus tetragonolobus) cropping systems Graham Eagleton
Biodiversitas Journal of Biological Diversity Vol. 21 No. 12 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d211258

Abstract

Abstract. Eagleton GE. 2020. Review: Winged bean (Psophocarpus tetragonolobus) cropping systems. Biodiversitas 21: 5927-5946. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is a rambling, nitrogen-rich, leguminous crop of the Old-World tropics. This review of winged bean (WB) within cropping systems of Southeast Asia and Melanesia revisited four traditional roles that the crop has played: as a minor courtyard vegetable of villages and suburbs throughout the region; as a popular tuber crop in the irrigated plains of Tada-U township in Central Myanmar; as a companion crop in the mixed garden fields of Wamena in Indonesian New Guinea; and as a niche tuber crop in rotation with sweet potato near Goroka in Papua New Guinea (PNG). Drawing upon such traditions, researchers since the 1970s have identified potential new roles for winged bean. In Malaysia, vegetable pod yields up to 35 t ha-1 over a 25-week growing period have been obtained from solidly trellised, branching cultivars. Ratooning the crop through a further two cycles covers the cost of the trellising. Tubers from un-trellised field crops in Myanmar, and of staked, pruned garden crops in highland PNG have been estimated to produce crude protein yields of at least 300 kg ha-1 and 600 kg ha-1, respectively. Synergies between the gene-pools and cultural traditions would be expected to expand the range, raise the yield and stabilize the quality of tuber crop production. Researchers in Sri Lanka intercropped maize with winged bean. At optimal plant densities, they recorded a corn cob yield of 5 t ha-1 together with a cumulative winged bean fresh pod yield of 27 t ha-1. In Kentucky (380N), the combination of maize with winged bean to produce silage resulted in 11-18% greater biomass with 39-67% greater nitrogen per hectare than maize monocrop control plots. Branching winged bean cultivars have significant potential for benign, high-nitrogen cover and forage crops. Promiscuous nodulation and the development of storage root-systems compensate for slow initial top growth which then accelerates to produce a substantial yield of highly digestible leaf protein and vitamins. Hard-seededness and daylength-sensitive phenology are significant, surmountable, barriers to an expanded role for winged beans.
Characterization of banana bunchy top virus on Sumatra (Indonesia) wild banana Ruth Feti Rahayuniati; Sedyo Hartono; Susamto Somowiyarjo; Siti Subandiyah; JOHN E. THOMAS
Biodiversitas Journal of Biological Diversity Vol. 22 No. 3 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220321

Abstract

Abstract. Rahayuniati RF, Hartono S, Somowiyarjo S, Subandiyah S, Thomas JE. 2021. Characterization of banana bunchy top virus on Sumatra (Indonesia) wild banana. Biodiversitas 22: 1243-1249. Banana bunchy top virus (BBTV) has been a major constrain on banana production worldwide. This virus infection is mostly found in banana cultivation.  The study aimed to characterize the BBTV on Sumatra wild bananas. The survey to collect seeds and typical symptomatic samples had been done in 2017 and 2019 in West Sumatra, South Sumatra, and Bengkulu. The transmission test of the virus was conducted by using the viruliferous vector on four wild banana species, while the identity of BBTV confirmed by nucleotide sequences analysis using primer pairs of DNA R and DNA S. Musa acuminata subsp. sumatrana (AA) have been found naturally infected by BBTV. The transmission confirmed on M. acuminata subsp. longipetiolata, M. acuminata subsp. malacensis, M. acuminata subsp. halabanensis and Musa sp. with typical bunchy top symptoms. The incidence on test plants were 40%, 80% 20%, 20% and 20%, respectively. The virus infection on Sumatra wild bananas prolonged the incubation periods in comparison to cv Mas. BBTV of M. acuminata subsp. sumatrana is similar to the BBTV MK940788 and MN073184 from Sumatra. This is the first report of BBTV on Sumatra wild banana. The result can be used as a reference to study the resistance of the banana against BBTV.
Drought adaptive prediction in potato (Solanum tuberosum) using in vitro and in vivo approaches JANE KATHRYNE JOLANDA LAISINA; AWANG MAHARIJAYA; SOBIR SOBIR; AGUS PURWITO
Biodiversitas Journal of Biological Diversity Vol. 22 No. 2 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220204

Abstract

Abstract. Laisina JKJ, Maharijaya A, Sobir, Purwito A. 2021. Drought adaptive prediction in potato (Solanum tuberosum) using in vitro and in vivo approaches. Biodiversitas 22: 537-545. Prediction of drought adaptive potatoes requires selection indicators. This study aimed to determine in vitro selection indicators for obtaining drought adaptive potato genotypes in vitro and in vivo. The in vitro study was performed using single-node explants from seven genotypes cultured for six weeks on MS medium added with 0.2 M sorbitol to achieve the research aims. The cultures were partially observed and followed by watering the in vitro tubing medium. For the in vivo study, drought stress was applied for 21 days when the plants reached 25 days after planting (DAP) and for 14 days when the plants reached 50 DAP, then plants were irrigated again until harvesting. The results showed that plant height and root length can be used as selection indicators because they had a relative decrease below 50%, a close relationship and had the same variance with the in vitro number of tubers, in vitro tuber fresh weight and in vivo tuber fresh weight in drought stress at 25 DAP. These characters were determinant characters for the clustering pattern in the heat map cluster analysis. Based on these characters, SSI analysis was also performed and it was found that the PKHT4 was more adaptive than the PKHT6 in vitro, but the two genotypes were classified in the medium adaptive in vivo. In conclusion, plant height and root length were determined as the in vitro selection indicators in predicting drought adaptive genotypes in vivo at the plant age of 25 DAP.
Endophytic bacteria associated with rice roots from suboptimal land as plant growth promoters Nur Prihatiningsih; HERU ADI DJATMIKO; PUJI LESTARI
Biodiversitas Journal of Biological Diversity Vol. 22 No. 1 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220153

Abstract

Abstract. Prihatiningsih N, Djatmiko HA, Lestari P. 2021. Endophytic bacteria associated with rice roots from suboptimal land as plant growth promoters. Biodiversitas 22: 432-437. Endophytic bacteria directly promoted plant growth and undirectly control the pathogens. This research was aimed to evaluate endophytic bacteria associated with rice root and their activity to promote plant growth and to control rice diseases. The study was conducted at the Laboratorium of Plant Protection and experimental farm Faculty of Agriculture Jenderal Soedirman University, from April to August 2020. The endophytic bacterial from suboptimal land were evaluated for promoting plant growth with soaking seed before seedling and spraying them at 10, 20, and 30 days after transplanting. The experiment was arranged with six replications and four treatments namely control (untreated endophytic bacteria) SM1 (endophytic bacteria isolate from Somagede); SB1 and SB3 (from Sumbang). Xanthomonas oyzae pv. oryzae was nature inoculation because the experiment location is in the endemic category of bacterial leaf blight. The variables observed were the plant growth components i.e plant height, number of tillers, number of panicles, incubation period, disease intensity, infection rate and effectiveness control. The result of this research shows that endophytic bacteria from Somagede (SM1) is the best to enhance plant height and number of tillers, and suppress disease intensity, and delay of incubation period.
Effects of Caulerpa lentillifera added into culture media on the growth and nutritional values of Phronima pacifica, a natural fish-feed crustacean Vivi Endar Herawati; Pinandoyo Pinandoyo; Restiana Wisnu Ariati; Nurmanita Rismaningsih; Seto Windarto; Slamet Budi Prayitno; Y.S. Darmanto; Ocky Karna Radjasa
Biodiversitas Journal of Biological Diversity Vol. 22 No. 1 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220152

Abstract

Abstract. Herawati VE, Pinandoyo, Ariyati RW, Rismaningsih N, Windarto S, Prayitno SB, Darmanto YS, Radjasa OK. 2021. Effects of Caulerpa lentillifera added into culture media on the growth and nutritional values of Phronima pacifica, a natural fish-feed crustacean Biodiversitas 22: 424-431. Phronima pacifica is a microcrustacean commonly used as natural feed in fish farming as it has high nutrient contents and is suitable based on larval fish mouth gap size and mass cultivation capacity. However, P. pacifica is not produced optimally and its supply is inadequate, so that P. pacifica culturing techniques need to be improved. The culture of P. pacifica is mostly done using sea grape seaweed (Caulerpa lentillifera). The aim of this study was to investigate the optimal stocking density of C. lentillifera added into media culture on the growth and nutritional values of P. pacifica. We applied a complete random design experiment with four treatments of stocking density of C. lentillifera (i.e., 0 g/m2 (Control), 20 g/m2, 40 g/m2, and 60 g/m2) with 3 replicates for each treatment. The following parameters were analyzed, namely specific growth rate (SGR) of C. lentillifera, and the growth, biomass, growth rate, proximate analysis, and amino and fatty acid concentrations of P. pacifica. This study found that the addition of C. lentillifera into culture media significantly enhanced the growth of P. pacifica. The highest effect on the growth was observed in the treatment of 60 g/m2 with C. lentillifera SGR value of 4.76 ± 0.12%/day, and P. pacifica growth rate, population density and biomass of 4.41 ± 0.12 ind/day, 53.81 ± 8.79 ind/L, and 1.14 ± 0.14 g, respectively. Similarly, the highest protein and fat contained in P. pacifica was obtained in the treatment of 60 g/m2 with 60.23% protein and 10.24% fat. Furthermore, the highest fatty acid profile was C20: 5n-3 of 13.23% ± 0.08% and amino acid profile of 45.23% ± 0.01%. The application of the optimal stocking density of C. lentillifera in culture media could increase the growth and nutritional quality of P. pacifica which in turn could enhance aquaculture productivity.
Agronomic characters, genetic and phenotypic diversity coefficients, and heritability of 12 genotypes of rice Jaenudin Kartahadimaja; SETYO DWI UTOMO; ERWIN YULIADI; ABDUL KADIR SALAM; WARSONO; Anung Wahyudi
Biodiversitas Journal of Biological Diversity Vol. 22 No. 3 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220302

Abstract

Abstract. Kartahadimaja J, Utomo SD, Yuliadi E, Salam AK, Warsono, Wahyudi A. 2021. Agronomic characters, genetic and phenotypic diversity coefficients, and heritability of 12 genotypes of rice. Biodiversitas 22: 1091-1097. The achievement of national rice production is always below the target. One of the causes is the low productivity of the varieties grown due to the stagnant genetic capacity of these varieties. The assembly of new lines through breeding is one solution that can increase the genetic capacity of new varieties. Genetic diversity is one of the factors that influence the success of plant breeding. Ten new F9 rice lines were successfully assembled showing various phenotypes. The identification of the specific advantages of each of these new rice lines was based largely on the phenotypic response. The research objective was to identify the genetic advantages of each line through the analysis approach of genetic diversity coefficient (GDC), Phenotific Diversity Coefficient (PDC), and broad-sense heritability. The research was designed on a randomized completely block design (RCBD) with ten new F9 rice lines and two comparison varieties as treatments, repeated three times. The variables observed were plant height, maximum number of tillers, number of productive tillers, flowering time, harvesting time, panicle length, number of grain per panicle, number of filled grains per panicle, number of empty grain per panicle, grain length, grain width, grain thickness, and grain yield per hectare. The data were analyzed using Analysis of Variance (ANOVA), if there was a difference between the mean values, it was continued with a 5% LSD test. The results showed that (i) the genotypes tested showed wide genetic and phenotypic diversity, (ii) based on the analysis of GDC, PDC, and broad sense heritability, the appearance of phenotypes of several agronomic characters was controlled by genetic factors.

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