1
|
Siregar IZ, Majiidu M, Dwiyanti FG, Harnelly E, Damayanti R, Karlinasari L, Rafi M, Septaningsih DA, Parker-Forney M. Collecting Wood Core Samples from Macassar Ebony (Diospyros celebica Bakh.) for Multi-Purpose Analysis using Pickering Punch. MethodsX 2022; 9:101728. [PMID: 35677845 PMCID: PMC9168166 DOI: 10.1016/j.mex.2022.101728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 05/08/2022] [Indexed: 11/02/2022] Open
Abstract
Sample collection activities for a study of population genetics across the natural distribution of targeted tree species require a lot of resources, mainly if repeated field visits are necessary. Conventionally, population genetic studies use good sample material like leaves. In addition, cambium or small pieces of fresh wood can be used to replace leaf samples. Currently, restrictions from the permit regulation have caused only a limited number of samples that can be collected. Therefore, efficient use of samples must be designed to maximize their uses for research. Due to the small amount of successfully sampled materials, hence there are limitations to extend their uses for other analyses and are often sufficient only for genetic analysis. Therefore, innovation in sampling methods using pickering punch (https://www.agroisolab.com/pickering-punch) to collect ebony wood cores in this study is required to cover multi-analyses not only limited to genetics but also for other analyses such as isotopes, near-infrared spectroscopy (NIRs), anatomy, and chemical compounds.Pickering punch is recommended for efficient wood core sample collection from ebony standing trees. 323 wood core samples were successfully collected from 16 natural populations across Celebes (Sulawesi). Multi-analyses studies on sampled wood cores are possible for ebony wood identification (e.g., species and origin/provenance).
Collapse
|
2
|
Matra DD, Fathoni MAN, Majiidu M, Wicaksono H, Sriyono A, Gunawan G, Susanti H, Sari R, Fitmawati F, Siregar IZ, Widodo WD, Poerwanto R. The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm. Sci Rep 2021; 11:19766. [PMID: 34611275 PMCID: PMC8492637 DOI: 10.1038/s41598-021-99381-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/23/2021] [Indexed: 11/09/2022] Open
Abstract
Mangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi's genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.
Collapse
Affiliation(s)
- Deden Derajat Matra
- Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Bogor, Indonesia.
- Molecular Science Research Group, Advanced Research Laboratory, Bogor Agricultural University (IPB University), Bogor, Indonesia.
| | - Muh Agust Nur Fathoni
- Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Bogor, Indonesia
| | - Muhammad Majiidu
- Molecular Science Research Group, Advanced Research Laboratory, Bogor Agricultural University (IPB University), Bogor, Indonesia
| | - Hanif Wicaksono
- Tunas Meratus Conservation Organization of South Kalimantan, Kandangan, Indonesia
| | - Agung Sriyono
- Banua Botanical Garden, Province of South Kalimantan, Banjarbaru, Indonesia
| | - Gunawan Gunawan
- Department of Biology, Faculty of Mathematics and Natural Sciences, Lambung Mangkurat University, Banjarbaru, Indonesia
| | - Hilda Susanti
- Department of Agronomy, Faculty of Agriculture, Lambung Mangkurat University, Banjarbaru, Indonesia
| | - Rismita Sari
- Research Centre for Plant Conservation and Botanic Gardens-Indonesian Institute of Sciences (LIPI), Bogor, Indonesia
| | - Fitmawati Fitmawati
- Department of Biology, Faculty of Mathematics and Natural Sciences, Riau University, Pekanbaru, Indonesia
| | - Iskandar Zulkarnaen Siregar
- Molecular Science Research Group, Advanced Research Laboratory, Bogor Agricultural University (IPB University), Bogor, Indonesia
- Department of Silviculture, Faculty of Forestry and Environment, Bogor Agricultural University (IPB University), Bogor, Indonesia
| | - Winarso Drajad Widodo
- Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Bogor, Indonesia
| | - Roedhy Poerwanto
- Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB University), Bogor, Indonesia
| |
Collapse
|
3
|
Siregar IZ, Dwiyanti FG, Pratama R, Matra DD, Majiidu M. Generating long-read sequences using Oxford Nanopore Technology from Diospyros celebica genomic DNA. BMC Res Notes 2021; 14:75. [PMID: 33640010 PMCID: PMC7913452 DOI: 10.1186/s13104-021-05484-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/12/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Development of sequencing technology has opened up vast opportunities for tree genomic research in the tropics. One of the aforesaid technologies named ONT (Oxford Nanopore Technology) has attracted researchers in undertaking testings and experiments due to its affordability and accessibility. To the best of our knowledge, there has been no published reports on the use of ONT for genomic analysis of Indonesian tree species. This progress is promising for further improvement in order to acquire more genomic data for research purposes. Therefore, the present study was carried out to determine the effectiveness of ONT in generating long-read DNA sequences using DNA isolated from leaves and wood cores of Macassar ebony (Diospyros celebica Bakh.). DATA DESCRIPTION Long-read sequences data of leaves and wood cores of Macassar ebony were generated by using the MinION device and MinKnow v3.6.5 (ONT). The obtained data, as the first long-read sequence dataset for Macassar ebony, is of great importance to conserve the genetic diversity, understanding the molecular mechanism, and sustainable use of plant genetic resources for downstream applications.
Collapse
Affiliation(s)
- Iskandar Zulkarnaen Siregar
- Department of Silviculture, Faculty of Forestry and Environment, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Molecular Science Research Group, Advanced Research Laboratory, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Fifi Gus Dwiyanti
- Department of Silviculture, Faculty of Forestry and Environment, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Molecular Science Research Group, Advanced Research Laboratory, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Rahadian Pratama
- Molecular Science Research Group, Advanced Research Laboratory, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Department of Biochemistry, Faculty of Mathematic and Natural Science, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Deden Derajat Matra
- Molecular Science Research Group, Advanced Research Laboratory, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Muhammad Majiidu
- Molecular Science Research Group, Advanced Research Laboratory, IPB University (Bogor Agricultural University), Bogor, Indonesia
| |
Collapse
|
4
|
Siregar IZ, Dwiyanti FG, Siregar UJ, Matra DD. De novo assembly of transcriptome dataset from leaves of Dryobalanops aromatica (Syn. Dryobalanops sumatrensis) seedlings grown in two contrasting potting media. BMC Res Notes 2020; 13:405. [PMID: 32859262 PMCID: PMC7456001 DOI: 10.1186/s13104-020-05251-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022] Open
Abstract
Objectives Efforts to restore tropical peat swamp forests in Indonesia face huge challenges of potential failures due to socio-economic factors and ecological dynamics attributed to lack of knowledge on the adaptive mechanisms of potential tree species such as Kapur (Dryobalanops aromatica C.F.Gaertn Syn. Dryobalanops sumatrensis J.F. Gmelin A.J.G.H Kostermans). This species is a multi-purpose tree that, commonly grows in mineral soils, but also in peat swamp as previously reported, which raised a fundamental question regarding the molecular mechanism of this adaptation. Therefore, a dataset was created aiming to detect candidates of adaptive genes in D. aromatica seedlings, cultivated in two contrasting potting media, namely mineral soil and peat media, based on RNA Sequencing Transcriptome Analysis. Data description The RNA transcriptome data of D. aromatica’s seedlings derived from young leaves of three one-year-old seedlings, raised in each dry mineral soil media and peat media, were generated by using Illumina HiSeq 4000 platform in NovogenAIT, Singapore. The acquired data, as the first transcriptome dataset for D. aromatica, is of a great importance in understanding molecular mechanism and responses of the involved genes of D. aromatica to the contrasting, growing potting media conditions that could also be useful to generate molecular markers.
Collapse
Affiliation(s)
- Iskandar Zulkarnaen Siregar
- Department of Silviculture, Faculty of Forestry and Environment, IPB University (Bogor Agricultural University), Bogor, Indonesia.
| | - Fifi Gus Dwiyanti
- Department of Silviculture, Faculty of Forestry and Environment, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Ulfah Juniarti Siregar
- Department of Silviculture, Faculty of Forestry and Environment, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Deden Derajat Matra
- Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University (Bogor Agricultural University), Bogor, Indonesia
| |
Collapse
|
5
|
Pramono AA, Palupi ER, Siregar IZ, Kusmana C. Characteristics of Surian Flower, Fruit and Seed Productions (Toona sinensis (A. Juss.) M. Roem.) in Sumedang, West Java. Trop Life Sci Res 2016; 27:77-91. [PMID: 27019683 PMCID: PMC4807964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Abstract
Community forest development requires a constant supply of high-quality seeds. In addition, sound management of Toona sinensis (surian) seed sources requires a deep understanding of factors affecting seed production. This present study investigated the reproduction characteristics of surian, including flower, fruit and seed productions, variations in the productions of fruits and seeds among trees and among branches, and dendrometric factors that influence the productions of fruits and seeds. Flower production characteristics were observed in 99 panicles, fruit production characteristics were observed in 128 panicles, and seed characteristics were evaluated based on 890 fruits. The number of fruits per panicle ranged from 38 to 646. The number of seeds in fruits ranged from 1 to 35. Fruit size was correlated to the number of filled seeds following a quadratic regression equation. The optimal number of filled seeds was 20 per fruit. Stem diameter, crown width, crown base height, and the number of sub-branches positively influenced the production of panicles per tree, while the crown base height (of the tree) negatively affected the fruit set.
Collapse
Affiliation(s)
- Agus Astho Pramono
- Forest Tree Seed Technology Research Institute, Forestry Research Development Agency, Ministry of Forestry, Bogor, Indonesia
| | - Endah Retno Palupi
- Department of Agronomy and Horticulture, Bogor Agricultural University, Bogor, Indonesia
| | | | - Cecep Kusmana
- Department of Tropical Silviculture, Bogor Agricultural University, Bogor, Indonesia
| |
Collapse
|
6
|
Irmayanti L, Zulkarnaen Siregar I, Pamoengkas P. Spatial Variability of Fruit and Seedling Growth of Mindi (Melia azedarach L.) in Community Forest, West Java, Indonesia. JTLS 2015. [DOI: 10.11594/jtls.05.03.09] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
|