@misc{ApriyantoCompartFettke2022, author = {Apriyanto, Ardha and Compart, Julia and Fettke, J{\"o}rg}, title = {A review of starch, a unique biopolymer - structure, metabolism and in planta modifications}, series = {Plant science : an international journal of experimental plant biology}, volume = {318}, journal = {Plant science : an international journal of experimental plant biology}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0168-9452}, doi = {10.1016/j.plantsci.2022.111223}, pages = {8}, year = {2022}, abstract = {Starch is a complex carbohydrate polymer produced by plants and especially by crops in huge amounts. It consists of amylose and amylopectin, which have alpha-1,4-and alpha-1,6-linked glucose units. Despite this simple chemistry, the entire starch metabolism is complex, containing various (iso)enzymes/proteins. However, whose interplay is still not yet fully understood. Starch is essential for humans and animals as a source of nutrition and energy. Nowadays, starch is also commonly used in non-food industrial sectors for a variety of purposes. However, native starches do not always satisfy the needs of a wide range of (industrial) applications. This review summarizes the structural properties of starch, analytical methods for starch characterization, and in planta starch modifications.}, language = {en} } @article{ApriyantoCompartZimmermannetal.2022, author = {Apriyanto, Ardha and Compart, Julia and Zimmermann, Vincent and Alseekh, Saleh and Fernie, Alisdair and Fettke, J{\"o}rg}, title = {Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.)}, series = {Food chemistry}, volume = {393}, journal = {Food chemistry}, publisher = {Elsevier}, address = {New York, NY [u.a.]}, issn = {0308-8146}, doi = {10.1016/j.foodchem.2022.133361}, pages = {11}, year = {2022}, abstract = {Oil palm (Elaeis guineensis Jacq.) is the most productive oil-producing crop per hectare of land. The oil that accumulates in the mesocarp tissue of the fruit is the highest observed among fruit-producing plants. A comparative analysis between high-, medium-, and low-yielding oil palms, particularly during fruit development, revealed unique characteristics. Metabolomics analysis was able to distinguish accumulation patterns defining of the various developmental stages and oil yield. Interestingly, high- and medium-yielding oil palms exhibited substantially increased sucrose levels compared to low-yielding palms. In addition, parameters such as starch granule morphology, granule size, total starch content, and starch chain length distribution (CLD) differed significantly among the oil yield categories with a clear correlation between oil yield and various starch parameters. These results provide new insights into carbohydrate and starch metabolism for biosynthesis of oil palm fruits, indicating that starch and sucrose can be used as novel, easy-to-analyze, and reliable biomarker for oil yield.}, language = {en} } @phdthesis{Apriyanto2023, author = {Apriyanto, Ardha}, title = {Analysis of starch metabolism in source and sink tissue of plants}, school = {Universit{\"a}t Potsdam}, pages = {166}, year = {2023}, abstract = {Starch is an essential biopolymer produced by plants. Starch can be made inside source tissue (such as leaves) and sink tissue (such as fruits and tubers). Nevertheless, understanding how starch metabolism is regulated in source and sink tissues is fundamental for improving crop production. Despite recent advances in the understanding of starch and its metabolism, there is still a knowledge gap in the source and sink metabolism. Therefore, this study aimed to summarize the state of the art regarding starch structure and metabolism inside plants. In addition, this study aimed to elucidate the regulation of starch metabolism in the source tissue using the leaves of a model organism, Arabidopsis thaliana, and the sink tissue of oil palm (Elaeis guineensis) fruit as a commercial crop. The research regarding the source tissue will focus on the effect of the blockage of starch degradation on the starch parameter in leaves, especially in those of A. thaliana, which lack both disproportionating enzyme 2 (DPE2) and plastidial glucan phosphorylase 1 (PHS1) (dpe2/phs1). The additional elimination of phosphoglucan water dikinase (PWD), starch excess 4 (SEX4), isoamylase 3 (ISA3), and disproportionating enzyme 1 (DPE1) in the dpe2/phs1 mutant background demonstrates the alteration of starch granule number per chloroplast. This study provides insights into the control mechanism of granule number regulation in the chloroplast. The research regarding the sink tissue will emphasize the relationship between starch metabolism and the lipid metabolism pathway in oil palm fruits. This study was conducted to observe the alteration of starch parameters, metabolite abundance, and gene expression during oil palm fruit development with different oil yields. This study shows that starch and sucrose can be used as biomarkers for oil yield in oil palms. In addition, it is revealed that the enzyme isoforms related to starch metabolism influence the oil production in oil palm fruit. Overall, this thesis presents novel information regarding starch metabolism in the source tissue of A.thaliana and the sink tissue of E.guineensis. The results shown in this thesis can be applied to many applications, such as modifying the starch parameter in other plants for specific needs.}, language = {en} } @article{ApriyantoTambunan2021, author = {Apriyanto, Ardha and Tambunan, Van Basten}, title = {Draft genome sequence, annotation, and SSR mining data of Elaeidobius kamerunicus Faust., an essential oil palm pollinating weevil}, series = {Data in Brief}, volume = {34}, journal = {Data in Brief}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2352-3409}, doi = {10.1016/j.dib.2021.106745}, pages = {7}, year = {2021}, abstract = {Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) is an essential insect pollinator in oil palm plantations. Recently, researches have been undertaken to improve pollination efficiency using this species. A fundamental understanding of the genes related to this pollinator behavior is necessary to achieve this goal. Here, we present the draft genome sequence, annotation, and simple sequence repeat (SSR) marker data for this pollinator. In total, 34.97 Gb of sequence data from one male individual (monoisolate) were obtained using Illumina short-read platform NextSeq 500. The draft genome assembly was found to be 269.79 Mb and about 59.9\% of completeness based on Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment. Functional gene annotation predicted about 26.566 genes. Also, a total of 281.668 putative SSR markers were identified. This draft genome sequence is a valuable resource for understanding the population genetics, phylogenetics, dispersal patterns, and behavior of this species.}, language = {en} } @article{ApriyantoAjambang2022, author = {Apriyanto, Ardha and Ajambang, Walter}, title = {Transcriptomic dataset for early inflorescence stages of oil palm in response to defoliation stress}, series = {Data in Brief}, volume = {41}, journal = {Data in Brief}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2352-3409}, doi = {10.1016/j.dib.2022.107914}, pages = {6}, year = {2022}, abstract = {Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.}, language = {en} } @article{ApriyantoTambunan2020, author = {Apriyanto, Ardha and Tambunan, Van Basten}, title = {The complete mitochondrial genome of oil palm pollinating weevil, Elaeidobius kamerunicus Faust}, series = {Mitochondrial DNA: Part B}, volume = {5}, journal = {Mitochondrial DNA: Part B}, number = {3}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {2380-2359}, doi = {10.1080/23802359.2020.1823899}, pages = {3450 -- 3452}, year = {2020}, abstract = {Elaeidobius kamerunicusis the most important insect pollinator in oil palm plantations. In this study, the mitochondrial genome (mitogenome) ofE. kamerunicus(17.729 bp), a member of the Curculionidae family, will be reported. The mitogenome consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a putative control region (CR). Phylogenetic analysis based on 13 protein-coding genes (PCGs) using maximum Likelihood (ML) methods indicated thatE. kamerunicusbelongs to the Curculionidae family. This mitochondrial genome provides essential information for understanding genetic populations, phylogenetics, molecular evolution, and other biological applications in this species.}, language = {en} } @article{LiApriyantoFloresCastellanosetal.2022, author = {Li, Xiaoping and Apriyanto, Ardha and Flores Castellanos, Junio and Compart, Julia and Muntaha, Sidratul Nur and Fettke, J{\"o}rg}, title = {Dpe2/phs1 revealed unique starch metabolism with three distinct phases characterized by different starch granule numbers per chloroplast, allowing insights into the control mechanism of granule number regulation by gene co-regulation and metabolic profiling}, series = {Frontiers in Plant Science}, journal = {Frontiers in Plant Science}, publisher = {Frontiers}, address = {Lausanne, Schweiz}, issn = {1664-462X}, doi = {10.3389/fpls.2022.1039534}, pages = {1 -- 16}, year = {2022}, abstract = {An Arabidopsis mutant lacking both the cytosolic Disproportionating enzyme 2 (DPE2) and the plastidial glucan Phosphorylase 1 (PHS1) revealed a unique starch metabolism. Dpe2/phs1 has been reported to have only one starch granule number per chloroplast when grown under diurnal rhythm. For this study, we analyzed dpe2/phs1 in details following the mutant development, and found that it showed three distinct periods of granule numbers per chloroplast, while there was no obvious change observed in Col-0. In young plants, the starch granule number was similar to that in Col-0 at first, and then decreased significantly, down to one or no granule per chloroplast, followed by an increase in the granule number. Thus, in dpe2/phs1, control over the starch granule number is impaired, but it is not defective in starch granule initiation. The data also indicate that the granule number is not fixed, and is regulated throughout plant growth. Furthermore, the chloroplasts revealed alterations during these three periods, with a partially strong aberrant morphology in the middle phase. Interestingly, the unique metabolism was perpetuated when starch degradation was further impaired through an additional lack of Isoamylase 3 (ISA3) or Starch excess 4 (SEX4). Transcriptomic studies and metabolic profiling revealed the co-regulation of starch metabolism-related genes and a clear metabolic separation between the periods. Most senescence-induced genes were found to be up-regulated more than twice in the starch-less mature leaves. Thus, dpe2/phs1 is a unique plant material source, with which we may study starch granule number regulation to obtain a more detailed understanding.}, language = {en} } @article{MuntahaLiCompartetal.2022, author = {Muntaha, Sidratul Nur and Li, Xiaoping and Compart, Julia and Apriyanto, Ardha and Fettke, J{\"o}rg}, title = {Carbon pathways during transitory starch degradation in Arabidopsis differentially affect the starch granule number and morphology in the dpe2/phs1 mutant background}, series = {Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology}, volume = {180}, journal = {Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology}, publisher = {Elsevier}, address = {Paris}, issn = {0981-9428}, doi = {10.1016/j.plaphy.2022.03.033}, pages = {35 -- 41}, year = {2022}, abstract = {The Arabidopsis knockout mutant lacking both the cytosolic disproportionating enzyme 2 (DPE2) and the plastidial phosphorylase (PHS1) had a dwarf-growth phenotype, a reduced and uneven distribution of starch within the plant rosettes, and a lower starch granule number per chloroplast under standard growth conditions. In contrast, a triple mutant impaired in starch degradation by its additional lack of the glucan, water dikinase (GWD) showed improved plant growth, a starch-excess phenotype, and a homogeneous starch distribution. Furthermore, the number of starch granules per chloroplast was increased and was similar to the wild type. We concluded that ongoing starch degradation is mainly responsible for the observed phenotype of dpe2/phs1. Next, we generated two further triple mutants lacking either the phosphoglucan, water dikinase (PWD), or the disproportionating enzyme 1 (DPE1) in the background of the double mutant. Analysis of the starch metabolism revealed that even minor ongoing starch degradation observed in dpe2/phs1/pwd maintained the double mutant phenotype. In contrast, an additional blockage in the glucose pathway of starch breakdown, as in dpe2/phs1/ dpe1, resulted in a nearly starch-free phenotype and massive chloroplast degradation. The characterized mutants were discussed in the context of starch granule formation.}, language = {en} }