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A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation

Genomics, Proteomics & Bioinformatics 2023年第3期21卷 440-454页

作者： Le Wang May Lee Zi Yi Wan Bin Bai Baoqing Ye Yuzer Alfiko Rahmadsyah Rahmadsyah sigit purwantomo Zhuojun Song Antonius Suwanto Gen Hua Yue Temasek Life Sciences Laboratory Singapore 117604Singapore Wheat Research Institute Gansu Academy of Agricultural SciencesLanzhou 730070China Biotech Lab Wilmar InternationalBekasi 17530Indonesia R&D Department Wilmar International PlantationPalembang 30118Indonesia Department of Biological Sciences National University of SingaporeSingapore 117558Singapore

The palm family(Arecaceae),consisting of2600 species,is the third most economically important family of *** African oil palm(Elaeis guineensis)is one of the most important ***,the genome sequences of palms that are currently available are still limited and ***,we report a high-quality chromosome-level reference genome of an oil palm,Dura,assembled by integrating long reads with150 genome *** assembled genome was 1.7 Gb in size,covering 94.5%of the estimated genome,of which 91.6%was assigned into 16 pseudochromosomes and 73.7%was repetitive *** on the conserved synteny with oil palm,the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal *** burst,particularly long terminal repeat retrotransposons,following the last whole-genome duplication,likely explains the genome size variation across *** analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit *** duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to ***-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses,suggesting adaptation to stresses in the new *** genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.

关键词： Oil palm Genome Evolution VIRESCENS Molecular breeding

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Association of core promoter mutations of hepatitis B virus and viral load is different in HBeAg(+) and HBeAg(-) patients

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World Journal of Gastroenterology 2011年第6期17卷 708-716页

作者： Andi Utama Marlinang Diarta Siburian sigit purwantomo Mariana Destila Bayu Intan Tri Shinta Kurniasih Susan Tai Rino Alvani Gani Laurentius Adrianus Lesmana All Sulaiman Wenny Astuti Achwan Soewignjo Soemohardjo Arnelis Nasrul Zubir Julius Syafruddin AR Lelosutan Benyamin Lukito Tantoro Harmono Molecular Epidemiology Division Mochtar Riady Institute for Nanotechnology Universitas Pelita Harapan Lippo Karawaci Tangerang 15810 Indonesia Hepatology Division Department of Intemal Medicine Faculty of Medicine University of Indonesia Jakarta 10430 Indonesia Department of Internal Medicine Mataram General Hospital Mataram 83127 Indonesia Gastroentero-Hepatology Division Department of Internal Medicine Dr. M. Jamil Hospital Padang 25127 Indonesia Gastroentero-Hepatology Division Department of Intemal Medicine Dr. Gatot Soebroto Hospital Jakarta 10410 Indonesia Department of Internal Medicine Siloam Hospital Lippo Village Tangerang 15810 Indonesia Department of Internal Medicine Dr. Moewardi Hospital Surakarta 57126 Indonesia

AIM:To identify the prevalence of hepatitis B e antigen (HBeAg) and to assess the association of hepatitis B virus (HBV) core promoter mutations and viral load in Indonesian ***:Sixty-four patients with chronic hepatitis,65 with liver cirrhosis and 50 with hepatocellular carcinoma were included in this *** and hepatitis B e antibody (HBeAb) tests were performed using enzyme-linked immunosorbent assay and the mutations were analyzed by *** load was measured by real-time polymerase chain ***:Of 179 patients,108 (60.3%) were HBeAg(-) and 86 (79.6%) of these HBeAg(-) patients had been *** A1896 mutation was not found in HBeAg(+) patients,however,this mutation was detected in 70.7% of HBeAg(-) *** mutation was frequently found when HBeAg was not expressed (87.7%),compared to that found in HBeAg seroconverted patients (65.1%).The A1899 mutation was also more prevalent in HBeAg(-) than in HBeAg(+) patients (P=0.004).The T1762/A1764 mutation was frequently found in both HBeAg(+) and HBeAg(-) patients,however,the prevalence of this mutation did not significantly differ among the two groups (P=0.054).In HBeAg(+) patients,the T1762/A1764 mutation was correlated with lower HBV DNA (P < 0.001).The A1899 mutation did not correlate with HBV DNA (P=0.609).In HBeAg(-) patients,the T1762/A1764 mutation alone was not correlated with HBV DNA (P=0.095),however,the presence of either the T1762/A1764 or A1896 mutations was associated with increased HBV DNA (P < 0.001).CONCLUSION:The percentage of HBeAg(-) patients is high in Indonesia,and most of the HBeAg(-) patients had been *** A1896 mutation was most likely the major cause of HBeAg *** T1762/A1764 mutation alone was associated with lower viral loads in HBeAg(+) patients,but not in HBeAg(-) patients.

关键词： Hepatitis B e antibody Hepatitis B e antigen Hepatitis B virus Indonesia Precore/core promoter mutations Viral load

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Hepatitis B virus subgenotypes and basal core promoter mutations in Indonesia

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World Journal of Gastroenterology 2009年第32期15卷 4028-4036页

作者： Andi Utama sigit purwantomo Marlinang Diarta Siburian Rama Dhenni Rino Alvani Gani Irsan Hasan Andri Sanityoso Upik Anderiani Miskad Fardah Akil Irawan Yusuf Wenny Astuti Achwan Soewignjo Soemohardjo Syafruddin AR Lelosutan Ruswhandi Martamala Benyamin Lukito Unggul Budihusodo Laurentius Adrianus Lesmana Ali Sulaiman Susan Tai Molecular Epidemiology Division Mochtar Riady Institute for NanotechnologyLippo KarawaciTangerangBanten 15810Indonesia Hepatology Division Department of Internal MedicineFaculty of MedicineUniversity of IndonesiaJakarta 10430Indonesia Center of Gastroentero-Hepatology Department of Internal MedicineFaculty of MedicineHasanuddin UniversityMakassar 90245Indonesia Department of Internal Medicine Mataram General HospitalMataram 83127Indonesia Gastroentero-Hepatology Division Department of Internal MedicineGatot Soebroto HospitalJakarta 10410Indonesia Department of Internal Medicine Siloam Hospital Lippo KarawaciTangerang Banten 15810Indonesia

AIM： To identify the distribution of hepatitis B virus （HBV） subgenotype and basal core promoter （BCP） mutations among patients with HBV-associated liver disease in Indonesia.METHODS： Patients with chronic hepatitis （CH, n =61）, liver cirrhosis （LC, n = 62）, and hepatocellular carcinoma （HCC, n = 48） were included in this study. HBV subgenotype was identified based on S or preS gene sequence, and mutations in the HBx gene including the overlapping BCP region were examined by direct sequencing.RESULTS： HBV genotype B （subgenotypes B2, B3, B4, 85 and B7） the major genotype in the samples, accounted for 75.4%, 71.0% and 75.0% of CH, LC and HCC patients, respectively, while the genotype C （subgenotypes C1, C2 and C3） was detected in 24.6%, 29.0%, and 25.0% of CH, LC, and HCC patients, respectively. Subgenotypes B3 （84.9%） and C1 （82.2%） were the main subgenotype in HBV genotype B and C, respectively. Serotype adw2 （84.9%） and adrq＋（89.4%） were the most prevalent in HBV genotype B and C, respectively. Double mutation （A1762T/G1764A） in the BCP was significantly higher in LC （59.7%） and HCC （54.2%） than in CH （19.7%）, suggesting that this mutation was associated with severity of liver disease. The T1753V was also higher in LC （46.8%）, but lower in HCC （22.9%） and CH （18.0%）, suggesting that this mutation may be an indicator of cirrhosis.CONCLUSION： HBV genotype B/B3 and C/C1 are the major genotypes in Indonesia. Mutations in BCP, such as A1762T/G1764A and T1753V, might have an association with manifestations of liver disease.

关键词： Basal core promoter mutation Hepatitis Bvirus Indonesia Liver disease Subgenotype

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