Expressed sequence tags (ESTs) from young leaves of Metroxylon sagu

Wee, Ching Ching; Roslan, Hairul Azman

doi:10.1007/s13205-012-0048-6

Cited by 7 publications

(4 citation statements)

References 34 publications

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“…RNA isolation was carried out according to the method described by Wee and Roslan [ 15 ] while total genomic DNA was extracted from young leaves by using modified Doyle and Doyle method [ 16 ].…”

Section: Methodsmentioning

confidence: 99%

Isolation of Alcohol Dehydrogenase cDNA and Basal Regulatory Region from Metroxylon sagu

Wee

Roslan

2012

ISRN Molecular Biology

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Alcohol dehydrogenase (Adh) is a versatile enzyme involved in many biochemical pathways in plants such as in germination and stress tolerance. Sago palm is plant with much importance to the state of Sarawak as one of the most important crops that bring revenue with the advantage of being able to withstand various biotic and abiotic stresses such as heat, pathogens, and water logging. Here we report the isolation of sago palm Adh cDNA and its putative promoter region via the use of rapid amplification of cDNA ends (RACE) and genomic walking. The isolated cDNA was characterized and determined to be 1464 bp long encoding for 380 amino acids. BLAST analysis showed that the Adh is similar to the Adh1 group with 91% and 85% homology with Elaeis guineensis and Washingtonia robusta, respectively. The putative basal msAdh1 regulatory region was further determined to contain promoter signals of TATA and AGGA boxes and predicted amino acids analyses showed several Adh-specific motifs such as the two zincbinding domains that bind to the adenosine ribose of the coenzyme and binding to alcohol substrate. A phylogenetic tree was also constructed using the predicted amino acid showed clear separation of Adh from bacteria and clustered within the plant Adh group.

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Section: Methodsmentioning

confidence: 99%

Isolation of Alcohol Dehydrogenase cDNA and Basal Regulatory Region from Metroxylon sagu

Wee

Roslan

2012

ISRN Molecular Biology

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“…In recent years, the sago palm has been placed in the limelight of agricultural molecular research subsequent to the whole chloroplast genome sequencing, orgnanellar genome copy number investigation, genome survey, genome size estimation, population genetics, transcriptomics as well as proteomics (Wee & Roslan, 2012;Abbas et al, 2017;Lim et al, 2020a;Lim et al, 2020b;Nisar & Hussain, 2020;Lim et al, 2021). The origin of life is often associated with the central dogma of molecular biology and genes are deemed the building blocks of life.…”

Section: Data Descriptionmentioning

confidence: 99%

First high-quality genome assembly data of sago palm (Metroxylon sagu Rottboll)

Lim¹,

Lau²,

Chung³

et al. 2021

Preprint

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The sago palm (Metroxylon sagu Rottboll) is a all-rounder palm, it is both a tropical halophytic starch-producing palm as well as an ornamental plant. Recently, a genome survey was conducted on this palm using Illumina sequencing platform but the BUSCO genome completeness is very low (21.5%) and most of them (~78%) are either fragmented or missing. Thus, in this study, the sago palm genome completeness was further improved with the utilization of the Nanopore sequencing platform that produced longer reads. A hybrid genome assembly was conducted and the outcome was a much complete sago palm genome with BUSCO completeness achieved at as high as 97.9% with only ~2% of them either fragmented or missing. The estimated genome size of the sago palm is 509,812,790 bp in this study. A sum of 33,242 protein-coding genes were revealed from the sago palm genome and around 96.39% of them had been functionally annotated. An investigation on the carbohydrate metabolism KEGG pathways also unearthed that starch synthesis was one of the major sago palm activities. These data are indispensable for future molecular evolutionary and genome-wide association studies.

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“…Dalam bidang molekuler, Ibrahim et al, (2014) menguji efisiensi beberapa metode transformasi pada tanaman ini. Dari konstruksi pustaka cDNA dan analisis EST yang dilakukan, Wee & Roslan (2012), mengidentifikasi transkrip yang terlibat dalam metabolisme primer dan toleran stres.…”

Section: Pendahuluanunclassified

Kloning dan karakterisasi daerah promoter gen penyandi ADP glucose pyrophosphorylase dari Metroxylon sagu rendemen pati-tinggi dan -rendah [Cloning and characterization of promoter region of ADP glucose pyrophosphorylase-encoding gene from Metroxylon sagu with high- and low-starch content]

Budiani¹,

Putranto²,

Minarsih³

et al. 2016

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ADP-glucose pyrophosphorylase (AGPase) is one of the key enzymes in the starch biosynthesis. In many plants, the activity of this enzyme was reported to affect the yield and composition of the produced starch. This research is a part of an effort to develop molecular markers for early selection of high starch-yielding of sago palm. The purpose of the research was to isolate promoters of AGP gene and to analyze the differences in their DNA sequences between sago palm with high starch content (MsHS) and low starch content (MsLS). DNA was isolated and purified from the leaves of the two sago palm. The promoter region of AGP was amplified by Genome Walking technique. The specific primers were designed by Primer3 program based on the information of DNA sequence of AGP genes of sago palm from previous studies. Selected DNA fragments resulted from Genome Walking were isolated from the gel, cloned into E. coli, and analyzed its DNA sequence. DNA sequence analysis showed that one DNA fragment from MsHS (± 1500 bp) and one DNA fragment from MsLS (> 2000 bp) were confirmed as a 5’ upstream of the AGP gene. Further in silico analysis using MEME program identified various DNA motifs of cis-acting elements, which confirmed that those DNA fragment were promoter region of the gene. Preliminary analysis showed the differences in DNA sequences and motives of cis-acting elements in the promoter region of the two samples which might influence or indirectly associated with the character of the starch yield in sago palm.

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Expressed sequence tags (ESTs) from young leaves of Metroxylon sagu

Cited by 7 publications

References 34 publications

Isolation of Alcohol Dehydrogenase cDNA and Basal Regulatory Region from Metroxylon sagu

Isolation of Alcohol Dehydrogenase cDNA and Basal Regulatory Region from Metroxylon sagu

First high-quality genome assembly data of sago palm (Metroxylon sagu Rottboll)

Kloning dan karakterisasi daerah promoter gen penyandi ADP glucose pyrophosphorylase dari Metroxylon sagu rendemen pati-tinggi dan -rendah [Cloning and characterization of promoter region of ADP glucose pyrophosphorylase-encoding gene from Metroxylon sagu with high- and low-starch content]

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