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Transcriptome analysis of Trunking and Non-trunking Metroxylon sagu leaf tissue

ABSTRACT: Sago palm is an important agricultural starch producing plant which contributes to the economics of Malaysia where the trunk is the main plant part which the starch is stored. However, there are sago palms that planted on peat soil failed to develop its trunk even after 17 years been planted. This phenomenon is known as 'non-trunking', which eliminates the economic value of the plants. Numeral researches have been done to address the phenomenon but the molecular mechanisms of sago palm respond toward the responsible stresses are still lacking. Therefore, in this study we collected samples from Trunking (Normal) and Non-Trunking sago palm leaf samples which planted on peat soil for total RNA extraction followed by next generation sequencing using BGISEQ-500 platform. The raw reads were cleaned and de novo assembled using TRINITY software package. Total of 40.11 Gb bases were sequenced from the sago palm leaf samples and after assembled producing 102,447 unigenes, with N50 score 1,809 bp and GC ratio of 44.34%. Unigenes by aligning with 7 (NR, NT, GO, KOG, KEGG, SwissProt & InterPro) functional databases and 65,523 (63.96%) unigenes were annotated. Functional annotation results in the detection of 46,335 Coding DNA sequences by Transdecoder. 30,039 Simple-sequence repeats distributed on 21,676 Unigenes were detected using Primer3 software, and 2,355 Transcription Factor coding Unigenes were predicted using getorf and hmmseach software. A total of 492 up-regulated and 444 down-regulated at least two-fold differential expressed gene were detected using DESeq2 algorithm with 95% confidence.

ORGANISM(S): Metroxylon sagu

PROVIDER: GSE189085 | GEO | 2021/12/13

REPOSITORIES: GEO

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Project description:Cotton (Gossypium hirsutum L) is an important crop world wide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. These reserves are not available to produce seed and fiber when cotton is usually grown as an annual crop. Analysis of developing cotton plants indicated that starch levels peaked about the time of first anthesis then began to decline. An earlier peak of levels of starch was occasionally observed and in some greenhouse-grown samples starch increased 2 week after first bloom. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with carbohydrate metabolism, transcription activity and the proteasome. Genes associated with starch synthesis, starch degradation, sucrose metabolism, hexose metabolism, raffinose synthesis and trehalose synthesis increased in expression in starch accumulating tissues. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in relevant tissues. We propose that altering expressions of genes and pathways identified in this work could be used to more efficiently mobilize stored carbohydrate to fiber production. Keywords: starch accumulating, stem, root Genes expression was compared between cotton stems that were low in starch and accumulating starch. Gene expression was also compared between cotton roots that were low in starch and accumulating starch. A total of three microarrays were used. One dye swap was used. Material from the field were harvested 2 weeks apart. Greenhouse grown material were planted at two week intervals and harvested at the same time. NOTE that the channel representing the low starch material only gave about half of the total signal than the high starch samples. QPCR of 9 genes confirmed differential expression of 8 of them. QPCR also confirmed similar expression of two genes not predicted to be differentially expressed by the microarray analysis. Therefore no correction was made for the apparent difference in the hybridization of high and low starch samples.

Dataset Information

Transcriptome analysis of Trunking and Non-trunking Metroxylon sagu leaf tissue

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