New Insight Into Early Somatic Embryogenesis of Mangosteen (Garcinia mangostana) Through de Novo and Comparative Transcriptome Analyses

Fatemeh Mahdavi-Darvari, Normah Mohd. Noor

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Somatic embryogenesis in mangosteen (Garcinia mangostana L.), an apomictic and recalcitrant-seeded species, allows stock improvement through genetic manipulation as well as mass propagation in a shortened time. To understand molecular events and gene expression during early somatic embryogenesis of mangosteen, we used RNA-Seq technology and assembled the mangosteen transcriptome de novo. Using the Trinity package, 186,203 transcripts were assembled with a mean size of 767 bp, 34.8 % of which showed significant similarities to known sequences in the GenBank non-redundant protein database. A total of 4001 transcripts were differentially expressed during somatic embryogenesis, while transcripts encoding signalling components of plant hormones such as auxin and cytokinin were significantly enriched. All the cytokinin-related genes were up-regulated, while some auxin-related genes were down-regulated and others were up-regulated. Somatic embryogenesis candidate genes such as SERK2, AGL15, CLVs, WUS and PIN1 were up-regulated in somatic embryos. Zinc finger and MADS family transcription factor genes were among the most presented differentially expressed transcripts in early somatic embryogenesis. Further qRT-PCR analysis confirmed the expression levels of the candidate genes. This study reports a de novo transcriptome assembly and analysis of gene expression during early somatic embryogenesis of mangosteen. Differentially expressed genes reveal that cytokinin has critical role in triggering somatic cell dedifferentiation and induction of somatic embryogenesis in mangosteen. The present work can serve as an important resource for further functional studies in woody plant embryogenesis.

Original languageEnglish
Pages (from-to)1-15
Number of pages15
JournalTropical Plant Biology
DOIs
Publication statusAccepted/In press - 29 Sep 2016

Fingerprint

Garcinia mangostana
mangosteens
Gene Expression Profiling
somatic embryogenesis
transcriptome
Embryonic Development
Cytokinins
cytokinins
Genes
genes
Indoleacetic Acids
auxins
cell dedifferentiation
Cell Dedifferentiation
gene expression
Gene Expression
zinc finger motif
Protein Databases
Plant Growth Regulators
somatic embryos

Keywords

  • De novo assembly
  • Differential gene expression
  • Mangosteen
  • RNA-seq Transcriptome
  • Trinity

ASJC Scopus subject areas

  • Genetics
  • Plant Science

Cite this

New Insight Into Early Somatic Embryogenesis of Mangosteen (Garcinia mangostana) Through de Novo and Comparative Transcriptome Analyses. / Mahdavi-Darvari, Fatemeh; Mohd. Noor, Normah.

In: Tropical Plant Biology, 29.09.2016, p. 1-15.

Research output: Contribution to journalArticle

@article{dfa72a7ba7914b5d9de284cf3edfecd7,
title = "New Insight Into Early Somatic Embryogenesis of Mangosteen (Garcinia mangostana) Through de Novo and Comparative Transcriptome Analyses",
abstract = "Somatic embryogenesis in mangosteen (Garcinia mangostana L.), an apomictic and recalcitrant-seeded species, allows stock improvement through genetic manipulation as well as mass propagation in a shortened time. To understand molecular events and gene expression during early somatic embryogenesis of mangosteen, we used RNA-Seq technology and assembled the mangosteen transcriptome de novo. Using the Trinity package, 186,203 transcripts were assembled with a mean size of 767 bp, 34.8 {\%} of which showed significant similarities to known sequences in the GenBank non-redundant protein database. A total of 4001 transcripts were differentially expressed during somatic embryogenesis, while transcripts encoding signalling components of plant hormones such as auxin and cytokinin were significantly enriched. All the cytokinin-related genes were up-regulated, while some auxin-related genes were down-regulated and others were up-regulated. Somatic embryogenesis candidate genes such as SERK2, AGL15, CLVs, WUS and PIN1 were up-regulated in somatic embryos. Zinc finger and MADS family transcription factor genes were among the most presented differentially expressed transcripts in early somatic embryogenesis. Further qRT-PCR analysis confirmed the expression levels of the candidate genes. This study reports a de novo transcriptome assembly and analysis of gene expression during early somatic embryogenesis of mangosteen. Differentially expressed genes reveal that cytokinin has critical role in triggering somatic cell dedifferentiation and induction of somatic embryogenesis in mangosteen. The present work can serve as an important resource for further functional studies in woody plant embryogenesis.",
keywords = "De novo assembly, Differential gene expression, Mangosteen, RNA-seq Transcriptome, Trinity",
author = "Fatemeh Mahdavi-Darvari and {Mohd. Noor}, Normah",
year = "2016",
month = "9",
day = "29",
doi = "10.1007/s12042-016-9182-3",
language = "English",
pages = "1--15",
journal = "Tropical Plant Biology",
issn = "1935-9756",
publisher = "Springer New York",

}

TY - JOUR

T1 - New Insight Into Early Somatic Embryogenesis of Mangosteen (Garcinia mangostana) Through de Novo and Comparative Transcriptome Analyses

AU - Mahdavi-Darvari, Fatemeh

AU - Mohd. Noor, Normah

PY - 2016/9/29

Y1 - 2016/9/29

N2 - Somatic embryogenesis in mangosteen (Garcinia mangostana L.), an apomictic and recalcitrant-seeded species, allows stock improvement through genetic manipulation as well as mass propagation in a shortened time. To understand molecular events and gene expression during early somatic embryogenesis of mangosteen, we used RNA-Seq technology and assembled the mangosteen transcriptome de novo. Using the Trinity package, 186,203 transcripts were assembled with a mean size of 767 bp, 34.8 % of which showed significant similarities to known sequences in the GenBank non-redundant protein database. A total of 4001 transcripts were differentially expressed during somatic embryogenesis, while transcripts encoding signalling components of plant hormones such as auxin and cytokinin were significantly enriched. All the cytokinin-related genes were up-regulated, while some auxin-related genes were down-regulated and others were up-regulated. Somatic embryogenesis candidate genes such as SERK2, AGL15, CLVs, WUS and PIN1 were up-regulated in somatic embryos. Zinc finger and MADS family transcription factor genes were among the most presented differentially expressed transcripts in early somatic embryogenesis. Further qRT-PCR analysis confirmed the expression levels of the candidate genes. This study reports a de novo transcriptome assembly and analysis of gene expression during early somatic embryogenesis of mangosteen. Differentially expressed genes reveal that cytokinin has critical role in triggering somatic cell dedifferentiation and induction of somatic embryogenesis in mangosteen. The present work can serve as an important resource for further functional studies in woody plant embryogenesis.

AB - Somatic embryogenesis in mangosteen (Garcinia mangostana L.), an apomictic and recalcitrant-seeded species, allows stock improvement through genetic manipulation as well as mass propagation in a shortened time. To understand molecular events and gene expression during early somatic embryogenesis of mangosteen, we used RNA-Seq technology and assembled the mangosteen transcriptome de novo. Using the Trinity package, 186,203 transcripts were assembled with a mean size of 767 bp, 34.8 % of which showed significant similarities to known sequences in the GenBank non-redundant protein database. A total of 4001 transcripts were differentially expressed during somatic embryogenesis, while transcripts encoding signalling components of plant hormones such as auxin and cytokinin were significantly enriched. All the cytokinin-related genes were up-regulated, while some auxin-related genes were down-regulated and others were up-regulated. Somatic embryogenesis candidate genes such as SERK2, AGL15, CLVs, WUS and PIN1 were up-regulated in somatic embryos. Zinc finger and MADS family transcription factor genes were among the most presented differentially expressed transcripts in early somatic embryogenesis. Further qRT-PCR analysis confirmed the expression levels of the candidate genes. This study reports a de novo transcriptome assembly and analysis of gene expression during early somatic embryogenesis of mangosteen. Differentially expressed genes reveal that cytokinin has critical role in triggering somatic cell dedifferentiation and induction of somatic embryogenesis in mangosteen. The present work can serve as an important resource for further functional studies in woody plant embryogenesis.

KW - De novo assembly

KW - Differential gene expression

KW - Mangosteen

KW - RNA-seq Transcriptome

KW - Trinity

UR - http://www.scopus.com/inward/record.url?scp=84989183223&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84989183223&partnerID=8YFLogxK

U2 - 10.1007/s12042-016-9182-3

DO - 10.1007/s12042-016-9182-3

M3 - Article

AN - SCOPUS:84989183223

SP - 1

EP - 15

JO - Tropical Plant Biology

JF - Tropical Plant Biology

SN - 1935-9756

ER -