Comparative transcriptome analysis of developmental stages of theLimonium bicolorleaf generates insights into salt gland differentiation

2015 ◽  
Vol 38 (8) ◽  
pp. 1637-1657 ◽  
Author(s):  
FANG YUAN ◽  
MING-JU AMY LYU ◽  
BING-YING LENG ◽  
GUANG-YONG ZHENG ◽  
ZHONG-TAO FENG ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Salt Gland ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis

scholarly journals Comparing Time Series Transcriptome Data Between Plants Using A Network Module Finding Algorithm

2019 ◽  
Author(s):  
Jiyoung Lee ◽  
Lenwood S. Heath ◽  
Ruth Grene ◽  
Song Li
Keyword(s):  
Plant Species ◽  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Network Module ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
R Programming Language ◽  
Homologous Genes ◽  
R Programming

ABSTRACTComparative transcriptome analysis is the comparison of expression patterns between homologous genes in different species. Since most molecular mechanistic studies in plants have been performed in model species including Arabidopsis and rice, comparative transcriptome analysis is particularly important for functional annotation of genes in other plant species. Many biological processes, such as embryo development, are highly conserved between different plant species. The challenge is to establish one-to-one mapping of the developmental stages between two species. In this protocol, we solve this problem by converting the gene expression patterns into a co-expression network and then apply network module-finding algorithms to the cross-species co-expression network. We describe how to perform such analysis using bash scripts for preliminary data processing and R programming language, which implemented simulated annealing method for module finding. We also provide instructions on how to visualize the resulting co-expression networks across species.

scholarly journals Comparative Transcriptome Analysis of Two Races of Heterodera glycines at Different Developmental Stages

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e91634 ◽  
Author(s):  
Gaofeng Wang ◽  
Deliang Peng ◽  
Bingli Gao ◽  
Wenkun Huang ◽  
Lingan Kong ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Heterodera Glycines ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis

scholarly journals Comparative transcriptome analysis of mulberry reveals anthocyanin biosynthesis mechanisms in black (Morus atropurpurea Roxb) and white (Morus alba L) fruit genotypes

2020 ◽  
Author(s):  
Gaiqun Huang ◽  
Yichun Zeng ◽  
Ling Wei ◽  
Yongquan Yao ◽  
Jie Dai ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Morus Alba ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Early Stages ◽  
New Genes ◽  
Mulberry Fruit ◽  
Late Stages

Abstract To better understand anthocyanin biosynthesis in mulberry fruit, we analyzed the transcriptome of Da 10 (Morus atropurpurea Roxb, black fruit) and Baisang (Morus alba L., white fruit). Although Da 10 had high levels of cyanidin 3-O-glucoside (Cy) and pelargonidin 3-O-glucoside (Pg), Baisang contained only Cy, at low levels. Comparative transcriptome analysis resulted in the annotation of more than 27,085 genes (including 1,735 new genes). Differentially expressed genes (DEGs) were detected at three developmental stages—S1 (4,256 genes, 10 DPA), S2 (5,612 genes, 19 DPA), and S3 (5,226 genes, 28 DPA)—when comparing Da 10 and Baisang. Anthocyanin biosynthesis was associated with the expression of 15 core genes and 5 transcription factors. Relative to Baisang, Da 10 showed significant upregulation of the genes involved in the early stages (production of the intermediate compounds, chalcone and dihydroflavonol) and late stages (production of Cy and Pg) of anthocyanin biosynthesis. Baisang showed significant downregulation of the genes involved in the early stages of anthocyanin biosynthesis, and overexpression of flavanone 3-hydroxylase, resulting in the generation of quercetin and/or myricetin but not anthocyanins. Anthocyanin biosynthesis in mulberry fruit was fueled by the precursor, phenylalanine, the intermediates, chalcone and dihydroflavonol, and the products, Cy and Pg, involving the anthocyanin biosynthesis pathways.

Sign in / Sign up

Export Citation Format

Share Document