scholarly journals Transcriptome analysis of maca (Lepidium meyenii ) root at different developmental stages

2018 ◽  
Vol 6 (12) ◽  
pp. e01206 ◽  
Author(s):  
Rui-Guang Shang ◽  
Pu Yang ◽  
Bing-Yi Wang ◽  
Zun-Ling Zhao
Keyword(s):  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Lepidium Meyenii

scholarly journals Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hangxia Jin ◽  
Xiaomin Yu ◽  
Qinghua Yang ◽  
Xujun Fu ◽  
Fengjie Yuan
Keyword(s):  
Developmental Stage ◽  
Phytic Acid ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

scholarly journals Identification, Expression and Evolution of Short-Chain Dehydrogenases/Reductases in Nile Tilapia (Oreochromis niloticus)

2021 ◽  
Vol 22 (8) ◽  
pp. 4201
Author(s):  
Shuai Zhang ◽  
Lang Xie ◽  
Shuqing Zheng ◽  
Baoyue Lu ◽  
Wenjing Tao ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Tandem Duplication ◽  
Developmental Stages ◽  
Short Chain ◽  
Sexually Dimorphic ◽  
Physiological Processes ◽  
Genome Wide ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Tandem Duplications

The short-chain dehydrogenases/reductases (SDR) superfamily is involved in multiple physiological processes. In this study, genome-wide identification and comprehensive analysis of SDR superfamily were carried out in 29 animal species based on the latest genome databases. Overall, the number of SDR genes in animals increased with whole genome duplication (WGD), suggesting the expansion of SDRs during evolution, especially in 3R-WGD and polyploidization of teleosts. Phylogenetic analysis indicated that vertebrates SDRs were clustered into five categories: classical, extended, undefined, atypical, and complex. Moreover, tandem duplication of hpgd-a, rdh8b and dhrs13 was observed in teleosts analyzed. Additionally, tandem duplications of dhrs11-a, dhrs7a, hsd11b1b, and cbr1-a were observed in all cichlids analyzed, and tandem duplication of rdh10-b was observed in tilapiines. Transcriptome analysis of adult fish revealed that 93 SDRs were expressed in more than one tissue and 5 in one tissue only. Transcriptome analysis of gonads from different developmental stages showed that expression of 17 SDRs were sexually dimorphic with 11 higher in ovary and 6 higher in testis. The sexually dimorphic expressions of these SDRs were confirmed by in situ hybridization (ISH) and qPCR, indicating their possible roles in steroidogenesis and gonadal differentiation. Taken together, the identification and the expression data obtained in this study contribute to a better understanding of SDR superfamily evolution and functions in teleosts.

scholarly journals Transcriptome Analysis and Discovery of Genes Relevant to Development in Bradysia odoriphaga at Three Developmental Stages

PLoS ONE ◽  
2016 ◽  
Vol 11 (2) ◽  
pp. e0146812 ◽  
Author(s):  
Huanhuan Gao ◽  
Yifan Zhai ◽  
Wenbo Wang ◽  
Hao Chen ◽  
Xianhong Zhou ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Developmental Stages

scholarly journals Transcriptome analysis of different developmental stages of amphioxus reveals dynamic changes of distinct classes of genes during development

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Kevin Yi Yang ◽  
Yuan Chen ◽  
Zuming Zhang ◽  
Patrick Kwok-Shing Ng ◽  
Wayne Junwei Zhou ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Dynamic Changes

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.

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