scholarly journals De novo sequencing of the transcriptome of Fargesia macclureana (Poaceae) reveals regulators of the floral transition and ecological adaptations to high altitude

2019 ◽  
Author(s):  
Ying Li ◽  
Chunxia Zhang ◽  
Kebin Yang ◽  
Jingjing Shi ◽  
Yulong Ding ◽  
...  
Keyword(s):  
Flowering Time ◽  
De Novo ◽  
Extreme Environments ◽  
Floral Transition ◽  
Tibet Plateau ◽  
Growing Period ◽  
Time Control ◽  
Illumina Deep Sequencing ◽  
Flowering Time Control ◽  
Plant Pathogen Interactions

Abstract Background Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2,000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigated the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs, and DEUs) and a weighted gene co-expression network analysis (WGCNA) revealed that changes in expressions of unigenes related to the circadian cycle may account for the differences in the floral transition of F. macclureana after being transplanted from the QTP to a laboratory outside. In addition, differences in active carbohydrate metabolism and signal transduction between the flowering and non-flowering plants. Moreover, we detected the expression of unigenes related to DNA repair and plant-pathogen interactions, which may be of adaptive importance. Finally, we detected 9,296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.

scholarly journals De novo sequencing of the transcriptome of Fargesia macclureana (Poaceae) reveals regulators of the floral transition and ecological adaptations to high altitude

2019 ◽  
Author(s):  
Ying Li ◽  
Chunxia Zhang ◽  
Kebin Yang ◽  
Jingjing Shi ◽  
Yulong Ding ◽  
...  
Keyword(s):  
Flowering Time ◽  
De Novo ◽  
Extreme Environments ◽  
Floral Transition ◽  
Tibet Plateau ◽  
Growing Period ◽  
Time Control ◽  
Illumina Deep Sequencing ◽  
Flowering Time Control ◽  
Plant Pathogen Interactions

Abstract Background Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2,000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigated the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs, and DEUs) and a weighted gene co-expression network analysis (WGCNA) revealed that changes in expressions of unigenes related to the circadian cycle may account for the differences in the floral transition of F. macclureana after being transplanted from the QTP to a laboratory outside. In addition, there were differences in active carbohydrate metabolism and signal transduction between the flowering and non-flowering plants. Moreover, we detected the expression of unigenes related to DNA repair and plant-pathogen interactions, which may be of adaptive importance. Finally, we detected 9,296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.

scholarly journals De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)

2020 ◽  
Author(s):  
Ying Li ◽  
Chunxia Zhang ◽  
Kebin Yang ◽  
Jingjing Shi ◽  
Yulong Ding ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Flowering Time ◽  
De Novo ◽  
Extreme Environments ◽  
Tibet Plateau ◽  
Kegg Pathways ◽  
Growing Period ◽  
Time Control ◽  
Illumina Deep Sequencing ◽  
Flowering Time Control

Abstract Background: Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2,000 ~ 3,800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results: Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9,296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions: F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.

scholarly journals De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ying Li ◽  
Chunxia Zhang ◽  
Kebin Yang ◽  
Jingjing Shi ◽  
Yulong Ding ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Flowering Time ◽  
De Novo ◽  
Extreme Environments ◽  
Tibet Plateau ◽  
Kegg Pathways ◽  
Growing Period ◽  
Time Control ◽  
Illumina Deep Sequencing ◽  
Flowering Time Control

Abstract Background Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.

scholarly journals De novo sequencing of the transcriptome of Fargesia macclureana (Poaceae) reveals regulators of the floral transition and ecological adaptations to high altitude

2019 ◽  
Author(s):  
Ying Li ◽  
Chunxia Zhang ◽  
Kebin Yang ◽  
Jingjing Shi ◽  
Yulong Ding ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Flowering Time ◽  
De Novo ◽  
Extreme Environments ◽  
Tibet Plateau ◽  
Kegg Pathways ◽  
Growing Period ◽  
Time Control ◽  
Illumina Deep Sequencing ◽  
Flowering Time Control

Abstract Background: Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2,000 ~ 3,800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results: Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9,296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions: F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.

scholarly journals Characterization of genes associated with TGA7 during the floral transition

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaorui Xu ◽  
Jingya Xu ◽  
Chen Yuan ◽  
Yikai Hu ◽  
Qinggang Liu ◽  
...  
Keyword(s):  
Flowering Time ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Defense Responses ◽  
Floral Transition ◽  
Differentially Expressed ◽  
Time Control ◽  
Delayed Flowering ◽  
Flowering Time Control

Abstract Background The TGACG-binding (TGA) family has 10 members that play vital roles in Arabidopsis thaliana defense responses and development. However, their involvement in controlling flowering time remains largely unknown and requires further investigation. Results To study the role of TGA7 during floral transition, we first investigated the tga7 mutant, which displayed a delayed-flowering phenotype under both long-day and short-day conditions. We then performed a flowering genetic pathway analysis and found that both autonomous and thermosensory pathways may affect TGA7 expression. Furthermore, to reveal the differential gene expression profiles between wild-type (WT) and tga7, cDNA libraries were generated for WT and tga7 mutant seedlings at 9 days after germination. For each library, deep-sequencing produced approximately 6.67 Gb of high-quality sequences, with the majority (84.55 %) of mRNAs being between 500 and 3,000 nt. In total, 325 differentially expressed genes were identified between WT and tga7 mutant seedlings. Among them, four genes were associated with flowering time control. The differential expression of these four flowering-related genes was further validated by qRT-PCR. Conclusions Among these four differentially expressed genes associated with flowering time control, FLC and MAF5 may be mainly responsible for the delayed-flowering phenotype in tga7, as TGA7 expression was regulated by autonomous pathway genes. These results provide a framework for further studying the role of TGA7 in promoting flowering.

New Nucleotide Polymorphisms in the BTC1 gene of Sugar Beet

2020 ◽  
Vol 36 (6) ◽  
pp. 49-54
Author(s):  
A.A. Nalbandyan ◽  
T.P. Fedulova ◽  
I.V. Cherepukhina ◽  
T.I. Kryukova ◽  
N.R. Mikheeva ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Flowering Time ◽  
Molecular Genetic ◽  
Bioinformatic Analysis ◽  
Early Flowering ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Substitutions ◽  
Time Control ◽  
Flowering Time Control ◽  
Exon 10

The flowering time control gene of various sugar beet plants has been studied. The BTC1 gene is a regulator for the suppressor (flowering time 1) and inducer (flowering time 2) genes of this physiological process. The F9/R9 primer pair was used for polymerase chain reaction; these primers are specific to the BTC1 gene region containing exon 9, as well as intron and exon 10. For the first time, nucleotide substitutions in exon 10 of BTC1 gene were identified in bolting sensitive samples (HF1 and BF1), which led to a change in the amino acid composition of the coded polypeptide chain. Based on the results of bioinformatic analysis, it can be assumed that certain nucleotide polymorphisms in the BTC1 gene may determine with a high probability the predisposition of sugar beet genotypes to early flowering. The use of the Geneious Prime tool for the analysis of the BTC1 gene sequences may allow the culling of genotypes prone to early flowering at early stages of selection. sugar beet, flowering gene, BTC1, genetic polymorphism, PCR, molecular genetic markers, selection

scholarly journals Message ends: RNA 3′ processing and flowering time control

2013 ◽  
Vol 65 (2) ◽  
pp. 353-363 ◽  
Author(s):  
Katarzyna Rataj ◽  
Gordon G. Simpson
Keyword(s):  
Flowering Time ◽  
Time Control ◽  
Flowering Time Control

scholarly journals Characterization of Genes Associated with TGA7 During the Floral Transition

2020 ◽  
Author(s):  
Xiaorui Xu ◽  
Jingya Xu ◽  
Chen Yuan ◽  
Yikai Hu ◽  
Qinggang Liu ◽  
...  
Keyword(s):  
Flowering Time ◽  
Expression Profiles ◽  
Plant Defence ◽  
Gene Expression Profiles ◽  
Floral Transition ◽  
Cdna Libraries ◽  
Genetic Pathways ◽  
Time Control ◽  
Pathways Analysis

Abstract BackgroundThe TGA family has ten members and plays vital roles in plant defence and development in Arabidopsis. However, involvement of TGAs in control of flowering time remains largely unknown and requires further investigation. ResultsTo study the role of TGA7 during the floral transition, we first tested phenotypes of tga7 mutant, which displayed delay-flowering phenotype under both long-day and short-day conditions. We then performed flowering genetic pathways analysis and found that both autonomous and thermosensory pathways may affect TGA7 expression. Furthermore, to reveal differential gene expression profiles between wild-type (WT) and tga7, cDNA libraries were generated for WT and tga7 mutant seedlings at 9 DAG (days after germination). For each library, deep-sequencing produced approximately 6.67 Gb of high-quality sequences with the majority (84.55%) of mRNAs between 500 and 3000 nucleotides in length. Three hundred and twenty-five differentially expressed genes (DEGs) were identified between WT and tga7 mutant seedlings. Among them, four genes are associated with flowering time control. Differential expression of the four flowering-related DEGs was further validated by qRT-PCR.ConclusionsTransciptomic sequencing coupled with flowering genetic pathways analysis provides a framework for further studying the role of TGA7 in promoting flowering.

Repeated rearrangement of the GSL‐AOP locus contributed to spatio‐temporal variation in defense chemistry in Arabidopsis

2020 ◽  
Author(s):  
Konrad Weber ◽  
Lucasz Krych ◽  
Meike Burow
Keyword(s):  
Flowering Time ◽  
Regulatory Networks ◽  
Structural Diversity ◽  
Sequence Information ◽  
Sequencing Data ◽  
Defense Compounds ◽  
Caucasus Region ◽  
Time Control ◽  
Spatio Temporal ◽  
Flowering Time Control

Abstract Plants coordinate metabolic and developmental processes with the help of genetically variable, interconnected regulatory networks. The GSL-AOP locus in Arabidopsis thaliana encodes enzymes involved in the biosynthesis of glucosinolate defense compounds and has been attributed regulatory functions e.g. in flowering time control. To correlate genetic and phenotypic variation linked to GSL-AOP, we conducted a phylogenetic analysis across 1135 accessions and found that the available short-read sequencing data does not fully resolve the structural diversity in the locus. We analyzed a selection of 74 accessions for glucosinolate profiles and flowering time under different conditions and acquired long-read sequence information for glucosinolate and flowering time loci. Especially in the Caucasus region, structural variation in GSL-AOP was associated with conditional, tissue-specific glucosinolate profiles. Variation in FLC among the Caucasian accessions correlated with variation in the flowering time response to vernalization, suggesting that local adaptation has shaped defense and development in an orchestrated manner.

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