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

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.

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

10.21203/rs.2.10521/v4 ◽

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

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

BMC Genomics ◽

10.1186/s12864-019-6418-2 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 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.

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

10.21203/rs.2.10521/v1 ◽

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.

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

10.21203/rs.2.10521/v2 ◽

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.

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Recent Advances in Flowering Time Control

10.3389/978-2-88945-115-9 ◽

2017 ◽

Keyword(s):

Flowering Time ◽

Time Control ◽

Recent Advances ◽

Flowering Time Control

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New Nucleotide Polymorphisms in the BTC1 gene of Sugar Beet

Biotekhnologiya ◽

10.21519/0234-2758-2020-36-6-49-54 ◽

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

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Message ends: RNA 3′ processing and flowering time control

Journal of Experimental Botany ◽

10.1093/jxb/ert439 ◽

2013 ◽

Vol 65 (2) ◽

pp. 353-363 ◽

Cited By ~ 14

Author(s):

Katarzyna Rataj ◽

Gordon G. Simpson

Keyword(s):

Flowering Time ◽

Time Control ◽

Flowering Time Control

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

10.21203/rs.3.rs-108131/v1 ◽

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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BBX32 Interacts with AGL24 Involved in Flowering Time Control in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha47111205 ◽

2018 ◽

Vol 47 (1) ◽

pp. 34-45

Author(s):

Guan-Peng MA ◽

Da-Qin ZHAO ◽

Tian-Wen WANG ◽

Lin-Bi ZHOU ◽

Gui-Lian LI

Keyword(s):

Arabidopsis Thaliana ◽

Circadian Clock ◽

Flowering Time ◽

Brassica Rapa ◽

Chinese Cabbage ◽

Protein Interactions ◽

Protein Protein Interactions ◽

Time Control ◽

Flowering Time Control ◽

Molecular Regulatory Mechanisms

B-box (BBX) zinc finger proteins play critical roles in both vegetative and reproductive development in plants. Many BBX proteins have been identified in Arabidopsis thaliana as floral transition regulatory factors, such as CO, BBX7 (COL9), BBX19, and BBX32. BBX32 is involved in flowering time control through repression of COL3 in Arabidopsis thaliana, but it is still elusive that whether and how BBX32 directly interacts with flowering signal integrators of AGAMOUS-LIKE 24 (AGL24) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) in Chinese cabbage (Brassica rapa L. ssp. pekinensis) or other plants. In this study, B-box-32(BBX32), a transcription factor in this family with one B-box motif was cloned from B. rapa, acted as a circadian clock protein, showing expression changes during the circadian period. Additional experiments using GST pull-down and yeast two-hybrid assays indicated that BrBBX32 interacts with BrAGL24 and does not interact with BrSOC1, while BrAGL24 does interact with BrSOC1. To investigate the domains involved in these protein-protein interactions, we tested three regions of BrBBX32. Only the N-terminus interacted with BrAGL24, indicating that the B-box domain may be the key region for protein interaction. Based on these data, we propose that BrBBX32 may act in the circadian clock pathway and relate to the mechanism of flowering time regulation by binding to BrAGL24 through the B-box domain. This study will provide valuable information for unraveling the molecular regulatory mechanisms of BrBBX32 in flowering time of B. rapa.

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