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Yunlong Yin - One of the best experts on this subject based on the ideXlab platform.
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Identification and Functional Analysis of ThADH1 and ThADH4 Genes Involved in Tolerance to Waterlogging Stress in Taxodium Hybrid ‘Zhongshanshan 406’
Genes, 2021Co-Authors: Lei Xuan, Ying Yang, Yunlong Yin, Jianfeng Hua, Zhiquan Wang, Fan Zhang, Xiaoxiao Pei, David L. CreechAbstract:The Taxodium hybrid ‘Zhongshanshan 406’ (T. hybrid ‘Zhongshanshan 406’) [Taxodium mucronatum Tenore × Taxodium distichum (L.). Rich] has an outstanding advantage in flooding tolerance and thus has been widely used in wetland afforestation in China. Alcohol dehydrogenase genes (ADHs) played key roles in ethanol metabolism to maintain energy supply for plants in low-oxygen conditions. Two ADH genes were isolated and characterized—ThADH1 and ThADH4（GenBank ID: AWL83216 and AWL83217—basing on the transcriptome data of T. hybrid ‘Zhongshanshan 406’ grown under waterlogging stress. Then the functions of these two genes were investigated through transient expression and overexpression. The results showed that the ThADH1 and ThADH4 proteins both fall under ADH III subfamily. ThADH1 was localized in the cytoplasm and nucleus, whereas ThADH4 was only localized in the cytoplasm. The expression of the two genes was stimulated by waterlogging and the expression level in roots was significantly higher than those in stems and leaves. The respective overexpression of ThADH1 and ThADH4 in Populus caused the opposite phenotype, while waterlogging tolerance of the two transgenic Populus significantly improved. Collectively, these results indicated that genes ThADH1 and ThADH4 were involved in the tolerance and adaptation to anaerobic conditions in T. hybrid ‘Zhongshanshan 406.’
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Comparative chloroplast genomics of the genus Taxodium
BMC genomics, 2020Co-Authors: Hao Duan, Yunlong Yin, Jinbo Guo, Lei Xuan, Ziyang Wang, Ying YangAbstract:Chloroplast (cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood. We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613 bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the 3 cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat (TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Hypothetical cp open reading frame 1(Ycf1) was the only one gene that has an indel in coding DNA sequence, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. This study added new evidence for the role of repeats in the dynamics mechanism of cp genome mutation and rearrangement. Moreover, the information of TRs and hypervariable regions would provide reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure and biodiversity for the genus Taxodium and Cupressophytes.
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Comparative Chloroplast Genomics of The Genus Taxodium
2019Co-Authors: Ying Yang, Jinbo Guo, Lei Xuan, Ziyang Wang, Hao Duan, Yunlong YinAbstract:Abstract Background: Chloroplast(cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood.Results: We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the three cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat(TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Ycf1 was the only one gene that has an indel in CDS, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. Conclusions: This study would advance our understanding of the complexity, dynamics, and evolution of cp genome in Cupressophytes.
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Identification and functional analysis of LecRLK genes in Taxodium 'Zhongshanshan'.
PeerJ, 2019Co-Authors: Jinbo Guo, Yunlong Yin, Jianfeng Hua, Lei Xuan, Ziyang Wang, Hao Duan, Ying YangAbstract:Background Lectin receptor-like protein kinases (LecRLKs) can transform external stimuli into intracellular signals and play important regulatory roles in plant development and response to environmental stressors. However, research on the LecRLK gene family of conifers has seldom been reported. Methods Putative LecRLK genes were identified in the transcriptome of Taxodium 'Zhongshanshan'. The classification, domain structures, subcellular localization prediction, and expression patterns of LecRLK genes, as well as co-expressed genes, were analyzed using bioinformatics methods. Fifteen representative genes were further selected for qRT-PCR analysis in six tissues and under five different environmental stressor conditions. Results In total, 297 LecRLK genes were identified, including 155 G-type, 140 L-type, and 2 C-type. According to the classification, G-type and L-type LecRLK genes both can be organized into seven groups. The domain architecture of G-type proteins were more complex compared with that of L- and C-type proteins. Conservative motifs were found in G-type and L-type diverse lectin domains. Prediction and transient expression experiments to determine subcellular localization showed that LecRLKs were mainly concentrated in the cell membrane system, and some members were located at multiple sites at the same time. RNA-seq-based transcriptomics analysis suggested functional redundancy and divergence within each group. Unigenes co-expressed with LecRLKs in the transcriptome were found to be enriched in pathways related to signal transduction and environmental adaptation. Furthermore, qRT-PCR analysis of representative genes showed evidence of functional divergence between different groups. Conclusions This is the first study to conduct an identification and expression analysis of the LecRLK gene family in Taxodium. These results provide a basis for future studies on the evolution and function of this important gene family in Taxodium.
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An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium 'Zhongshanshan'.
International journal of molecular sciences, 2019Co-Authors: Zhiquan Wang, Yunlong Yin, Jianfeng Hua, Qin Shi, Jinbo Guo, Lei XuanAbstract:Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative proteomic (iTRAQ) analysis to measure changes in gene and protein expression levels during AR formation in Taxodium ‘Zhongshanshan’. Three comparison groups were established to represent the three developmental stages in the AR formation process. At the transcript level, 4743 genes showed an expression difference in the comparison groups as detected by RNA sequencing. At the protein level, 4005 proteins differed in their relative abundance levels, as indicated by the quantitative proteomic analysis. A comparison of the transcriptome and proteome data revealed regulatory aspects of metabolism during AR formation and development. In summary, hormonal signal transduction is different at different developmental stages during AR formation. Other factors related to carbohydrate and energy metabolism and protein degradation and some transcription factor activity levels, were also correlated with AR formation. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling AR formation.
Fitzpatrick-cooper Julia - One of the best experts on this subject based on the ideXlab platform.
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\u3cem\u3e Metasequoia glyptostroboides\u3c/em\u3e Whole Plant/Habit
DigitalCommons@COD, 2014Co-Authors: Fitzpatrick-cooper JuliaAbstract:Metasequoia glyptostroboides (dawn redwood) and Taxodium distichum (baldcypress) have a similar pyramidal habit; however, dawn redwood is generally narrower and slightly pointed at the top.https://dc.cod.edu/horticulture-2242-metasequoia-glyptostroboides/1002/thumbnail.jp
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\u3cem\u3eTaxodium distichum\u3c/em\u3e Branch/Twig
DigitalCommons@COD, 2014Co-Authors: Fitzpatrick-cooper JuliaAbstract:Similar to Metasequoia, Taxodium has two types of branches; persistent woody branches and deciduous branchlets. The persistent woody branches with the alternate/spiral leaf arrangement is a useful identification feature and helps to separate this species from dawn redwood which is opposite. Note: The long drooping structures in this image are male pollen cones, not stem structure.https://dc.cod.edu/horticulture-2242-Taxodium-distichum/1006/thumbnail.jp
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\u3cem\u3eTaxodium distichum\u3c/em\u3e Whole Plant/Habit
DigitalCommons@COD, 2014Co-Authors: Fitzpatrick-cooper JuliaAbstract:The pyramidal to conical habit is most apparent in the dormant season. It can look very similar to Metasequoia. However, baldcypress seems to have a more rounded top, dawn redwood comes more to a point. Slight difference but apparent with practice.https://dc.cod.edu/horticulture-2242-Taxodium-distichum/1001/thumbnail.jp
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\u3cem\u3e Metasequoia glyptostroboides\u3c/em\u3e Special ID Features
DigitalCommons@COD, 2014Co-Authors: Fitzpatrick-cooper JuliaAbstract:The habit, foliage and bark features of dawn redwood can easily be confused with Taxodium distichum. In addition to the bud/leaf arrangement already discussed, a unique feature of dawn redwood is the dark “armpit” or depression that forms under the attachment of larger branches to the trunk. Great identification feature!https://dc.cod.edu/horticulture-2242-metasequoia-glyptostroboides/1013/thumbnail.jp
Ying Yang - One of the best experts on this subject based on the ideXlab platform.
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Identification and Functional Analysis of ThADH1 and ThADH4 Genes Involved in Tolerance to Waterlogging Stress in Taxodium Hybrid ‘Zhongshanshan 406’
Genes, 2021Co-Authors: Lei Xuan, Ying Yang, Yunlong Yin, Jianfeng Hua, Zhiquan Wang, Fan Zhang, Xiaoxiao Pei, David L. CreechAbstract:The Taxodium hybrid ‘Zhongshanshan 406’ (T. hybrid ‘Zhongshanshan 406’) [Taxodium mucronatum Tenore × Taxodium distichum (L.). Rich] has an outstanding advantage in flooding tolerance and thus has been widely used in wetland afforestation in China. Alcohol dehydrogenase genes (ADHs) played key roles in ethanol metabolism to maintain energy supply for plants in low-oxygen conditions. Two ADH genes were isolated and characterized—ThADH1 and ThADH4（GenBank ID: AWL83216 and AWL83217—basing on the transcriptome data of T. hybrid ‘Zhongshanshan 406’ grown under waterlogging stress. Then the functions of these two genes were investigated through transient expression and overexpression. The results showed that the ThADH1 and ThADH4 proteins both fall under ADH III subfamily. ThADH1 was localized in the cytoplasm and nucleus, whereas ThADH4 was only localized in the cytoplasm. The expression of the two genes was stimulated by waterlogging and the expression level in roots was significantly higher than those in stems and leaves. The respective overexpression of ThADH1 and ThADH4 in Populus caused the opposite phenotype, while waterlogging tolerance of the two transgenic Populus significantly improved. Collectively, these results indicated that genes ThADH1 and ThADH4 were involved in the tolerance and adaptation to anaerobic conditions in T. hybrid ‘Zhongshanshan 406.’
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Comparative chloroplast genomics of the genus Taxodium
BMC genomics, 2020Co-Authors: Hao Duan, Yunlong Yin, Jinbo Guo, Lei Xuan, Ziyang Wang, Ying YangAbstract:Chloroplast (cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood. We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613 bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the 3 cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat (TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Hypothetical cp open reading frame 1(Ycf1) was the only one gene that has an indel in coding DNA sequence, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. This study added new evidence for the role of repeats in the dynamics mechanism of cp genome mutation and rearrangement. Moreover, the information of TRs and hypervariable regions would provide reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure and biodiversity for the genus Taxodium and Cupressophytes.
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Comparative Chloroplast Genomics of The Genus Taxodium
2019Co-Authors: Ying Yang, Jinbo Guo, Lei Xuan, Ziyang Wang, Hao Duan, Yunlong YinAbstract:Abstract Background: Chloroplast(cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood.Results: We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the three cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat(TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Ycf1 was the only one gene that has an indel in CDS, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. Conclusions: This study would advance our understanding of the complexity, dynamics, and evolution of cp genome in Cupressophytes.
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Identification and functional analysis of LecRLK genes in Taxodium 'Zhongshanshan'.
PeerJ, 2019Co-Authors: Jinbo Guo, Yunlong Yin, Jianfeng Hua, Lei Xuan, Ziyang Wang, Hao Duan, Ying YangAbstract:Background Lectin receptor-like protein kinases (LecRLKs) can transform external stimuli into intracellular signals and play important regulatory roles in plant development and response to environmental stressors. However, research on the LecRLK gene family of conifers has seldom been reported. Methods Putative LecRLK genes were identified in the transcriptome of Taxodium 'Zhongshanshan'. The classification, domain structures, subcellular localization prediction, and expression patterns of LecRLK genes, as well as co-expressed genes, were analyzed using bioinformatics methods. Fifteen representative genes were further selected for qRT-PCR analysis in six tissues and under five different environmental stressor conditions. Results In total, 297 LecRLK genes were identified, including 155 G-type, 140 L-type, and 2 C-type. According to the classification, G-type and L-type LecRLK genes both can be organized into seven groups. The domain architecture of G-type proteins were more complex compared with that of L- and C-type proteins. Conservative motifs were found in G-type and L-type diverse lectin domains. Prediction and transient expression experiments to determine subcellular localization showed that LecRLKs were mainly concentrated in the cell membrane system, and some members were located at multiple sites at the same time. RNA-seq-based transcriptomics analysis suggested functional redundancy and divergence within each group. Unigenes co-expressed with LecRLKs in the transcriptome were found to be enriched in pathways related to signal transduction and environmental adaptation. Furthermore, qRT-PCR analysis of representative genes showed evidence of functional divergence between different groups. Conclusions This is the first study to conduct an identification and expression analysis of the LecRLK gene family in Taxodium. These results provide a basis for future studies on the evolution and function of this important gene family in Taxodium.
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Genetic linkage map construction and QTL mapping of seedling height, basal diameter and crown width of Taxodium ‘Zhongshanshan 302’ × T. mucronatum
SpringerPlus, 2016Co-Authors: Ziyang Wang, Ying Yang, Yunlong Yin, Qin Shi, Yanli Cheng, Ziyuan HaoAbstract:Taxodium is a genus renowned for its fast growth, good form and tolerance of flooding, salt, alkalinity, disease and strong winds. In this study, a genetic linkage map was constructed using sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers based on an F1 population containing 148 individuals generated from a cross between T. ‘Zhongshanshan 302’ and T. mucronatum. The map has a total length of 976.5 cM, with a mean distance of 7.0 cM between markers, and contains 34 linkage groups with 179 markers (171 SRAPs and 8 SSRs). Quantitative trait loci (QTLs) affecting growth traits, such as seedling height, basal diameter and crown width, were detected based on the constructed linkage map. Four significant QTLs were identified, three of which, namely qtSH-1 for seedling height, qtBD-1 for basal diameter and qtCW-1 for crown width, were located at 2.659 cM of LG7 with logarithm odds values of 3.72, 3.49 and 3.93, respectively, and explained 24.9, 27.0 and 21.7 % of the total variation of the three grown traits, respectively. Another QTL for crown width (qtCW-2) was detected at 1.0 cM on LG13, with a logarithm of odds value of 3.15, and explained 31.7 % of the total variation of crown width. This is the first report on the construction of a genetic linkage map and QTL analysis in Taxodium, laying the groundwork for the construction of a high-density genetic map and QTL mapping in the genus Taxodium.
Lei Xuan - One of the best experts on this subject based on the ideXlab platform.
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Identification and Functional Analysis of ThADH1 and ThADH4 Genes Involved in Tolerance to Waterlogging Stress in Taxodium Hybrid ‘Zhongshanshan 406’
Genes, 2021Co-Authors: Lei Xuan, Ying Yang, Yunlong Yin, Jianfeng Hua, Zhiquan Wang, Fan Zhang, Xiaoxiao Pei, David L. CreechAbstract:The Taxodium hybrid ‘Zhongshanshan 406’ (T. hybrid ‘Zhongshanshan 406’) [Taxodium mucronatum Tenore × Taxodium distichum (L.). Rich] has an outstanding advantage in flooding tolerance and thus has been widely used in wetland afforestation in China. Alcohol dehydrogenase genes (ADHs) played key roles in ethanol metabolism to maintain energy supply for plants in low-oxygen conditions. Two ADH genes were isolated and characterized—ThADH1 and ThADH4（GenBank ID: AWL83216 and AWL83217—basing on the transcriptome data of T. hybrid ‘Zhongshanshan 406’ grown under waterlogging stress. Then the functions of these two genes were investigated through transient expression and overexpression. The results showed that the ThADH1 and ThADH4 proteins both fall under ADH III subfamily. ThADH1 was localized in the cytoplasm and nucleus, whereas ThADH4 was only localized in the cytoplasm. The expression of the two genes was stimulated by waterlogging and the expression level in roots was significantly higher than those in stems and leaves. The respective overexpression of ThADH1 and ThADH4 in Populus caused the opposite phenotype, while waterlogging tolerance of the two transgenic Populus significantly improved. Collectively, these results indicated that genes ThADH1 and ThADH4 were involved in the tolerance and adaptation to anaerobic conditions in T. hybrid ‘Zhongshanshan 406.’
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Comparative chloroplast genomics of the genus Taxodium
BMC genomics, 2020Co-Authors: Hao Duan, Yunlong Yin, Jinbo Guo, Lei Xuan, Ziyang Wang, Ying YangAbstract:Chloroplast (cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood. We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613 bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the 3 cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat (TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Hypothetical cp open reading frame 1(Ycf1) was the only one gene that has an indel in coding DNA sequence, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. This study added new evidence for the role of repeats in the dynamics mechanism of cp genome mutation and rearrangement. Moreover, the information of TRs and hypervariable regions would provide reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure and biodiversity for the genus Taxodium and Cupressophytes.
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Comparative Chloroplast Genomics of The Genus Taxodium
2019Co-Authors: Ying Yang, Jinbo Guo, Lei Xuan, Ziyang Wang, Hao Duan, Yunlong YinAbstract:Abstract Background: Chloroplast(cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood.Results: We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the three cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat(TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Ycf1 was the only one gene that has an indel in CDS, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. Conclusions: This study would advance our understanding of the complexity, dynamics, and evolution of cp genome in Cupressophytes.
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Identification and functional analysis of LecRLK genes in Taxodium 'Zhongshanshan'.
PeerJ, 2019Co-Authors: Jinbo Guo, Yunlong Yin, Jianfeng Hua, Lei Xuan, Ziyang Wang, Hao Duan, Ying YangAbstract:Background Lectin receptor-like protein kinases (LecRLKs) can transform external stimuli into intracellular signals and play important regulatory roles in plant development and response to environmental stressors. However, research on the LecRLK gene family of conifers has seldom been reported. Methods Putative LecRLK genes were identified in the transcriptome of Taxodium 'Zhongshanshan'. The classification, domain structures, subcellular localization prediction, and expression patterns of LecRLK genes, as well as co-expressed genes, were analyzed using bioinformatics methods. Fifteen representative genes were further selected for qRT-PCR analysis in six tissues and under five different environmental stressor conditions. Results In total, 297 LecRLK genes were identified, including 155 G-type, 140 L-type, and 2 C-type. According to the classification, G-type and L-type LecRLK genes both can be organized into seven groups. The domain architecture of G-type proteins were more complex compared with that of L- and C-type proteins. Conservative motifs were found in G-type and L-type diverse lectin domains. Prediction and transient expression experiments to determine subcellular localization showed that LecRLKs were mainly concentrated in the cell membrane system, and some members were located at multiple sites at the same time. RNA-seq-based transcriptomics analysis suggested functional redundancy and divergence within each group. Unigenes co-expressed with LecRLKs in the transcriptome were found to be enriched in pathways related to signal transduction and environmental adaptation. Furthermore, qRT-PCR analysis of representative genes showed evidence of functional divergence between different groups. Conclusions This is the first study to conduct an identification and expression analysis of the LecRLK gene family in Taxodium. These results provide a basis for future studies on the evolution and function of this important gene family in Taxodium.
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An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium 'Zhongshanshan'.
International journal of molecular sciences, 2019Co-Authors: Zhiquan Wang, Yunlong Yin, Jianfeng Hua, Qin Shi, Jinbo Guo, Lei XuanAbstract:Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative proteomic (iTRAQ) analysis to measure changes in gene and protein expression levels during AR formation in Taxodium ‘Zhongshanshan’. Three comparison groups were established to represent the three developmental stages in the AR formation process. At the transcript level, 4743 genes showed an expression difference in the comparison groups as detected by RNA sequencing. At the protein level, 4005 proteins differed in their relative abundance levels, as indicated by the quantitative proteomic analysis. A comparison of the transcriptome and proteome data revealed regulatory aspects of metabolism during AR formation and development. In summary, hormonal signal transduction is different at different developmental stages during AR formation. Other factors related to carbohydrate and energy metabolism and protein degradation and some transcription factor activity levels, were also correlated with AR formation. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling AR formation.
Jianfeng Hua - One of the best experts on this subject based on the ideXlab platform.
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Identification and Functional Analysis of ThADH1 and ThADH4 Genes Involved in Tolerance to Waterlogging Stress in Taxodium Hybrid ‘Zhongshanshan 406’
Genes, 2021Co-Authors: Lei Xuan, Ying Yang, Yunlong Yin, Jianfeng Hua, Zhiquan Wang, Fan Zhang, Xiaoxiao Pei, David L. CreechAbstract:The Taxodium hybrid ‘Zhongshanshan 406’ (T. hybrid ‘Zhongshanshan 406’) [Taxodium mucronatum Tenore × Taxodium distichum (L.). Rich] has an outstanding advantage in flooding tolerance and thus has been widely used in wetland afforestation in China. Alcohol dehydrogenase genes (ADHs) played key roles in ethanol metabolism to maintain energy supply for plants in low-oxygen conditions. Two ADH genes were isolated and characterized—ThADH1 and ThADH4（GenBank ID: AWL83216 and AWL83217—basing on the transcriptome data of T. hybrid ‘Zhongshanshan 406’ grown under waterlogging stress. Then the functions of these two genes were investigated through transient expression and overexpression. The results showed that the ThADH1 and ThADH4 proteins both fall under ADH III subfamily. ThADH1 was localized in the cytoplasm and nucleus, whereas ThADH4 was only localized in the cytoplasm. The expression of the two genes was stimulated by waterlogging and the expression level in roots was significantly higher than those in stems and leaves. The respective overexpression of ThADH1 and ThADH4 in Populus caused the opposite phenotype, while waterlogging tolerance of the two transgenic Populus significantly improved. Collectively, these results indicated that genes ThADH1 and ThADH4 were involved in the tolerance and adaptation to anaerobic conditions in T. hybrid ‘Zhongshanshan 406.’
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Identification and functional analysis of LecRLK genes in Taxodium 'Zhongshanshan'.
PeerJ, 2019Co-Authors: Jinbo Guo, Yunlong Yin, Jianfeng Hua, Lei Xuan, Ziyang Wang, Hao Duan, Ying YangAbstract:Background Lectin receptor-like protein kinases (LecRLKs) can transform external stimuli into intracellular signals and play important regulatory roles in plant development and response to environmental stressors. However, research on the LecRLK gene family of conifers has seldom been reported. Methods Putative LecRLK genes were identified in the transcriptome of Taxodium 'Zhongshanshan'. The classification, domain structures, subcellular localization prediction, and expression patterns of LecRLK genes, as well as co-expressed genes, were analyzed using bioinformatics methods. Fifteen representative genes were further selected for qRT-PCR analysis in six tissues and under five different environmental stressor conditions. Results In total, 297 LecRLK genes were identified, including 155 G-type, 140 L-type, and 2 C-type. According to the classification, G-type and L-type LecRLK genes both can be organized into seven groups. The domain architecture of G-type proteins were more complex compared with that of L- and C-type proteins. Conservative motifs were found in G-type and L-type diverse lectin domains. Prediction and transient expression experiments to determine subcellular localization showed that LecRLKs were mainly concentrated in the cell membrane system, and some members were located at multiple sites at the same time. RNA-seq-based transcriptomics analysis suggested functional redundancy and divergence within each group. Unigenes co-expressed with LecRLKs in the transcriptome were found to be enriched in pathways related to signal transduction and environmental adaptation. Furthermore, qRT-PCR analysis of representative genes showed evidence of functional divergence between different groups. Conclusions This is the first study to conduct an identification and expression analysis of the LecRLK gene family in Taxodium. These results provide a basis for future studies on the evolution and function of this important gene family in Taxodium.
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An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium 'Zhongshanshan'.
International journal of molecular sciences, 2019Co-Authors: Zhiquan Wang, Yunlong Yin, Jianfeng Hua, Qin Shi, Jinbo Guo, Lei XuanAbstract:Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative proteomic (iTRAQ) analysis to measure changes in gene and protein expression levels during AR formation in Taxodium ‘Zhongshanshan’. Three comparison groups were established to represent the three developmental stages in the AR formation process. At the transcript level, 4743 genes showed an expression difference in the comparison groups as detected by RNA sequencing. At the protein level, 4005 proteins differed in their relative abundance levels, as indicated by the quantitative proteomic analysis. A comparison of the transcriptome and proteome data revealed regulatory aspects of metabolism during AR formation and development. In summary, hormonal signal transduction is different at different developmental stages during AR formation. Other factors related to carbohydrate and energy metabolism and protein degradation and some transcription factor activity levels, were also correlated with AR formation. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling AR formation.
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Lateral Root Traits of Taxodium Hybrid ‘Zhongshanshan 406’ in Response to Drought Stress
HortScience, 2018Co-Authors: Qin Shi, Yunlong Yin, Zhiquan Wang, Wencai Fan, Jinbo Guo, Jianfeng HuaAbstract:Roots are vital organs for resource uptake. However, the knowledge regarding the extent by which responses in roots influence plant resistance is still poorly known. In this study, we examined the morphological and physiological responses of lateral roots of Taxodium hybrid ‘Zhongshanshan 406’ (Taxodium mucronatum♀ and Taxodium distichum♂, T. 406) to 8 (DS-8) and 12 days (DS-12) drought. Control plants (CK-8 and CK-12) were well-watered throughout the experiment. Results indicated that drought resulted in significantly decreased root length, surface area, volume, and biomass and a relatively high death rate of roots (>2 mm). Specific root length (SRL) and specific root surface area (SRA) of drought-stressed T. 406 plants were reduced to enhance resource uptake. Meanwhile, root relative water content (RWC) of T. 406 plants in CK-12 treatment was 5.81 times of those in DS-12 treatment. Under drought stress and root superoxide dismutase and ascorbic acid (ASA) activities, proline and hydrogen peroxide (H2O2) contents consistently increased to benefit the elimination of O2−. At the ultrastructural level, the organelle structure of T. 406 plant root tip was visibly damaged because of dehydration. The nucleus swelled and then exhibited uncommon features of disorganization and disruption. In short, our results provided substantial information about lateral root traits of T. 406 plants in response to drought stress, which is crucial to improve the drought resistance of Taxodium hybrid in the future breeding.
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Morpho-anatomical and photosynthetic responses of Taxodium hybrid 'Zhongshanshan' 406 to prolonged flooding
Flora, 2017Co-Authors: Jianfeng Hua, Luwan Han, Zhiquan Wang, Yunlong YinAbstract:Abstract Taxodium hybrid ‘Zhongshanshan 406’ ( T. mucronatum Tenore ♀ × T. distichum (L.) Rich ♂; Taxodium 406) has been selected as a species for reforestation in flooding areas, China. To elucidate its adaptive strategies to prolonged flooding environments, morpho-anatomical, photosynthetic and growth responses of Taxodium 406 were investigated during three months of flooding stress, i.e. half-flooding (HF) and total-submergence (TS). Taxodium 406 showed 100% survival rate under both flooding treatments. Compared to control (CK), root biomass and root/shoot ratio of HF plants were reduced, while height and shoot biomass were increased by 40% and 58% respectively, and thus total biomass was unchanged. For TS plants, their root biomass, total biomass and root/shoot ratio were 69, 48 and 58% lower respectively, than those of CK plants. Compared to initial values, however, non-elongating height and increased basal diameter of TS plants were observed. Besides, TS plants had greater chlorophyll contents than the other two treatments at the end of the experiment. Well-developed aerenchyma, hypertrophied lenticels, large intercellular spaces and adventitious roots of Taxodium 406 plants were formed under HF flooding treatment. Additionally, tested root morphological parameters, i.e. total length, surface area, volume, tips and length in diameter of four classes were lower for HF and TS plants than for CK plants, and no significant difference was found between HF and TS plants. Compared to CK plants, net photosynthetic rate of HF plants was unchanged, while stomatal conductance, transpiration rate and intercellular carbon dioxide concentration were enhanced across the experiment. Therefore, morpho-anatomical adaption and maintenance of photosynthesis of HF plants and the growth retardation of TS plants are responsible for the survival and growth of Taxodium 406 plants under extreme flooding environments.
