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De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response.

Zhang HB, Xia EH, Huang H, Jiang JJ, Liu BY, Gao LZ - BMC Genomics (2015)

Bottom Line: To gain insights into the evolution of these genes, we aligned them to the previously cloned orthologous genes in C. sinensis, and found that considerable nucleotide variation within several genes involved in important secondary metabolic biosynthesis pathways, of which flavone synthase II gene (FNSII) is the most variable between these two species.Moreover, comparative analyses revealed that C. taliensis shows a remarkable expansion of LEA genes, compared to C. sinensis, which might contribute to the observed stronger stress resistance of C. taliensis.Such comprehensive EST datasets provide an unprecedented opportunity for identifying genes involved in several major metabolic pathways and will accelerate functional genomic studies and genetic improvement efforts of tea trees in the future.

View Article: PubMed Central - PubMed

Affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650204, China. zhanghaibin@mail.kib.ac.cn.

ABSTRACT

Background: Camellia taliensis is one of the most important wild relatives of cultivated tea tree, C. sinensis. The species extensively occupies mountainous habitats representing a wide-range abiotic tolerance and biotic resistance and thus harbors valuable gene resources that may greatly benefit genetic improvement of cultivated tea tree. However, owning to a large genome size of ~3 Gb and structurally complex genome, there are fairly limited genetic information and particularly few genomic resources publicly available for this species. To better understand the key pathways determining tea flavor and enhance tea tree breeding programs, we performed a high-throughput transcriptome sequencing for C. taliensis.

Results: In this study, approximate 241.5 million high-quality paired-end reads, accounting for ~24 Gb of sequence data, were generated from tender shoots, young leaves, flower buds and flowers using Illumina HiSeq 2000 platform. De novo assembly with further processing and filtering yielded a set of 67,923 transcripts with an average length of 685 bp and an N50 of 995 bp. Based on sequence similarity searches against public databases, a total of 39,475 transcripts were annotated with gene descriptions, conserved protein domains or gene ontology (GO) terms. Candidate genes for major metabolic pathways involved in tea quality were identified and experimentally validated using RT-qPCR. Further gene expression profiles showed that they are differentially regulated at different developmental stages. To gain insights into the evolution of these genes, we aligned them to the previously cloned orthologous genes in C. sinensis, and found that considerable nucleotide variation within several genes involved in important secondary metabolic biosynthesis pathways, of which flavone synthase II gene (FNSII) is the most variable between these two species. Moreover, comparative analyses revealed that C. taliensis shows a remarkable expansion of LEA genes, compared to C. sinensis, which might contribute to the observed stronger stress resistance of C. taliensis.

Conclusion: We reported the first large-coverage transcriptome datasets for C. taliensis using the next-generation sequencing technology. Such comprehensive EST datasets provide an unprecedented opportunity for identifying genes involved in several major metabolic pathways and will accelerate functional genomic studies and genetic improvement efforts of tea trees in the future.

No MeSH data available.


Related in: MedlinePlus

Comparative analysis of stress resistance related genes between C. taliensis and C. sinensis transcriptome.a) The members of LEA family identified in C. taliensis and C. sinensis. The y-axes represent the numbers of LEA members found in C. taliensis, while x-axes shows the number identified in C. sinensis. Red dashed line means the number of LEA members that are equivalent in these two species. b) The largest LEA family identified in C. taliensis and C. sinensis. c) The number of cold tolerance related TFs identified from C. taliensis and C. sinensis.
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Fig8: Comparative analysis of stress resistance related genes between C. taliensis and C. sinensis transcriptome.a) The members of LEA family identified in C. taliensis and C. sinensis. The y-axes represent the numbers of LEA members found in C. taliensis, while x-axes shows the number identified in C. sinensis. Red dashed line means the number of LEA members that are equivalent in these two species. b) The largest LEA family identified in C. taliensis and C. sinensis. c) The number of cold tolerance related TFs identified from C. taliensis and C. sinensis.

Mentions: Transcription factors (TFs) are kinds of DNA-binding proteins that can activate or repress gene expression through specific interactions with cis-acting elements in promoters of eukaryotic genes [39]. The activation of a large number of stress-related genes is mediated by specific TFs [40]. Over the past decades, many TFs related to stress responses have been identified from different plants [41], but little has been known in tea tree so far. To identify putative genes that could be involved in freezing tolerance, we searched for members of the TFs families potentially involved in cold resistance, including AP2, bZIP, NAC, BHLH, WYBR, ERF, WRKY, MYB, HSF and RAV, in both C. taliensis and C. sinensis using a domain-based pipeline (see Methods). As a result, a total of 408 and 457 members were detected in C. taliensis and C. sinensis, respectively (see Additional file 7a). Of them, RAV represents the smallest group with only one and two members in C. taliensis and C. sinensis, respectively. While bHLH is the most preponderance class with 73 and 82 members were identified in C. taliensis and C. sinensis. Comparative analysis showed that some TF family sizes of C. sinensis are slightly larger than those in C. taliensis, but others are in opposite (see FigureĀ 8c). For example, AP2, NAC and WRKY respectively have 12, 65 and 61 copies in C. sinensis, while 6, 44, 47 members in C. taliensis. Interestingly, the number of ERF gene family in C. taliensis is 67, which is much larger than those in C. sinensis (52 copies).Figure 8


De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response.

Zhang HB, Xia EH, Huang H, Jiang JJ, Liu BY, Gao LZ - BMC Genomics (2015)

Comparative analysis of stress resistance related genes between C. taliensis and C. sinensis transcriptome.a) The members of LEA family identified in C. taliensis and C. sinensis. The y-axes represent the numbers of LEA members found in C. taliensis, while x-axes shows the number identified in C. sinensis. Red dashed line means the number of LEA members that are equivalent in these two species. b) The largest LEA family identified in C. taliensis and C. sinensis. c) The number of cold tolerance related TFs identified from C. taliensis and C. sinensis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4404113&req=5

Fig8: Comparative analysis of stress resistance related genes between C. taliensis and C. sinensis transcriptome.a) The members of LEA family identified in C. taliensis and C. sinensis. The y-axes represent the numbers of LEA members found in C. taliensis, while x-axes shows the number identified in C. sinensis. Red dashed line means the number of LEA members that are equivalent in these two species. b) The largest LEA family identified in C. taliensis and C. sinensis. c) The number of cold tolerance related TFs identified from C. taliensis and C. sinensis.
Mentions: Transcription factors (TFs) are kinds of DNA-binding proteins that can activate or repress gene expression through specific interactions with cis-acting elements in promoters of eukaryotic genes [39]. The activation of a large number of stress-related genes is mediated by specific TFs [40]. Over the past decades, many TFs related to stress responses have been identified from different plants [41], but little has been known in tea tree so far. To identify putative genes that could be involved in freezing tolerance, we searched for members of the TFs families potentially involved in cold resistance, including AP2, bZIP, NAC, BHLH, WYBR, ERF, WRKY, MYB, HSF and RAV, in both C. taliensis and C. sinensis using a domain-based pipeline (see Methods). As a result, a total of 408 and 457 members were detected in C. taliensis and C. sinensis, respectively (see Additional file 7a). Of them, RAV represents the smallest group with only one and two members in C. taliensis and C. sinensis, respectively. While bHLH is the most preponderance class with 73 and 82 members were identified in C. taliensis and C. sinensis. Comparative analysis showed that some TF family sizes of C. sinensis are slightly larger than those in C. taliensis, but others are in opposite (see FigureĀ 8c). For example, AP2, NAC and WRKY respectively have 12, 65 and 61 copies in C. sinensis, while 6, 44, 47 members in C. taliensis. Interestingly, the number of ERF gene family in C. taliensis is 67, which is much larger than those in C. sinensis (52 copies).Figure 8

Bottom Line: To gain insights into the evolution of these genes, we aligned them to the previously cloned orthologous genes in C. sinensis, and found that considerable nucleotide variation within several genes involved in important secondary metabolic biosynthesis pathways, of which flavone synthase II gene (FNSII) is the most variable between these two species.Moreover, comparative analyses revealed that C. taliensis shows a remarkable expansion of LEA genes, compared to C. sinensis, which might contribute to the observed stronger stress resistance of C. taliensis.Such comprehensive EST datasets provide an unprecedented opportunity for identifying genes involved in several major metabolic pathways and will accelerate functional genomic studies and genetic improvement efforts of tea trees in the future.

View Article: PubMed Central - PubMed

Affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650204, China. zhanghaibin@mail.kib.ac.cn.

ABSTRACT

Background: Camellia taliensis is one of the most important wild relatives of cultivated tea tree, C. sinensis. The species extensively occupies mountainous habitats representing a wide-range abiotic tolerance and biotic resistance and thus harbors valuable gene resources that may greatly benefit genetic improvement of cultivated tea tree. However, owning to a large genome size of ~3 Gb and structurally complex genome, there are fairly limited genetic information and particularly few genomic resources publicly available for this species. To better understand the key pathways determining tea flavor and enhance tea tree breeding programs, we performed a high-throughput transcriptome sequencing for C. taliensis.

Results: In this study, approximate 241.5 million high-quality paired-end reads, accounting for ~24 Gb of sequence data, were generated from tender shoots, young leaves, flower buds and flowers using Illumina HiSeq 2000 platform. De novo assembly with further processing and filtering yielded a set of 67,923 transcripts with an average length of 685 bp and an N50 of 995 bp. Based on sequence similarity searches against public databases, a total of 39,475 transcripts were annotated with gene descriptions, conserved protein domains or gene ontology (GO) terms. Candidate genes for major metabolic pathways involved in tea quality were identified and experimentally validated using RT-qPCR. Further gene expression profiles showed that they are differentially regulated at different developmental stages. To gain insights into the evolution of these genes, we aligned them to the previously cloned orthologous genes in C. sinensis, and found that considerable nucleotide variation within several genes involved in important secondary metabolic biosynthesis pathways, of which flavone synthase II gene (FNSII) is the most variable between these two species. Moreover, comparative analyses revealed that C. taliensis shows a remarkable expansion of LEA genes, compared to C. sinensis, which might contribute to the observed stronger stress resistance of C. taliensis.

Conclusion: We reported the first large-coverage transcriptome datasets for C. taliensis using the next-generation sequencing technology. Such comprehensive EST datasets provide an unprecedented opportunity for identifying genes involved in several major metabolic pathways and will accelerate functional genomic studies and genetic improvement efforts of tea trees in the future.

No MeSH data available.


Related in: MedlinePlus