The Experts below are selected from a list of 6744 Experts worldwide ranked by ideXlab platform

Haikuo Fan - One of the best experts on this subject based on the ideXlab platform.

  • The genome draft of coconut (Cocos nucifera).
    GigaScience, 2017
    Co-Authors: Yong Xiao, Haikuo Fan, Luc Baudouin, Wei Xia, Stéphanie Bocs, Anping Guo, Lixia Zhou
    Abstract:

    Coconut palm (Cocos nucifera,2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 main categories: “Tall” (flowering 8–10 years after planting) and “Dwarf” (flowering 4–6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years, which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, variety “Hainan Tall”) to an estimated ×173.32 read depth. A total scaffold length of 2.20 Gb was generated (N50 = 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28 039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that the obtained scaffold sequences covered 90.8% of the coconut genome and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome consisted of transposable elements, of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species. (Resume d'auteur)

  • The genome draft of coconut (Cocos nucifera)
    GigaScience, 2017
    Co-Authors: Yong Xiao, Haikuo Fan, Luc Baudouin, Wei Xia, Stéphanie Bocs, Anping Guo, Lixia Zhou, Alix Armero, Auguste Emmanuel Issali, Na Liu
    Abstract:

    Coconut palm (Cocos nucifera, 2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 main categories: "Tall" (flowering 8-10 years after planting) and " Dwarf" (flowering 4-6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years, which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, variety " Hainan Tall") to an estimated x173.32 read depth. A total scaffold length of 2.20 Gb was generated (N50 = 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28 039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that the obtained scaffold sequences covered 90.8% of the coconut genome and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome consisted of transposable elements, of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species.

  • Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera.
    Plant Omics, 2013
    Co-Authors: Yong Xiao, Haikuo Fan, Wei Xia, Yaodong Yang, Annaliese S. Mason, Songlin Zhao, Yi Luo, Ross Sager, Fei Qiao
    Abstract:

    Cocos nucifera (coconut) is an economically important tropical crop, but opportunities for molecular breeding are limited by lack of DNA sequence information for this species. Previous assessments of coconut germplasm have been conducted based solely on phenotypic data for agronomic and quality traits, due to lack of available molecular markers. In this study, we developed 30 novel microsatellite markers from Illumina transcriptome sequence data, and used these markers to evaluate coconut genetic diversity in 30 individuals representing accessions from China (12 samples) and Southeast Asia (18 samples). The microsatellite markers displayed low to high genetic polymorphism across the population: observed heterozygosity varied from 0.06 to 0.79, with an average of 0.39 ± 0.15. Our results indicated that the Southeast Asian population had a significantly higher number of alleles (p = 0.02), but not significantly different (p

  • RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.
    PloS one, 2013
    Co-Authors: Haikuo Fan, Yong Xiao, Wei Xia, Yaodong Yang, Annaliese S. Mason, Zhihui Xia, Fei Qiao, Songlin Zhao, Haoru Tang
    Abstract:

    Cocos nucifera (coconut), a member of the Arecaceae family, is an economically important woody palm grown in tropical regions. Despite its agronomic importance, previous germplasm assessment studies have relied solely on morphological and agronomical traits. Molecular biology techniques have been scarcely used in assessment of genetic resources and for improvement of important agronomic and quality traits in Cocos nucifera, mostly due to the absence of available sequence information. To provide basic information for molecular breeding and further molecular biological analysis in Cocos nucifera, we applied RNA-seq technology and de novo assembly to gain a global overview of the Cocos nucifera transcriptome from mixed tissue samples. Using Illumina sequencing, we obtained 54.9 million short reads and conducted de novo assembly to obtain 57,304 unigenes with an average length of 752 base pairs. Sequence comparison between assembled unigenes and released cDNA sequences of Cocos nucifera and Elaeis guineensis indicated that the assembled sequences were of high quality. Approximately 99.9% of unigenes were novel compared to the released coconut EST sequences. Using BLASTX, 68.2% of unigenes were successfully annotated based on the Genbank non-redundant (Nr) protein database. The annotated unigenes were then further classified using the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Our study provides a large quantity of novel genetic information for Cocos nucifera. This information will act as a valuable resource for further molecular genetic studies and breeding in coconut, as well as for isolation and characterization of functional genes involved in different biochemical pathways in this important tropical crop species.

  • rna seq analysis of Cocos nucifera transcriptome sequencing and de novo assembly for subsequent functional genomics approaches
    PLOS ONE, 2013
    Co-Authors: Yong Xiao, Haikuo Fan, Wei Xia, Yaodong Yang, Annaliese S. Mason, Zhihui Xia, Fei Qiao, Songlin Zhao, Haoru Tang
    Abstract:

    Background: Cocos nucifera (coconut), a member of the Arecaceae family, is an economically important woody palm grown in tropical regions. Despite its agronomic importance, previous germplasm assessment studies have relied solely on morphological and agronomical traits. Molecular biology techniques have been scarcely used in assessment of genetic resources and for improvement of important agronomic and quality traits in Cocos nucifera, mostly due to the absence of available sequence information. Methodology/Principal Findings: To provide basic information for molecular breeding and further molecular biological analysis in Cocos nucifera, we applied RNA-seq technology and de novo assembly to gain a global overview of the Cocos nucifera transcriptome from mixed tissue samples. Using Illumina sequencing, we obtained 54.9 million short reads and conducted de novo assembly to obtain 57,304 unigenes with an average length of 752 base pairs. Sequence comparison between assembled unigenes and released cDNA sequences of Cocos nucifera and Elaeis guineensis indicated that the assembled sequences were of high quality. Approximately 99.9% of unigenes were novel compared to the released coconut EST sequences. Using BLASTX, 68.2% of unigenes were successfully annotated based on the Genbank non-redundant (Nr) protein database. The annotated unigenes were then further classified using the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Conclusions/Significance: Our study provides a large quantity of novel genetic information for Cocos nucifera. This information will act as a valuable resource for further molecular genetic studies and breeding in coconut, as well as for isolation and characterization of functional genes involved in different biochemical pathways in this important tropical crop species.

Haoru Tang - One of the best experts on this subject based on the ideXlab platform.

  • RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.
    PloS one, 2013
    Co-Authors: Haikuo Fan, Yong Xiao, Wei Xia, Yaodong Yang, Annaliese S. Mason, Zhihui Xia, Fei Qiao, Songlin Zhao, Haoru Tang
    Abstract:

    Cocos nucifera (coconut), a member of the Arecaceae family, is an economically important woody palm grown in tropical regions. Despite its agronomic importance, previous germplasm assessment studies have relied solely on morphological and agronomical traits. Molecular biology techniques have been scarcely used in assessment of genetic resources and for improvement of important agronomic and quality traits in Cocos nucifera, mostly due to the absence of available sequence information. To provide basic information for molecular breeding and further molecular biological analysis in Cocos nucifera, we applied RNA-seq technology and de novo assembly to gain a global overview of the Cocos nucifera transcriptome from mixed tissue samples. Using Illumina sequencing, we obtained 54.9 million short reads and conducted de novo assembly to obtain 57,304 unigenes with an average length of 752 base pairs. Sequence comparison between assembled unigenes and released cDNA sequences of Cocos nucifera and Elaeis guineensis indicated that the assembled sequences were of high quality. Approximately 99.9% of unigenes were novel compared to the released coconut EST sequences. Using BLASTX, 68.2% of unigenes were successfully annotated based on the Genbank non-redundant (Nr) protein database. The annotated unigenes were then further classified using the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Our study provides a large quantity of novel genetic information for Cocos nucifera. This information will act as a valuable resource for further molecular genetic studies and breeding in coconut, as well as for isolation and characterization of functional genes involved in different biochemical pathways in this important tropical crop species.

  • rna seq analysis of Cocos nucifera transcriptome sequencing and de novo assembly for subsequent functional genomics approaches
    PLOS ONE, 2013
    Co-Authors: Yong Xiao, Haikuo Fan, Wei Xia, Yaodong Yang, Annaliese S. Mason, Zhihui Xia, Fei Qiao, Songlin Zhao, Haoru Tang
    Abstract:

    Background: Cocos nucifera (coconut), a member of the Arecaceae family, is an economically important woody palm grown in tropical regions. Despite its agronomic importance, previous germplasm assessment studies have relied solely on morphological and agronomical traits. Molecular biology techniques have been scarcely used in assessment of genetic resources and for improvement of important agronomic and quality traits in Cocos nucifera, mostly due to the absence of available sequence information. Methodology/Principal Findings: To provide basic information for molecular breeding and further molecular biological analysis in Cocos nucifera, we applied RNA-seq technology and de novo assembly to gain a global overview of the Cocos nucifera transcriptome from mixed tissue samples. Using Illumina sequencing, we obtained 54.9 million short reads and conducted de novo assembly to obtain 57,304 unigenes with an average length of 752 base pairs. Sequence comparison between assembled unigenes and released cDNA sequences of Cocos nucifera and Elaeis guineensis indicated that the assembled sequences were of high quality. Approximately 99.9% of unigenes were novel compared to the released coconut EST sequences. Using BLASTX, 68.2% of unigenes were successfully annotated based on the Genbank non-redundant (Nr) protein database. The annotated unigenes were then further classified using the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Conclusions/Significance: Our study provides a large quantity of novel genetic information for Cocos nucifera. This information will act as a valuable resource for further molecular genetic studies and breeding in coconut, as well as for isolation and characterization of functional genes involved in different biochemical pathways in this important tropical crop species.

Yong Xiao - One of the best experts on this subject based on the ideXlab platform.

  • The genome draft of coconut (Cocos nucifera).
    GigaScience, 2017
    Co-Authors: Yong Xiao, Haikuo Fan, Luc Baudouin, Wei Xia, Stéphanie Bocs, Anping Guo, Lixia Zhou
    Abstract:

    Coconut palm (Cocos nucifera,2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 main categories: “Tall” (flowering 8–10 years after planting) and “Dwarf” (flowering 4–6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years, which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, variety “Hainan Tall”) to an estimated ×173.32 read depth. A total scaffold length of 2.20 Gb was generated (N50 = 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28 039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that the obtained scaffold sequences covered 90.8% of the coconut genome and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome consisted of transposable elements, of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species. (Resume d'auteur)

  • The genome draft of coconut (Cocos nucifera)
    GigaScience, 2017
    Co-Authors: Yong Xiao, Haikuo Fan, Luc Baudouin, Wei Xia, Stéphanie Bocs, Anping Guo, Lixia Zhou, Alix Armero, Auguste Emmanuel Issali, Na Liu
    Abstract:

    Coconut palm (Cocos nucifera, 2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 main categories: "Tall" (flowering 8-10 years after planting) and " Dwarf" (flowering 4-6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years, which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, variety " Hainan Tall") to an estimated x173.32 read depth. A total scaffold length of 2.20 Gb was generated (N50 = 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28 039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that the obtained scaffold sequences covered 90.8% of the coconut genome and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome consisted of transposable elements, of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species.

  • Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera.
    Plant Omics, 2013
    Co-Authors: Yong Xiao, Haikuo Fan, Wei Xia, Yaodong Yang, Annaliese S. Mason, Songlin Zhao, Yi Luo, Ross Sager, Fei Qiao
    Abstract:

    Cocos nucifera (coconut) is an economically important tropical crop, but opportunities for molecular breeding are limited by lack of DNA sequence information for this species. Previous assessments of coconut germplasm have been conducted based solely on phenotypic data for agronomic and quality traits, due to lack of available molecular markers. In this study, we developed 30 novel microsatellite markers from Illumina transcriptome sequence data, and used these markers to evaluate coconut genetic diversity in 30 individuals representing accessions from China (12 samples) and Southeast Asia (18 samples). The microsatellite markers displayed low to high genetic polymorphism across the population: observed heterozygosity varied from 0.06 to 0.79, with an average of 0.39 ± 0.15. Our results indicated that the Southeast Asian population had a significantly higher number of alleles (p = 0.02), but not significantly different (p

  • RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.
    PloS one, 2013
    Co-Authors: Haikuo Fan, Yong Xiao, Wei Xia, Yaodong Yang, Annaliese S. Mason, Zhihui Xia, Fei Qiao, Songlin Zhao, Haoru Tang
    Abstract:

    Cocos nucifera (coconut), a member of the Arecaceae family, is an economically important woody palm grown in tropical regions. Despite its agronomic importance, previous germplasm assessment studies have relied solely on morphological and agronomical traits. Molecular biology techniques have been scarcely used in assessment of genetic resources and for improvement of important agronomic and quality traits in Cocos nucifera, mostly due to the absence of available sequence information. To provide basic information for molecular breeding and further molecular biological analysis in Cocos nucifera, we applied RNA-seq technology and de novo assembly to gain a global overview of the Cocos nucifera transcriptome from mixed tissue samples. Using Illumina sequencing, we obtained 54.9 million short reads and conducted de novo assembly to obtain 57,304 unigenes with an average length of 752 base pairs. Sequence comparison between assembled unigenes and released cDNA sequences of Cocos nucifera and Elaeis guineensis indicated that the assembled sequences were of high quality. Approximately 99.9% of unigenes were novel compared to the released coconut EST sequences. Using BLASTX, 68.2% of unigenes were successfully annotated based on the Genbank non-redundant (Nr) protein database. The annotated unigenes were then further classified using the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Our study provides a large quantity of novel genetic information for Cocos nucifera. This information will act as a valuable resource for further molecular genetic studies and breeding in coconut, as well as for isolation and characterization of functional genes involved in different biochemical pathways in this important tropical crop species.

  • rna seq analysis of Cocos nucifera transcriptome sequencing and de novo assembly for subsequent functional genomics approaches
    PLOS ONE, 2013
    Co-Authors: Yong Xiao, Haikuo Fan, Wei Xia, Yaodong Yang, Annaliese S. Mason, Zhihui Xia, Fei Qiao, Songlin Zhao, Haoru Tang
    Abstract:

    Background: Cocos nucifera (coconut), a member of the Arecaceae family, is an economically important woody palm grown in tropical regions. Despite its agronomic importance, previous germplasm assessment studies have relied solely on morphological and agronomical traits. Molecular biology techniques have been scarcely used in assessment of genetic resources and for improvement of important agronomic and quality traits in Cocos nucifera, mostly due to the absence of available sequence information. Methodology/Principal Findings: To provide basic information for molecular breeding and further molecular biological analysis in Cocos nucifera, we applied RNA-seq technology and de novo assembly to gain a global overview of the Cocos nucifera transcriptome from mixed tissue samples. Using Illumina sequencing, we obtained 54.9 million short reads and conducted de novo assembly to obtain 57,304 unigenes with an average length of 752 base pairs. Sequence comparison between assembled unigenes and released cDNA sequences of Cocos nucifera and Elaeis guineensis indicated that the assembled sequences were of high quality. Approximately 99.9% of unigenes were novel compared to the released coconut EST sequences. Using BLASTX, 68.2% of unigenes were successfully annotated based on the Genbank non-redundant (Nr) protein database. The annotated unigenes were then further classified using the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Conclusions/Significance: Our study provides a large quantity of novel genetic information for Cocos nucifera. This information will act as a valuable resource for further molecular genetic studies and breeding in coconut, as well as for isolation and characterization of functional genes involved in different biochemical pathways in this important tropical crop species.

Wei Xia - One of the best experts on this subject based on the ideXlab platform.

  • The genome draft of coconut (Cocos nucifera).
    GigaScience, 2017
    Co-Authors: Yong Xiao, Haikuo Fan, Luc Baudouin, Wei Xia, Stéphanie Bocs, Anping Guo, Lixia Zhou
    Abstract:

    Coconut palm (Cocos nucifera,2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 main categories: “Tall” (flowering 8–10 years after planting) and “Dwarf” (flowering 4–6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years, which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, variety “Hainan Tall”) to an estimated ×173.32 read depth. A total scaffold length of 2.20 Gb was generated (N50 = 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28 039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that the obtained scaffold sequences covered 90.8% of the coconut genome and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome consisted of transposable elements, of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species. (Resume d'auteur)

  • The genome draft of coconut (Cocos nucifera)
    GigaScience, 2017
    Co-Authors: Yong Xiao, Haikuo Fan, Luc Baudouin, Wei Xia, Stéphanie Bocs, Anping Guo, Lixia Zhou, Alix Armero, Auguste Emmanuel Issali, Na Liu
    Abstract:

    Coconut palm (Cocos nucifera, 2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 main categories: "Tall" (flowering 8-10 years after planting) and " Dwarf" (flowering 4-6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years, which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, variety " Hainan Tall") to an estimated x173.32 read depth. A total scaffold length of 2.20 Gb was generated (N50 = 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28 039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that the obtained scaffold sequences covered 90.8% of the coconut genome and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome consisted of transposable elements, of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species.

  • Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera.
    Plant Omics, 2013
    Co-Authors: Yong Xiao, Haikuo Fan, Wei Xia, Yaodong Yang, Annaliese S. Mason, Songlin Zhao, Yi Luo, Ross Sager, Fei Qiao
    Abstract:

    Cocos nucifera (coconut) is an economically important tropical crop, but opportunities for molecular breeding are limited by lack of DNA sequence information for this species. Previous assessments of coconut germplasm have been conducted based solely on phenotypic data for agronomic and quality traits, due to lack of available molecular markers. In this study, we developed 30 novel microsatellite markers from Illumina transcriptome sequence data, and used these markers to evaluate coconut genetic diversity in 30 individuals representing accessions from China (12 samples) and Southeast Asia (18 samples). The microsatellite markers displayed low to high genetic polymorphism across the population: observed heterozygosity varied from 0.06 to 0.79, with an average of 0.39 ± 0.15. Our results indicated that the Southeast Asian population had a significantly higher number of alleles (p = 0.02), but not significantly different (p

  • RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.
    PloS one, 2013
    Co-Authors: Haikuo Fan, Yong Xiao, Wei Xia, Yaodong Yang, Annaliese S. Mason, Zhihui Xia, Fei Qiao, Songlin Zhao, Haoru Tang
    Abstract:

    Cocos nucifera (coconut), a member of the Arecaceae family, is an economically important woody palm grown in tropical regions. Despite its agronomic importance, previous germplasm assessment studies have relied solely on morphological and agronomical traits. Molecular biology techniques have been scarcely used in assessment of genetic resources and for improvement of important agronomic and quality traits in Cocos nucifera, mostly due to the absence of available sequence information. To provide basic information for molecular breeding and further molecular biological analysis in Cocos nucifera, we applied RNA-seq technology and de novo assembly to gain a global overview of the Cocos nucifera transcriptome from mixed tissue samples. Using Illumina sequencing, we obtained 54.9 million short reads and conducted de novo assembly to obtain 57,304 unigenes with an average length of 752 base pairs. Sequence comparison between assembled unigenes and released cDNA sequences of Cocos nucifera and Elaeis guineensis indicated that the assembled sequences were of high quality. Approximately 99.9% of unigenes were novel compared to the released coconut EST sequences. Using BLASTX, 68.2% of unigenes were successfully annotated based on the Genbank non-redundant (Nr) protein database. The annotated unigenes were then further classified using the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Our study provides a large quantity of novel genetic information for Cocos nucifera. This information will act as a valuable resource for further molecular genetic studies and breeding in coconut, as well as for isolation and characterization of functional genes involved in different biochemical pathways in this important tropical crop species.

  • rna seq analysis of Cocos nucifera transcriptome sequencing and de novo assembly for subsequent functional genomics approaches
    PLOS ONE, 2013
    Co-Authors: Yong Xiao, Haikuo Fan, Wei Xia, Yaodong Yang, Annaliese S. Mason, Zhihui Xia, Fei Qiao, Songlin Zhao, Haoru Tang
    Abstract:

    Background: Cocos nucifera (coconut), a member of the Arecaceae family, is an economically important woody palm grown in tropical regions. Despite its agronomic importance, previous germplasm assessment studies have relied solely on morphological and agronomical traits. Molecular biology techniques have been scarcely used in assessment of genetic resources and for improvement of important agronomic and quality traits in Cocos nucifera, mostly due to the absence of available sequence information. Methodology/Principal Findings: To provide basic information for molecular breeding and further molecular biological analysis in Cocos nucifera, we applied RNA-seq technology and de novo assembly to gain a global overview of the Cocos nucifera transcriptome from mixed tissue samples. Using Illumina sequencing, we obtained 54.9 million short reads and conducted de novo assembly to obtain 57,304 unigenes with an average length of 752 base pairs. Sequence comparison between assembled unigenes and released cDNA sequences of Cocos nucifera and Elaeis guineensis indicated that the assembled sequences were of high quality. Approximately 99.9% of unigenes were novel compared to the released coconut EST sequences. Using BLASTX, 68.2% of unigenes were successfully annotated based on the Genbank non-redundant (Nr) protein database. The annotated unigenes were then further classified using the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Conclusions/Significance: Our study provides a large quantity of novel genetic information for Cocos nucifera. This information will act as a valuable resource for further molecular genetic studies and breeding in coconut, as well as for isolation and characterization of functional genes involved in different biochemical pathways in this important tropical crop species.

Vivian M Rumjanek - One of the best experts on this subject based on the ideXlab platform.

  • The Effect of a Catechin-rich Extract of Cocos nucifera on Lymphocytes Proliferation
    Phytotherapy Research, 2003
    Co-Authors: Clarice Kirszberg, Daniele Esquenazi, Celuta Sales Alviano, Vivian M Rumjanek
    Abstract:

    Catechins are polyphenols with antioxidant activity. The fruit Cocos nucifera (Palmae) has a fi ber husk rich in catechins and the local population of northeast Brazil uses it as a medicine against various diseases. An anti-bacterial and anti-viral activity has been already observed using this substance. Plant extracts, from other sources, rich in catechins are inhibitory to tumour cells, suppressing their proliferation. The aim of the present work was to verify if catechins isolated from Cocos nucifera were capable of inhibiting cell proliferation. An extract obtained from Cocos nucifera was purified through adsorption chromatography using the resin XAD-2. The purified material was used in cultures of an erythroleukaemia cell line (K562) and on normal human peripheral blood lymphocytes. Cell viability was assessed using MTT. Cellular proliferation was measured by [(3)H]-thymidine incorporation and cell cycle analysis in a fl ow cytometer. A dose-dependent inhibitory effect was observed on tumour cells and on lymphocytes activated by phytohemaglutinin (PHA) or phorbol ester. For PHA this effect was irreversible being already established on the fi rst four hours of culture.

  • The effect of a catechin‐rich extract of Cocos nucifera on lymphocytes proliferation
    Phytotherapy research : PTR, 2003
    Co-Authors: Clarice Kirszberg, Daniele Esquenazi, Celuta S. Alviano, Vivian M Rumjanek
    Abstract:

    Catechins are polyphenols with antioxidant activity. The fruit Cocos nucifera (Palmae) has a fi ber husk rich in catechins and the local population of northeast Brazil uses it as a medicine against various diseases. An anti-bacterial and anti-viral activity has been already observed using this substance. Plant extracts, from other sources, rich in catechins are inhibitory to tumour cells, suppressing their proliferation. The aim of the present work was to verify if catechins isolated from Cocos nucifera were capable of inhibiting cell proliferation. An extract obtained from Cocos nucifera was purified through adsorption chromatography using the resin XAD-2. The purified material was used in cultures of an erythroleukaemia cell line (K562) and on normal human peripheral blood lymphocytes. Cell viability was assessed using MTT. Cellular proliferation was measured by [(3)H]-thymidine incorporation and cell cycle analysis in a fl ow cytometer. A dose-dependent inhibitory effect was observed on tumour cells and on lymphocytes activated by phytohemaglutinin (PHA) or phorbol ester. For PHA this effect was irreversible being already established on the fi rst four hours of culture.