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Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences.

Terol J, Naranjo MA, Ollitrault P, Talon M - BMC Genomics (2008)

Bottom Line: Comparative genomic studies showed that citrus gene homology and microsyntheny with Populus trichocarpa was rather higher than with Arabidopsis thaliana, a species phylogenetically closer to citrus.In addition, BAC end sequencing has provided a first insight on the basic structure and organization of the citrus genome and has yielded valuable molecular markers for genetic mapping and cloning of genes of agricultural interest.Paired end sequences also may be very helpful for whole-genome sequencing programs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada, Náquera, Km. 4,5 Moncada, Valencia, E46113, Spain. terol_javalc@gva.es

ABSTRACT

Background: Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-term nature of tree breeding mostly impair citrus variety improvement. In woody plants, genomic science holds promise of improvements and in the Citrus genera the development of genomic tools may be crucial for further crop improvements. In this work we report the characterization of three BAC libraries from Clementine (Citrus clementina), one of the most relevant citrus fresh fruit market cultivars, and the analyses of 46.000 BAC end sequences. Clementine is a diploid plant with an estimated haploid genome size of 367 Mb and 2n = 18 chromosomes, which makes feasible the use of genomics tools to boost genetic improvement.

Results: Three genomic BAC libraries of Citrus clementina were constructed through EcoRI, MboI and HindIII digestions and 56,000 clones, representing an estimated genomic coverage of 19.5 haploid genome-equivalents, were picked. BAC end sequencing (BES) of 28,000 clones produced 28.1 Mb of genomic sequence that allowed the identification of the repetitive fraction (12.5% of the genome) and estimation of gene content (31,000 genes) of this species. BES analyses identified 3,800 SSRs and 6,617 putative SNPs. Comparative genomic studies showed that citrus gene homology and microsyntheny with Populus trichocarpa was rather higher than with Arabidopsis thaliana, a species phylogenetically closer to citrus.

Conclusion: In this work, we report the characterization of three BAC libraries from C. clementina, and a new set of genomic resources that may be useful for isolation of genes underlying economically important traits, physical mapping and eventually crop improvement in Citrus species. In addition, BAC end sequencing has provided a first insight on the basic structure and organization of the citrus genome and has yielded valuable molecular markers for genetic mapping and cloning of genes of agricultural interest. Paired end sequences also may be very helpful for whole-genome sequencing programs.

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GC content in BES of Citrus clementina BAC libraries. Distribution of GC content in coding and non-coding regions of BES of Citrus clementina BAC libraries.
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Figure 4: GC content in BES of Citrus clementina BAC libraries. Distribution of GC content in coding and non-coding regions of BES of Citrus clementina BAC libraries.

Mentions: Furthermore, total GC content in BESs estimated with EMBOSS was 39% while in coding and non-coding sequences, was 41% and 37%, respectively (Figure 4). No significant differences were found when the GC content was compared between the 3 BAC libraries constructed (see Additional File 1). The GC contents reported in other woody plants such as Scots Pine (Pinus sylvestris; 39.5%) [46] or yellow-poplar (Liriodendron tulipifera; 41%) [28] as well as in coding sequences from Solanaceae species i.e. Nicotiana tabacum (40.4%), Solanum tuberosum (39.0%), and Solanum esculentum (39.8%), or the Fabaceae Pisum sativum (39.2%) were also on the same range. The percentage of GC in Glycine max (46.5%) and A. thaliana (45.4%) was significantly higher [47].


Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences.

Terol J, Naranjo MA, Ollitrault P, Talon M - BMC Genomics (2008)

GC content in BES of Citrus clementina BAC libraries. Distribution of GC content in coding and non-coding regions of BES of Citrus clementina BAC libraries.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2561056&req=5

Figure 4: GC content in BES of Citrus clementina BAC libraries. Distribution of GC content in coding and non-coding regions of BES of Citrus clementina BAC libraries.
Mentions: Furthermore, total GC content in BESs estimated with EMBOSS was 39% while in coding and non-coding sequences, was 41% and 37%, respectively (Figure 4). No significant differences were found when the GC content was compared between the 3 BAC libraries constructed (see Additional File 1). The GC contents reported in other woody plants such as Scots Pine (Pinus sylvestris; 39.5%) [46] or yellow-poplar (Liriodendron tulipifera; 41%) [28] as well as in coding sequences from Solanaceae species i.e. Nicotiana tabacum (40.4%), Solanum tuberosum (39.0%), and Solanum esculentum (39.8%), or the Fabaceae Pisum sativum (39.2%) were also on the same range. The percentage of GC in Glycine max (46.5%) and A. thaliana (45.4%) was significantly higher [47].

Bottom Line: Comparative genomic studies showed that citrus gene homology and microsyntheny with Populus trichocarpa was rather higher than with Arabidopsis thaliana, a species phylogenetically closer to citrus.In addition, BAC end sequencing has provided a first insight on the basic structure and organization of the citrus genome and has yielded valuable molecular markers for genetic mapping and cloning of genes of agricultural interest.Paired end sequences also may be very helpful for whole-genome sequencing programs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada, Náquera, Km. 4,5 Moncada, Valencia, E46113, Spain. terol_javalc@gva.es

ABSTRACT

Background: Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-term nature of tree breeding mostly impair citrus variety improvement. In woody plants, genomic science holds promise of improvements and in the Citrus genera the development of genomic tools may be crucial for further crop improvements. In this work we report the characterization of three BAC libraries from Clementine (Citrus clementina), one of the most relevant citrus fresh fruit market cultivars, and the analyses of 46.000 BAC end sequences. Clementine is a diploid plant with an estimated haploid genome size of 367 Mb and 2n = 18 chromosomes, which makes feasible the use of genomics tools to boost genetic improvement.

Results: Three genomic BAC libraries of Citrus clementina were constructed through EcoRI, MboI and HindIII digestions and 56,000 clones, representing an estimated genomic coverage of 19.5 haploid genome-equivalents, were picked. BAC end sequencing (BES) of 28,000 clones produced 28.1 Mb of genomic sequence that allowed the identification of the repetitive fraction (12.5% of the genome) and estimation of gene content (31,000 genes) of this species. BES analyses identified 3,800 SSRs and 6,617 putative SNPs. Comparative genomic studies showed that citrus gene homology and microsyntheny with Populus trichocarpa was rather higher than with Arabidopsis thaliana, a species phylogenetically closer to citrus.

Conclusion: In this work, we report the characterization of three BAC libraries from C. clementina, and a new set of genomic resources that may be useful for isolation of genes underlying economically important traits, physical mapping and eventually crop improvement in Citrus species. In addition, BAC end sequencing has provided a first insight on the basic structure and organization of the citrus genome and has yielded valuable molecular markers for genetic mapping and cloning of genes of agricultural interest. Paired end sequences also may be very helpful for whole-genome sequencing programs.

Show MeSH