Limits...
Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes.

Guyot R, de la Mare M, Viader V, Hamon P, Coriton O, Bustamante-Porras J, Poncet V, Campa C, Hamon S, de Kochko A - BMC Plant Biol. (2009)

Bottom Line: This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome.The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago.Altogether, these results provide valuable information to identify candidate genes in C. canephora genome and serve as a foundation to establish strategies for whole genome sequencing.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR GDP, IRD BP 64501, Centre IRD de Montpellier, Montpellier Cedex 5, France. romain.guyot@mpl.ird.fr

ABSTRACT

Background: Coffea canephora, also called Robusta, belongs to the Rubiaceae, the fourth largest angiosperm family. This diploid species (2x = 2n = 22) has a fairly small genome size of approximately 690 Mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. Here, we report the 160 kb of the first C. canephora Bacterial Artificial Chromosome (BAC) clone ever sequenced and its fine analysis.

Results: This clone contains the CcEIN4 gene, encoding an ethylene receptor, and twenty other predicted genes showing a high gene density of one gene per 7.8 kb. Most of them display perfect matches with C. canephora expressed sequence tags or show transcriptional activities through PCR amplifications on cDNA libraries. Twenty-three transposable elements, mainly Class II transposon derivatives, were identified at this locus. Most of these Class II elements are Miniature Inverted-repeat Transposable Elements (MITE) known to be closely associated with plant genes. This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome. Comparative sequence analysis indicated an extensive conservation between C. canephora and most of the reference dicotyledonous genomes studied in this work, such as tomato (S. lycopersicum), grapevine (V. vinifera), barrel medic M. truncatula, black cottonwood (Populus trichocarpa) and Arabidopsis thaliana. The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago.

Conclusion: This study provides a first glimpse of C. canephora genome composition and evolution. Our data revealed a remarkable conservation of the microcollinearity between C. canephora and V. vinifera and a high conservation with other distant dicotyledonous reference genomes. Altogether, these results provide valuable information to identify candidate genes in C. canephora genome and serve as a foundation to establish strategies for whole genome sequencing. Future large-scale sequence comparison between C. canephora and reference sequenced genomes will help in understanding the evolutionary history of dicotyledonous plants.

Show MeSH

Related in: MedlinePlus

Physical map of the 160,404 bp sequence of the coffee BAC 46C02. Black boxes represent identified coding regions and arrowheads indicate transcriptional orientation of genes. The CcEIN4 gene is indicated in red. Colored boxes represent identified transposable elements as follows: violet for transposons, blue for MITEs and brown for LINE. Markers used for genetic mapping on LGH (EIN4 and BAC-37) are indicated by a yellow triangle. P indicates partial gene, whereas a and E symbolize respectively successful gene amplification on C. canephora cDNA libraries and strong identities with C. canephora coffee ESTs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2656508&req=5

Figure 2: Physical map of the 160,404 bp sequence of the coffee BAC 46C02. Black boxes represent identified coding regions and arrowheads indicate transcriptional orientation of genes. The CcEIN4 gene is indicated in red. Colored boxes represent identified transposable elements as follows: violet for transposons, blue for MITEs and brown for LINE. Markers used for genetic mapping on LGH (EIN4 and BAC-37) are indicated by a yellow triangle. P indicates partial gene, whereas a and E symbolize respectively successful gene amplification on C. canephora cDNA libraries and strong identities with C. canephora coffee ESTs.

Mentions: In total, 21 genes were identified and validated by sequence alignments, giving an overall gene density of about one gene per 7.8 kb, considering the partial gene (g1) that covers the 5' part of the BAC insert (Table 1; Figure 2). Similarities with plant Expressed Sequence Tag sequences (EST) were found for the 21 identified genes (Table 1). Eight genes (g2, g4, g5, g6, g7, g14, g15 and g16) have almost perfect matches with C. canephora ESTs and mRNA, with sequence identities higher than 97%, suggesting that these genes are expressed. All the remaining genes have significant matches with plant ESTs (> 70% identity). On the 10 genes analyzed, seven (g3, g7, g8, g9, g10, g11 and g13) showed PCR amplifications on two C. canephora cDNA libraries (Table 1). For genes g3 and g7, sequencing of PCR products allowed the fine determination of the gene model and then the re-annotation of the gene predictions. Gene 6 (g6) encodes an ethylene receptor with a high sequence identity (85.7%) with the tomato ethylene receptor neverripe gene (ETR5 accession AY600439, [17]). This gene, called CcEIN4 (position from 36174 to 40482 bp), was previously cloned and analyzed in our lab [15]. On the 19 remaining coding genes, 16 contain known protein domains in pfam database [18] (Table 1). Among them, a gene coding for an ERF/AP2 transcription factor has been identified from 75,661 to 76,365 bp (g12, CcERF1).


Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes.

Guyot R, de la Mare M, Viader V, Hamon P, Coriton O, Bustamante-Porras J, Poncet V, Campa C, Hamon S, de Kochko A - BMC Plant Biol. (2009)

Physical map of the 160,404 bp sequence of the coffee BAC 46C02. Black boxes represent identified coding regions and arrowheads indicate transcriptional orientation of genes. The CcEIN4 gene is indicated in red. Colored boxes represent identified transposable elements as follows: violet for transposons, blue for MITEs and brown for LINE. Markers used for genetic mapping on LGH (EIN4 and BAC-37) are indicated by a yellow triangle. P indicates partial gene, whereas a and E symbolize respectively successful gene amplification on C. canephora cDNA libraries and strong identities with C. canephora coffee ESTs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2656508&req=5

Figure 2: Physical map of the 160,404 bp sequence of the coffee BAC 46C02. Black boxes represent identified coding regions and arrowheads indicate transcriptional orientation of genes. The CcEIN4 gene is indicated in red. Colored boxes represent identified transposable elements as follows: violet for transposons, blue for MITEs and brown for LINE. Markers used for genetic mapping on LGH (EIN4 and BAC-37) are indicated by a yellow triangle. P indicates partial gene, whereas a and E symbolize respectively successful gene amplification on C. canephora cDNA libraries and strong identities with C. canephora coffee ESTs.
Mentions: In total, 21 genes were identified and validated by sequence alignments, giving an overall gene density of about one gene per 7.8 kb, considering the partial gene (g1) that covers the 5' part of the BAC insert (Table 1; Figure 2). Similarities with plant Expressed Sequence Tag sequences (EST) were found for the 21 identified genes (Table 1). Eight genes (g2, g4, g5, g6, g7, g14, g15 and g16) have almost perfect matches with C. canephora ESTs and mRNA, with sequence identities higher than 97%, suggesting that these genes are expressed. All the remaining genes have significant matches with plant ESTs (> 70% identity). On the 10 genes analyzed, seven (g3, g7, g8, g9, g10, g11 and g13) showed PCR amplifications on two C. canephora cDNA libraries (Table 1). For genes g3 and g7, sequencing of PCR products allowed the fine determination of the gene model and then the re-annotation of the gene predictions. Gene 6 (g6) encodes an ethylene receptor with a high sequence identity (85.7%) with the tomato ethylene receptor neverripe gene (ETR5 accession AY600439, [17]). This gene, called CcEIN4 (position from 36174 to 40482 bp), was previously cloned and analyzed in our lab [15]. On the 19 remaining coding genes, 16 contain known protein domains in pfam database [18] (Table 1). Among them, a gene coding for an ERF/AP2 transcription factor has been identified from 75,661 to 76,365 bp (g12, CcERF1).

Bottom Line: This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome.The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago.Altogether, these results provide valuable information to identify candidate genes in C. canephora genome and serve as a foundation to establish strategies for whole genome sequencing.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR GDP, IRD BP 64501, Centre IRD de Montpellier, Montpellier Cedex 5, France. romain.guyot@mpl.ird.fr

ABSTRACT

Background: Coffea canephora, also called Robusta, belongs to the Rubiaceae, the fourth largest angiosperm family. This diploid species (2x = 2n = 22) has a fairly small genome size of approximately 690 Mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. Here, we report the 160 kb of the first C. canephora Bacterial Artificial Chromosome (BAC) clone ever sequenced and its fine analysis.

Results: This clone contains the CcEIN4 gene, encoding an ethylene receptor, and twenty other predicted genes showing a high gene density of one gene per 7.8 kb. Most of them display perfect matches with C. canephora expressed sequence tags or show transcriptional activities through PCR amplifications on cDNA libraries. Twenty-three transposable elements, mainly Class II transposon derivatives, were identified at this locus. Most of these Class II elements are Miniature Inverted-repeat Transposable Elements (MITE) known to be closely associated with plant genes. This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome. Comparative sequence analysis indicated an extensive conservation between C. canephora and most of the reference dicotyledonous genomes studied in this work, such as tomato (S. lycopersicum), grapevine (V. vinifera), barrel medic M. truncatula, black cottonwood (Populus trichocarpa) and Arabidopsis thaliana. The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago.

Conclusion: This study provides a first glimpse of C. canephora genome composition and evolution. Our data revealed a remarkable conservation of the microcollinearity between C. canephora and V. vinifera and a high conservation with other distant dicotyledonous reference genomes. Altogether, these results provide valuable information to identify candidate genes in C. canephora genome and serve as a foundation to establish strategies for whole genome sequencing. Future large-scale sequence comparison between C. canephora and reference sequenced genomes will help in understanding the evolutionary history of dicotyledonous plants.

Show MeSH
Related in: MedlinePlus