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Organization and molecular evolution of a disease-resistance gene cluster in coffee trees.

Ribas AF, Cenci A, Combes MC, Etienne H, Lashermes P - BMC Genomics (2011)

Bottom Line: All these R-gene sequences appeared to be members of a CC-NBS-LRR (CNL) gene family that was only found at the SH3 locus in C. arabica.Furthermore, while homologs were found in several dicot species, comparative genomic analysis failed to find any CNL R-gene in the orthologous regions of other eudicot species.Gene conversion between paralog members, inter-subgenome sequence exchanges and positive selection appear to be the major forces acting on the evolution of SH3-CNL in coffee trees.

View Article: PubMed Central - HTML - PubMed

Affiliation: IRD - Institut de Recherche pour le Développement, UMR RPB, Montpellier Cedex, France.

ABSTRACT

Background: Most disease-resistance (R) genes in plants encode NBS-LRR proteins and belong to one of the largest and most variable gene families among plant genomes. However, the specific evolutionary routes of NBS-LRR encoding genes remain elusive. Recently in coffee tree (Coffea arabica), a region spanning the SH3 locus that confers resistance to coffee leaf rust, one of the most serious coffee diseases, was identified and characterized. Using comparative sequence analysis, the purpose of the present study was to gain insight into the genomic organization and evolution of the SH3 locus.

Results: Sequence analysis of the SH3 region in three coffee genomes, Ea and Ca subgenomes from the allotetraploid C. arabica and Cc genome from the diploid C. canephora, revealed the presence of 5, 3 and 4 R genes in Ea, Ca, and Cc genomes, respectively. All these R-gene sequences appeared to be members of a CC-NBS-LRR (CNL) gene family that was only found at the SH3 locus in C. arabica. Furthermore, while homologs were found in several dicot species, comparative genomic analysis failed to find any CNL R-gene in the orthologous regions of other eudicot species. The orthology relationship among the SH3-CNL copies in the three analyzed genomes was determined and the duplication/deletion events that shaped the SH3 locus were traced back. Gene conversion events were detected between paralogs in all three genomes and also between the two sub-genomes of C. arabica. Significant positive selection was detected in the solvent-exposed residues of the SH3-CNL copies.

Conclusion: The ancestral SH3-CNL copy was inserted in the SH3 locus after the divergence between Solanales and Rubiales lineages. Moreover, the origin of most of the SH3-CNL copies predates the divergence between Coffea species. The SH3-CNL family appeared to evolve following the birth-and-death model, since duplications and deletions were inferred in the evolution of the SH3 locus. Gene conversion between paralog members, inter-subgenome sequence exchanges and positive selection appear to be the major forces acting on the evolution of SH3-CNL in coffee trees.

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Alignment of the predicted amino acid sequences from SH3-CNL members. The coiled-coil, NBS and LRR domains are highlighted in lilac, blue and green, respectively. The motif EDVID [79] as well as the motifs P-loop/kinase 1, RNBS-A, kinase II, RNBS-B, RNBS-C, hydrophobic domain in NBS domain are underlined. The first sequence is shown in full, while for other proteins only amino acids that differ from the first one are indicated. A 8 bp deletions in B2_Ea and an 1 bp insertion in A2_Ea modifying the reading frame were disregarded. The xxLxLxx motif in the LRR domain is boxed, where L is any aliphatic amino acid and x is any amino acid. Gaps introduced at alignment are indicated by dashes, while asterisks indicate the presence of stop codons. NBS probe used in Southern hybridization is highlighted by a frame. The tryptophan residue (W), specific to the non-TIR-NBS-LRR class of plant disease R gene, located at the end of the kinase 2 motif [20], is highlighted in yellow.
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Figure 6: Alignment of the predicted amino acid sequences from SH3-CNL members. The coiled-coil, NBS and LRR domains are highlighted in lilac, blue and green, respectively. The motif EDVID [79] as well as the motifs P-loop/kinase 1, RNBS-A, kinase II, RNBS-B, RNBS-C, hydrophobic domain in NBS domain are underlined. The first sequence is shown in full, while for other proteins only amino acids that differ from the first one are indicated. A 8 bp deletions in B2_Ea and an 1 bp insertion in A2_Ea modifying the reading frame were disregarded. The xxLxLxx motif in the LRR domain is boxed, where L is any aliphatic amino acid and x is any amino acid. Gaps introduced at alignment are indicated by dashes, while asterisks indicate the presence of stop codons. NBS probe used in Southern hybridization is highlighted by a frame. The tryptophan residue (W), specific to the non-TIR-NBS-LRR class of plant disease R gene, located at the end of the kinase 2 motif [20], is highlighted in yellow.

Mentions: The coding sequence of all SH3-CNL members is composed of two exons separated by an intron ranging from 157 to 272 nucleotides in length. The first exon spanned 1042 nt while the second exon extended from 1703 to 2003 nt (Table 1). The protein sequence extended from 915 to 1015 aa (Table 1). The protein sequence alignment of the identified 12 SH3-CNL members (eight from C. arabica and four from C. canephora) is shown in figure 6. SH3-CNL_A2_Ca was chosen as query to annotate protein domains. BLASTp analysis against the Pfam database predicted a NBS domain between positions 173 and 465 aa, while analysis of the Conserved Domain Database predicted the beginning of the LRR region at position 625 aa of the query protein. COILS analysis revealed a coiled-coil region located between position 17 and 56 aa, confirming that this family belongs to the CC sub-family of NBS-LRR genes (or non-TIR sub-family). The LRR region of all genes consists of 12 repeats ranging from 23 to 31 aa. These repeats are sufficiently different to ensure an unambiguous alignment of amino-acid sequences. A 8 bp deletions modified the reading frame of B2_Ea and induced an early stop codon after the 10th LRR; similarly, an 1 bp insertion in the A2_Ea made this member a pseudogene. Both INDEL modifying the reading frame were disregarded in figure 6 and in the following analyses.


Organization and molecular evolution of a disease-resistance gene cluster in coffee trees.

Ribas AF, Cenci A, Combes MC, Etienne H, Lashermes P - BMC Genomics (2011)

Alignment of the predicted amino acid sequences from SH3-CNL members. The coiled-coil, NBS and LRR domains are highlighted in lilac, blue and green, respectively. The motif EDVID [79] as well as the motifs P-loop/kinase 1, RNBS-A, kinase II, RNBS-B, RNBS-C, hydrophobic domain in NBS domain are underlined. The first sequence is shown in full, while for other proteins only amino acids that differ from the first one are indicated. A 8 bp deletions in B2_Ea and an 1 bp insertion in A2_Ea modifying the reading frame were disregarded. The xxLxLxx motif in the LRR domain is boxed, where L is any aliphatic amino acid and x is any amino acid. Gaps introduced at alignment are indicated by dashes, while asterisks indicate the presence of stop codons. NBS probe used in Southern hybridization is highlighted by a frame. The tryptophan residue (W), specific to the non-TIR-NBS-LRR class of plant disease R gene, located at the end of the kinase 2 motif [20], is highlighted in yellow.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113787&req=5

Figure 6: Alignment of the predicted amino acid sequences from SH3-CNL members. The coiled-coil, NBS and LRR domains are highlighted in lilac, blue and green, respectively. The motif EDVID [79] as well as the motifs P-loop/kinase 1, RNBS-A, kinase II, RNBS-B, RNBS-C, hydrophobic domain in NBS domain are underlined. The first sequence is shown in full, while for other proteins only amino acids that differ from the first one are indicated. A 8 bp deletions in B2_Ea and an 1 bp insertion in A2_Ea modifying the reading frame were disregarded. The xxLxLxx motif in the LRR domain is boxed, where L is any aliphatic amino acid and x is any amino acid. Gaps introduced at alignment are indicated by dashes, while asterisks indicate the presence of stop codons. NBS probe used in Southern hybridization is highlighted by a frame. The tryptophan residue (W), specific to the non-TIR-NBS-LRR class of plant disease R gene, located at the end of the kinase 2 motif [20], is highlighted in yellow.
Mentions: The coding sequence of all SH3-CNL members is composed of two exons separated by an intron ranging from 157 to 272 nucleotides in length. The first exon spanned 1042 nt while the second exon extended from 1703 to 2003 nt (Table 1). The protein sequence extended from 915 to 1015 aa (Table 1). The protein sequence alignment of the identified 12 SH3-CNL members (eight from C. arabica and four from C. canephora) is shown in figure 6. SH3-CNL_A2_Ca was chosen as query to annotate protein domains. BLASTp analysis against the Pfam database predicted a NBS domain between positions 173 and 465 aa, while analysis of the Conserved Domain Database predicted the beginning of the LRR region at position 625 aa of the query protein. COILS analysis revealed a coiled-coil region located between position 17 and 56 aa, confirming that this family belongs to the CC sub-family of NBS-LRR genes (or non-TIR sub-family). The LRR region of all genes consists of 12 repeats ranging from 23 to 31 aa. These repeats are sufficiently different to ensure an unambiguous alignment of amino-acid sequences. A 8 bp deletions modified the reading frame of B2_Ea and induced an early stop codon after the 10th LRR; similarly, an 1 bp insertion in the A2_Ea made this member a pseudogene. Both INDEL modifying the reading frame were disregarded in figure 6 and in the following analyses.

Bottom Line: All these R-gene sequences appeared to be members of a CC-NBS-LRR (CNL) gene family that was only found at the SH3 locus in C. arabica.Furthermore, while homologs were found in several dicot species, comparative genomic analysis failed to find any CNL R-gene in the orthologous regions of other eudicot species.Gene conversion between paralog members, inter-subgenome sequence exchanges and positive selection appear to be the major forces acting on the evolution of SH3-CNL in coffee trees.

View Article: PubMed Central - HTML - PubMed

Affiliation: IRD - Institut de Recherche pour le Développement, UMR RPB, Montpellier Cedex, France.

ABSTRACT

Background: Most disease-resistance (R) genes in plants encode NBS-LRR proteins and belong to one of the largest and most variable gene families among plant genomes. However, the specific evolutionary routes of NBS-LRR encoding genes remain elusive. Recently in coffee tree (Coffea arabica), a region spanning the SH3 locus that confers resistance to coffee leaf rust, one of the most serious coffee diseases, was identified and characterized. Using comparative sequence analysis, the purpose of the present study was to gain insight into the genomic organization and evolution of the SH3 locus.

Results: Sequence analysis of the SH3 region in three coffee genomes, Ea and Ca subgenomes from the allotetraploid C. arabica and Cc genome from the diploid C. canephora, revealed the presence of 5, 3 and 4 R genes in Ea, Ca, and Cc genomes, respectively. All these R-gene sequences appeared to be members of a CC-NBS-LRR (CNL) gene family that was only found at the SH3 locus in C. arabica. Furthermore, while homologs were found in several dicot species, comparative genomic analysis failed to find any CNL R-gene in the orthologous regions of other eudicot species. The orthology relationship among the SH3-CNL copies in the three analyzed genomes was determined and the duplication/deletion events that shaped the SH3 locus were traced back. Gene conversion events were detected between paralogs in all three genomes and also between the two sub-genomes of C. arabica. Significant positive selection was detected in the solvent-exposed residues of the SH3-CNL copies.

Conclusion: The ancestral SH3-CNL copy was inserted in the SH3 locus after the divergence between Solanales and Rubiales lineages. Moreover, the origin of most of the SH3-CNL copies predates the divergence between Coffea species. The SH3-CNL family appeared to evolve following the birth-and-death model, since duplications and deletions were inferred in the evolution of the SH3 locus. Gene conversion between paralog members, inter-subgenome sequence exchanges and positive selection appear to be the major forces acting on the evolution of SH3-CNL in coffee trees.

Show MeSH
Related in: MedlinePlus