Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements
- Minkyu Park†1, 2,
- SungHwan Jo†3, 4,
- Jin-Kyung Kwon2, 5,
- Jongsun Park1, 6, 7, 8,
- Jong Hwa Ahn2, 5,
- Seungill Kim1, 2,
- Yong-Hwan Lee6, 7, 8,
- Tae-Jin Yang2, 5,
- Cheol-Goo Hur4,
- Byoung-Cheorl Kang2, 5,
- Byung-Dong Kim2, 5 and
- Doil Choi2, 5Email author
© Park et al; licensee BioMed Central Ltd. 2011
Received: 27 February 2010
Accepted: 29 January 2011
Published: 29 January 2011
Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato.
For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation.
Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.
The Solanaceae is an unusually divergent family consisting of approximately 90 genera and 3,000-4,000 species . Members of the Solanaceae have evolved into extremely divergent forms, ranging from trees to annual herbs, and they occupy diverse habitats ranging from deserts to aquatic areas . Such hyper-diversity in one family makes it useful to study plant adaptation and diversification. Despite this diversity, all Solanaceous species evolved during the last 40 million years . Furthermore, almost all members share the same chromosome number (x = 12) .
To date, diversity within the Solanaceae has been studied by comparative genome analyses using common genetic markers. As a result, we know that the Solanaceae genomes have undergone relatively small numbers of chromosomal rearrangements (e.g., about 5 rearrangements between potato and tomato and about 30 rearrangements between pepper and tomato), maintaining well-conserved gene content and order [3–8]. The conservation of the Solanaceae genic region was also identified by the comparison of a syntenic segment in eggplant, pepper, petunia and tomato .
Despite such conservation, the genome sizes of the Solanaceae family members are diverse. For example, the genome size of the Solanum tuberosum (potato) is 840 Mb, S. lycopersicum (tomato) 950 Mb, Petunia hybrida (petunia) 1200 Mb, and Capsicum annuum (pepper) 2700 Mb. However, the genetic analyses conducted to date were not successful at explaining genome size diversity due to limitations in the genetic markers. Hence, a sequence-level analysis to investigate the cause of the genome size diversity is required.
Among the Solanaceous species, pepper and tomato show strong advantages for the study of genome size difference because of following reasons. First, the genome size of pepper is three times larger than that of tomato. Second, the duplication of the whole genome did not occur during the evolution of both species . Third, although pepper and tomato show large size differences in their genomes, their speciation is estimated to have occurred recently (approximately 16.2-22.2 million years ago) , which makes them not as closely related as potato and tomato, but more closely related than tobacco and tomato within the Solanaceae family . Therefore, the investigation of genome diversity between pepper and tomato can represent the general trend of genome diversification among Solanaceous members that have not undergone the whole genome duplication.
To date, most studies related to the pepper genome have been carried out by generating genetic maps [6, 10–14]. In contrast, the structure of the tomato euchromatic and heterochromatic regions has been the subject of several studies through the analyses of tomato BAC sequences [15–17]. Furthermore, the tomato genome sequencing project is currently underway, with the goal of generating a reference genome in the Solanaceae[18–21].
As a first study concerning the expansion of the pepper genome, the present work addresses the causes behind the expansion of pepper euchromatic regions. For this purpose, 35.6 Mb of pepper sequences from 1,245 BAC clones selected from euchromatin-enriched regions were generated. Using information from the tomato genome project, 39.9 Mb BAC sequences of tomato were chosen for comparing orthologous gene-rich sequences and the constitution of repetitive elements between the pepper and tomato genomes. We used fluorescence in situ hybridization (FISH) to support the results. This study presents an example of the Solanaceae genome diversity revealing how the pepper euchromatic region was expanded.
Sequencing of pepper BAC clones
Comparison of visible genome structures
Comparison of repetitive elements in the orthologous gene-rich regions
Statistics of the compared pepper and tomato gene-rich sequences
Total length of compared sequence
Number of predicted genes
Total length of predicted genes
Genes paired into orthologous set
Genes that have no ortholog
Average length of coding region
Average length of intron
The comparative analysis of the orthologous gene-rich sequences revealed many insertions found exclusively in the pepper sequences. The insertions were transposable elements, and there were 35 transposable elements in the compared pepper sequences (Figure 3; colored boxes and Additional file 2). Boundary of the LTR-retrotransposons was determined in 16 elements by manual inspection (Figure 3; marked with asterisks in the colored boxes). The else transposons were found by gene prediction and repeat BLAST search in Repbase [24, 25]. All of the transposable elements were found in the inter-genic regions, therefore without a disruption of the other structural genes. The insertion of the transposable elements resulted in a doubling of the pepper sequence size in comparison to that of tomato. Accordingly, the gene density was lower in pepper (13,136 bp per one gene) than in tomato (7,011 bp per one gene).
Among identified transposable elements, LTR-retrotransposon sequences were the most abundant. Most of the LTR-retrotransposons were found in the pepper sequences (Figure 4). In addition, 28 of the 35 transposable elements found in pepper sequences were identified as LTR retrotransposons. The pepper sequences contained LTR-retrotransposon sequences with a frequency approximately 22 times higher than in the tomato sequences. The other two repeat classes also presented higher proportions in pepper than in tomato. Pepper had about 1.7 times as many DNA transposons, 4 times the number of non-LTR retrotransposons (Figure 4).
According to our transposon annotation results, the total length of the transposons found was 210,341 bp (see Additional file 2). Among them, Ty3/Gypsy-like element was the most abundant as 134,523 bp in total length (approximately 64% of the annotated repeats), which suggests its important role in pepper euchromatin expansion. The next was Ty1/Copia-like elements as 55,173 bp (approximately 26% of the annotated repeats). The Non-LTR retrotransposon and DNA transposon was 12,159 bp and 5,486 bp, respectively.
Similar gene composition between pepper and tomato
In contrast to the repetitive elements, gene constitution less affected the difference in the sequence size. In the compared sequences, a total of 145 genes were predicted excluding the transposable element genes. These included 75 pepper genes and 70 tomato genes (Table 1). The total length of the genes combined was 247,338 bp in pepper and 195,342 bp in tomato, showing a length difference of 51,996 bp. The total gene-length difference corresponded to approximately 10% of the total length difference of the compared sequences. The total gene-length difference was mainly caused by the intron-length difference. A total of 136 out of 145 genes were paired into 56 orthologous sets (see Additional file 2). In these sets the average length of the pepper coding regions was 1,366 bp, which was 34 bp longer than that of tomato (1,332 bp), whereas the average intron length in pepper was 1,815 bp, which was 356 bp longer than that of tomato (1,459 bp). Among the 56 orthologous sets, six sets (10.7%) consisted of duplicated genes. These six sets corresponded to 37 of the 145 genes (25%), of which 18 genes were in pepper and 19 in tomato (see Additional file 3). Hence, there was no remarkable bias in gene duplication number between both species (Table 1).
Identification of LTR retrotransposons in the pepper and tomato genome sequences
The causes for the accumulation of LTR retrotransposons in the pepper euchromatic regions were investigated by comparing the overall constitution of LTR retrotransposons between pepper and tomato by phylogenetic analysis. For this analysis, reverse transcriptase (RT) sequences, which are constitutive genes in LTR retrotransposons , were identified from the pepper and tomato genome sequences. The RTs were classified into Ty3/Gypsy and Ty1/Copia types by BLAST search in Repbase [24, 25]. A total of 155 Ty3/Gypsy-like and 166 Ty1/Copia-like tomato RTs were identified from 39.9 Mb of tomato BAC sequences (http://sgn.cornell.edu/about/tomato_sequencing.pl; downloaded in August, 2008) and 312 Ty3/Gypsy-like and 48 Ty1/Copia-like pepper RTs were found in the 35.6 Mb pepper BAC sequences. Because the tomato genome project focused on the gene-rich region, the number of heterochromatin-preferential LTR retrotransposons might be underestimated in this comparison.
Differential accumulation of a group of Ty3/Gypsy-like elements
The Ty3/Gypsy-like elements in the Del subgroup were identified as being accumulated in the pericentromeric heterochromatin. Yang et al. reported that the PCRT1 in the Del subgroup is a tomato Ty3/Gypsy-like element distributed throughout pericentromeric heterochromatin of tomato . This result was consistent with our FISH result of another tomato Del element (Figure 5; indicated by yellow triangle). Furthermore, the FISH result of the pepper Del element exhibited the same distribution pattern as that of tomato (Figure 5; indicated by purple triangle). These results suggest that the Del elements constitute pericentromeric heterochromatin in both genomes, which means they do not affect euchromatin expansion.
The differences that may affect the expansion of pepper euchromatic regions were observed in the Tat and Athila subgroups. The number of pepper Tat and Athila elements was approximately twice the number in tomato (42 in pepper and 23 in tomato). According to the previous report by Yang et al., PCRT2 and PCRT3 are the tomato Ty3/Gypsy-like elements preferentially distributed in the tomato heterochromatic regions . These two elements belonged to Athila and Tat respectively, suggesting that the tomato Ty3/Gypsy-like elements in these groups are accumulated in heterochromatic regions. In contrast, the FISH result of the pepper Tat element showed randomly distributed signals throughout the pepper chromosomes including the euchromatic regions (Figure 5; indicated by green triangle). Furthermore, four of the nine black arrows indicating the pepper Ty3/Gypsy-like elements found in the compared pepper gene-rich sequences belonged to Tat. Likewise, two of the nine elements belonged to the Athila subgroup, indicating the elements in this group are also found in pepper gene-rich regions. However, the Del subgroup didn't contain any of the Ty3/Gypsy-like elements found in the pepper gene-rich sequences (Figure 5). These results show that, in contrast to the distribution in tomato, the pepper Ty3/Gypsy-like elements in the Tat and Athila subgroups are randomly inserted throughout the whole genome, including the euchromatic regions.
Chromodomains in the Ty3/Gypsy-like elements
Proportion of the intact pepper Ty3/Gypsy-like elements in the genome
The proportion of the pepper Ty3/Gypsy-like elements in the genome was estimated using the intact LTR retrotransposons (see methods for detail) (Figure 6B). The proportion of the individual elements was broadly different according to the classified groups. The average proportion of the Tat elements was 1.28% but the Athila was 0.64%, suggesting more active accumulation of the Tat elements. The elements in the Del showed higher proportion than other classified groups in the genome as 2.01% of average proportion.
Highly diversified features with similar lineage collections of Ty1/Copia-like elements
The results of the present study revealed that one of the important factors for the expansion of pepper euchromatic regions was the massive accumulation of the pepper Tat and Athila elements. In the Tat and Athila subgroups, the Ty3/Gypsy-like elements were found to be approximately two times more abundant in pepper than tomato. Considering that the pepper sequences used in this study were smaller than those of tomato in terms of total length (three-quarters of tomato) and in each contig length (Figure 1), the number of pepper Tat and Athila elements would further exceed that of tomato. Given that the tomato Tat and Athila elements preferentially accumulated in the heterochromatic regions (Figure 7), the higher copy number and random insertion of the pepper Tat and Athila elements suggests their important role in the expansion of pepper euchromatic regions.
According to the FISH analyses, the Del elements in both pepper and tomato genomes were identified as forming the pericentromeric heterochromatin blocks. Unlike the Ty1/Copia-like elements, the Ty3/Gypsy-like elements that constitute pericentromeric heterochromatin blocks are known to be selectively inserted into the heterochromatic regions in A. thaliana. The existence of the chromodomain in both pepper and tomato Del intact elements can explain this insertion selectivity. The insertion site preferences of LTR retrotransposons have also been observed in other plant genomes, including conifers, and members of the genus Helianthus[31, 32]. Although the number of Del elements is predominant in the phylogenetic tree, accumulation of the Del elements would have expanded the pericentromeric heterochromatin, not affecting euchromatin expansion in both species.
Pereira reported that the Ty1/Copia-like elements in A. thaliana were randomly inserted into the whole genome, after which they underwent purifying selection in euchromatic regions . This resulted in the preferential accumulation of the Ty1/Copia-like elements in the pericentromeric heterochromatin blocks of A. thaliana genome. In the present study, a similar phenomenon was detected in the heterochromatin preferential accumulation of the tomato Ty3/Gypsy-like elements that belong to Tat and Athila (Figure 7). The absence of the chromodomain in the elements indicates its initial random insertions in the genome. However, the purifying selection may have been eliminated the tomato Tat and Athila elements from the tomato euchromatic regions, resulting in their preferential accumulation in the heterochromatic regions.
The comparative analysis of the LTR retrotransposons in the present study revealed a similar collection of lineages in both Ty3/Gypsy-like and Ty1/Copia-like elements. Given that the LTR retrotransposons of the same lineage have similar characteristics, both genomes would have accumulated the Ty1/Copia-like elements and Ty3/Gypsy-like elements of the Tat and Athila in their euchromatic regions. However, the copy number of the elements in the tomato euchromatic regions may have been reduced due to the purifying selection, which could have resulted in the lower accumulation of the LTR retrotransposons in the tomato euchromatic regions than in those of pepper.
The number of pepper Del elements corresponded to twice the number of tomato Del elements (256 in pepper and 122 in tomato). This difference was partially due to the euchromatin selective sequencing of the tomato genome project. Although the pepper BAC clones were selected by the labelled cDNAs of mRNAs, our bioinformatics survey suggested that a large portion of pepper BAC clones contained heterochromatic regions. This phenomenon can be caused by contamination with the transcripts of repetitive elements, such as retrotransposons, during the selection of the BAC clones.
The expansion of genome sizes through the accumulation of LTR retrotransposons is well documented among flowering plants [30, 33–35]. Based on the results of the present study, the expansion of the pepper genome is also due to the accumulation of LTR retrotransposons. A similar comparative analysis of repetitive elements in close species was carried out between A. thaliana and Brassica oleracea by Zang et al.. Zang et al. reported that the large size of the B. oleracea genome is accounted by the higher copy number of each type of transposable elements within a similar collection of lineages, explaining the overall genome expansion . However, the gene densities of both genomes were 4.5 kb/gene in A. thaliana and 6.6 kb/gene in B. oleracea, indicating that the euchromatic regions of both genomes are highly gene-rich, as is the case in tomato. In contrast with B. oleracea, pepper has an expanded euchromatin structure, and the present results explained the expansion of the euchromatic regions. Hence, the comparison of the pepper and tomato genomes can provide new insights into the expansion of euchromatic regions by the accumulation of repetitive elements.
The results of the present study show that the Ty3/Gypsy-like elements in the Tat and Athila play an important role in the expansion of the pepper euchromatic regions. The genic regions of pepper and tomato were found to be well conserved with regards to gene order and content. However, the euchromatic regions in pepper were expanded to twice the size of those in tomato, mainly due to the insertion of LTR retrotransposons. The LTR retrotransposons in the pepper euchromatic regions may also explain why the pepper euchromatic regions look like intermixed with the heterochromatin structures.
Sequencing of the pepper and tomato BAC clones
The selection of pepper BAC clones for the comparison of the orthologous gene-rich regions was performed as described in this section: seven tomato BAC sequences that are distributed on chromosome 2 were chosen. The tomato sequences were used as queries in a BLASTN search of the pepper EST database to find orthologous pepper ESTs. Two or three pepper ESTs that were orthologous to sequences about 30 kb apart in each tomato BAC clone were used as probes. The probes were labelled via PCR amplification using specific primers and 32P-labeled dCTP. Seven or eight labelled probes were pooled, and the Southern hybridizations were carried out on pepper BAC library filters. The filters were sequentially washed in 2 X SSC for 60 min, 1 X SSC for 60 min, and 0.5 X SSC 60 min. The positive clones were confirmed by colony PCR using the same primers. The pepper BAC clones that showed positive PCR results were used for sequencing. Each BAC clone was fully sequenced and analyzed by NICEM (http://nicem.snu.ac.kr/) using the ABI 3730xl system (Applied Biosystems Inc [ABI], Foster City, CA). From each pepper BAC clone, a shotgun sequencing library was constructed using the pUC118 vector with an average insert size of 3-5 kb. BigDye Terminator chemistry version 3.1 (ABI) was used for the sequencing reactions. All of the sequences were analyzed by Phred/Pharp/Consed processing . Base-calling and assembling of the sequences were carried out using the Phred/Phrap software. The Phred scores of the sequences were 30 or higher. The assembled sequences were edited using Consed software. Sequence editing for consensus contig formation was carried out using the Sequencher 4.1.5 (Gene codes Corp., Ann Arbor, USA). The tomato BAC sequences were generated by the same method as part of the International Tomato Sequencing Project of Korea .
A total of 1,235 pepper BAC clones were additionally selected for next-generation sequencing using 454 GS FLX-Titanium (454 Life Science, Roche). Each BAC clone DNA was manually extracted and normalized. The normalized BAC clone DNAs were pooled into 125 clones per a reaction channel of 454 GS FLX-Ti. Each sequencing reaction of 454 GS FLX-Ti was divided into two. The sequencing procedures for the 454 GS FLX-Ti were carried out using manufacturer-supplied protocols and reagents. The sequences were assembled by Newbler 2.0.1. The average coverage of the contigs was 18.22×. Among the assembled contigs, the contigs longer than 30 kb were used in the analyses.
Gene prediction and comparative analysis
For accurate gene structure analysis, we predicted genes using three steps as follows: (1) Genes were predicted by FGENESH using a trained data set from tomato . (2) The predicted genes were confirmed by BLASTP searches of the GenBank database (http://www.ncbi.nlm.nih.gov/) using the protein sequences of the predicted genes as queries. Among the predicted genes, those with scores greater than 100 and e-values less than e-20 were used in the next step. (3) Among the BLASTP results for each predicted gene, the protein sequence that had the highest score was chosen as a reference, and the gene models were predicted again by FGENESH+ using the trained data set from tomato. These results were used as gene models for the pepper and tomato sequences. The visualization of compared orthologous sequences was carried out using GATA  with minimum bits of 30 and maximum bits of 35.6. The repeat sequences were found by BLAST search in the Repbase repeat masking (http://girinst.org/censor/index.php) [24, 25].
Phylogenetic analysis of LTR retrotransposons
The RTs were found by Hmmer 2.1  using the RTs reported in the Pfam database (http://pfam.sanger.ac.uk/, Accession No. PF00078 and PF07727) as a training set. The super family of the RTs was determined by the Rebase repeat masking. The RTs were confirmed by BLASTP searches in the GenBank database, and the RTs with a score over 200 were used in the analyses. The RTs containing any frame shift mutations or deletions were manually deleted in the alignment. Intact LTR retrotransposons were predicted using LTR_FINDER  with the default settings or by manual inspection using DOT-PLOT analysis. These analyses were conducted in the environment of the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr/) .
The phylogenetic trees were generated using the MEGA 4.0 software . The alignments were carried out using ClustalW of MEGA 4.0 with the default settings (see Additional file 7, 8 and 9). The aligned RT sequences were used for generating the phylogenetic trees. The Poisson correction model and Neighbor-Joining method were used, and the phylogeny test was carried out by bootstrapping with 1,000 replications.
Chromodomain search and proportion calculation of the intact LTR retrotransposon in the genome
The chromodomains were found by BLASTX search of the intact LTR retrotransposons with the chromodomain proteins in the Pfam database (PF00385). The chromodomains found in the intact LTR retrotransposons were used again in finding the chromodomains in the other sequences. The intact LTR retrotransposons that have no chromodomain were confirmed again by the conserved domain search service in the NCBI (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi).
The proportions of the individual intact LTR retrotransposons in the pepper genome were calculated using the 90.8 Mbp of the assembled sequence and 3.2 Mbp of additional BAC sequences of pepper. By BLASTN search against the total 94 Mbp pepper sequence, total matched sequence length of each intact LTR retrotransposon was calculated. The threshold e-value of the search was e-5. The total matched sequence length of the individual intact LTR retrotransposon was divided by the 94 Mbp of pepper sequence size.
The FISH probes for analyzing the LTR retrotransposons were produced by PCR amplification using the primer sets listed in Additional file 10 online. Pachytene chromosomes of tomato (Lycopersicon esculentum cv. Micro-Tom) were prepared according to the methods of Koo et al. . Metaphase and pachytene chromosomes of pepper (Capsicum annuum cv. CM334) were prepared as described by Kwon et al. . All probes were labelled with biotin 16-dUTP or digoxygenin 11-dUTP by nick translation as described by the manufacturer's protocol (Roche, Germany). The FISH experiments for tomato and pepper were performed according to the methods described by Koo et al.  and Kwon et al. , respectively. The hybridization solutions contained 50% formamide (w/v), 10% dextran sulfate (w/v), 5 ng/μl salmon sperm DNA, and 20 ng of each probe in 2 X SSC. The probes were detected using fluorescein avidin DCS (Roche, Germany) and rhodamine anti-digoxygenin (Roche, Germany). Pachytene chromosomes were counterstained with DAPI (1 mg/ml) in Vectashield antifade (Vector Laboratories). All images were captured and analyzed using the DeltaVision imaging system and associated software (Applied Precision, USA) with a cool SNAP CCD camera at NICEM. All images were improved for optimal brightness and contrast using Adobe Photoshop.
bacterial artificial chromosome
expressed sequence tag
fluorescence in situ hybridization
long terminal repeat
This research was supported by a grant from Crop Functional Genomics Center (CG1132) of the 21st Century Frontier Research Program and National Research Foundation (Project No. 2010-0015105) funded by the Ministry of Education, Science and Technology of Republic of Korea.
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