Insight into pepper genome in comparison to tomato
Authors: Arpita Srivastava and Manisha Mangal

Pepper (Capsicum annuum) is the most widely grown spice crop in the world. Though most members of the Solanacea family have the same number of chromosomes (n = 12) yet they differ drastically in genome size and the pepper genome also consists of 12 chromosomes. The pepper genome is extraordinarily large compared to other Solanaceous species though it has not undergone whole genome duplication or polyploidization since its speciation within the Solanaceae. The average genome size of the other well known Solanaceous species, such as tomato, potato and tobacco is approximately 1000 Mb, whereas the pepper genome is approximately three times larger. Compared to the tomato genome, the pepper genome is approximately three times larger and has a different chromosome structure.

The size of 12 Capsicum species has been estimated. The estimated sizes of the pepper haploid chromosomes ranged from 3090 Mbp to 5643 Mbp. It has been reported that genome size of the most popular commercial species C. annuum, was the smallest (3090 Mbp) among the various species known. The genomes of the other cultivatedCapsicum species which includes frutescens, chinense and baccatum have also been found to be smaller than those of the wild races.

Comparison between chilli peppers and tomato genome

Euchromatin and the heterochromatin content also differs between the two genus. Tomato is characterized by distinct the boundary between the euchromatin and the heterochromatin while the same is absent in pepper. Heterochromatin in tomato is centered on the peri-centromeric regions. In contrast to this the pepper heterochromatin is quite diffused and extended and is also found in the euchromatic regions. Studies on the basis of the comparative analysis of the genetic maps generated by conserved ortholog sequence (COS) markers revealed conserved synteny and gene content at the sequence level and the time of speciation between pepper and tomato was estimated to be 19.2 million years ago.

A total of 34,903 protein-coding genes have been predicted in pepper. This gene number is approximately the same as for tomato and potato which suggests a similar gene number in Solanaceae plants. Genome-wide analysis of small RNAs has identified 177 microRNAs corresponding to 37 microRNA families. The distribution of small RNAs correlated well with gene density in the hot pepper genome and is also similar to in tomato.

Studies on the cause of genome expansion in pepper were done by comparing orthologous BAC sequence pairs between pepper and tomato. The total size of the orthologous sequence pairs was double in pepper when compared to tomato. The average lengths of the coding regions has been found to be similar between the two species, however, the average intron length was 356 bp longer in pepper. Although the gene synteny is well conserved between the two crops, the gene density in pepper is much less.

Comparative analysis has revealed that the major reason for the genome expansion in the pepper was the insertion of transposable elements. All of the transposable elements were found in the intronic regions of the pepper sequences without any disruption of the coding genes. The insertion of the transposable elements was identified in most of the pepper sequences studied, but it was completely absent in the tomato sequences. The insertions resulted in a doubling of the total length of the pepper sequences. Long-terminal repeat (LTR) retro transposons were the most abundant among the identified transposable elements. The pepper sequences when compared with tomato sequences contained approximately 22 times more LTR retrotransposons. Pepper had other two repeat classes of DNA transposons and non-LTR retrotransposons which were again more abundant in pepper than in tomato. Pepper had about 1.7 times as many DNA transposons and four times as many non-LTR retro transposons as the tomato had. Among the repeat sequences found in pepper, approximately 64 percent were Ty3/Gypsy-like elements, suggesting an important role for these elements in the expansion of the pepper euchromatin.

Ty3/Gypsy -like elements were studied to investigate their effects on the structure of the pepper genome. Using the phylogenetic tree, it was possible to compare the composition of the Ty3/Gypsy-like elements in pepper and tomato genomes. The phylogenetic tree was largely divided into three major subgroups: Tat, Athila and Del. The Del elements show preferential accumulation in heterochromatic regions of pepper and tomato both. The number of Tat and Athila elements found in pepper was approximately twice that found in tomato which provides the evidence that pepper heterochromatin expanded via the accumulation of Tat and Athila subgroups. TheTy3/ Gypsy-like elements are preferentially distributed in the heterochromatic regions of the tomato. These two elements belonged to the Athila and Tat subgroups, respectively, suggesting that these subgroups accumulate in the heterochromatic regions of the tomato. In contrast Tat subgroup showed random distribution throughout the pepper chromosomes, including the euchromatic regions. The Tat and Athila elements are relatively common in the gene-rich regions of the pepper. In contrast to their distribution in tomato, the Ty3/Gypsy -like elements in the Tat and Athila subgroups are distributed randomly throughout the whole genome of pepper, resulting in euchromatin expansion.

Statistics for the hot pepper genome and gene annotation (Source: Kim et al., 2014)

Number of scaffolds 37,989
Total length of scaffolds 3.06 Gb
Anchored scaffolds 2.63 Gb (86.0%)
N50 of scaffolds 2.47 Mb
Longest (shortest) scaffolds 18.6 Mb (264 bp)
Number of contigs 337,328
Total length of contigs 2.96 Gb
N50 of contigs 30.0 kb (24,618th)
Longest (shortest) contigs 442.1 kb (71 bp)
GC content 35.03%
Number of genes 34,903
Average/total coding sequence length 1,009.9/35.2 Mb
Average exon/intron length 286.5 bp/541.6 bp
Total length of transposable elements 2.34 Gb (76.4%)

Kim Seungill, Park, Minkyu, Yeom, Seon-In, Kim, Yong-Min, Lee, Je Min, Lee, Hyun et al. (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nature Genetics . 46: 270 UR -

About Author / Additional Info:
I am working as a scientist at Indian Agricultural Research Institute, New Delhi with specialisation in Genetics and Plant Breeding. Basically involved in hot pepper improvement programs.