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Pepper Sequencing Study Provides Fodder for Understanding Capsicum Traits, Evolution

NEW YORK (GenomeWeb News) – In a study appearing online this week in the Proceedings of the National Academy of Sciences, researchers from China, Mexico, France, the US, and Denmark described details of pepper evolution and biology that they detected through genome sequencing and population re-sequencing of cultivated peppers and their wild ancestors.

The team started by generating genome sequences for the cultivated pepper accession called Capsicum annuum Zunla-1 as well as the pepper's wild progenitor Chiltepin, also known as C. annuum var. glabriusculum. Along with transcriptome profiling, the genomes highlighted key features of the pepper genome while providing a look at changes that accompanied the plant's domestication.

Additional domestication details stemmed from the researchers' efforts to re-sequence another 20 plants from cultivated, wild, and semi-wild pepper accessions, along with genome and transcriptome sequence comparisons to related plants. For instance, they detected signs of artificial selection in some peppers that seem to coincide with domestication-related genes, as well as genes expressed during pepper fruit development.

"The two pepper genomes together with 20 re-sequencing accessions, including [three] accessions that are classified as semi-wild/wild, provide a better understanding of the evolution, domestication, and divergence of various pepper species," the study's authors wrote, "and ultimately, will enhance future genetic improvement of this important worldwide crop."

Findings from the analysis, together with the availability of the new sequences, are expected to prove useful for those focused on improving pepper production and understanding the roots of sought-after pepper traits such as spiciness and medicinal compound production.

The researchers used Illumina instruments to do shotgun sequencing on genomic DNA from a cultivated C. annuum accession called Zunla-1 that is grown in China's Guizhou province. They used a similar strategy to sequence Chiltepin, a wild pepper landrace from the north-central region of Mexico.

After putting the reads together into de novo assemblies spanning 3.35 billion bases, in the case of the cultivated plant, and 3.48 billion bases for the wild Chiltepin progenitor, the team assigned the sequences to pepper chromosomes with help from a high-density linkage map centered on almost 7,700 SNPs.

The researchers then annotated the genomes with the help of RNA sequence data from various pepper tissues at different developmental stages, uncovering 35,336 predicted protein-coding genes in the cultivated pepper genome and an estimated 34,476 protein-coding genes in the wild plant. They also detected thousands of long, non-coding and small, interfering RNAs, along with hundreds of candidate microRNAs.

The group's comparisons with other plants from the Solanaceae plant family — particularly potato, tomato, and Arabidopsis — highlighted almost 10,300 gene families shared in all of the species and more than 1,200 gene families found only in the pepper genome.

A phylogenetic analysis based on thousands of orthologous genes from that group of Solanaceae plants and a few others put pepper plant divergence from the potato and tomato lineage roughly 36 million years ago. From that phylogeny, the study's authors also traced the advent of the broader Solanaceae family back to about 156 million years ago.

Meanwhile, a look at translocation and duplication patterns in the plant genomes pointed to a recent whole-genome duplication in the ancestor of pepper and tomato lineage prior to a split between those plants.

When they re-sequenced peppers from 18 cultivated and two wild or semi-wild accessions to depths of 10-fold to 30-fold average coverage, the researchers detected more than 9.8 suspected SNPs and around 237,500 small insertions and deletions.

The team harnessed these variants as part of their search for signs of artificial selection in the pepper, digging up more than 100 parts of the pepper genome showing strong selective sweeps. Among the 511 genes in these regions were genes contributing to functions ranging from transcriptional regulation, stress response, and disease resistance to plant growth and fruit development.

That analysis revealed transcription factors that affect the expression of genes suspected of contributing to cultivated pepper traits, researchers reported. In addition, their comparison of expression patterns at play during pepper and tomato fruit development highlighted transcriptional differences that coincide with known fruit features in each of the plants.

Similarly, by comparing gene expression across pepper tissues, the team was able to take a closer look at the genes that contribute to the production of characteristic pepper products, particularly the capsaicinod compounds that give peppers their spicy flavor.

Although further research is needed to unravel the genetic differences that dictate pungency, fruit size, and other features that vary across the dozens of pepper species found in the Capsicum genus, authors of the current analysis argued that "[t]he Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but the Solanaceae family," adding that it will "facilitate the establishment of more effective pepper breeding programs."