Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

Abstract

As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.de novo genome sequence | genome expansion | Solanaceae evolution

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

“…Files of Amborella trichopoda, Capsicum annuum, Sesamum indicum, Phyllostachys heterocycla, and Musa acuminata were downloaded from the Pepper Genome Database (http://peppersequence. genomics.cn/page/species/index.jsp; Qin et al, 2014), Sinbase (http://ocrigenomics.org/Sinbase/manual.htm; Wang et al, 2014), BambooGDB (http:// www.bamboogdb.org/page/download.jsp; Peng et al, 2013), Banana Genome Hub (http://banana-genome.cirad.fr; D 'Hont et al, 2012), and the Amborella genome database (http://www.amborella.org; Amborella-Genome-Project, 2013), respectively.…”

Genome-wide characterization and expression analysis of GRAS gene family in pepper (Capsicum annuum L.)

“…SCL13 (PAT1 subfamily) in Arabidopsis has been reported to participate in phytochrome-B (phyB) sional transduction (Bolle et al 2000), whereas other members of the same subfamily includino PAT1, SCL5 and SCL21 mainly function as positive reoulators mediatino phyA sionalino pathway to control plant development (Torres-Galea et al 2006). Another GRAS member MOC1 is a positive reoulator of rice tillerino, which is directly related to the increase of orain yield.Pepper (Capsicum annuum L.) is an economically important veoetable and has tremendous value for providino food, spice, colorino aoent, pharmaceuticals and ornamental products (Kim et al 2014;Qin et al 2014). In 2013, the total pepper production of the world already reached 34.9 million tons, makino it the second laroest Solanaceae crop after tomato (Kim et al 2014).…”

“…CM334 and cv. Zunla-1 were used for this study, and their oenome information were downloaded from http://pepperoenome.snu.ac.kr/download.php and http://peppersequence.oenomics.cn/ respectively (Kim et al 2014;Qin et al 2014). Arabidopsis GRAS protein sequences previously reported were obtained from Arabidopsis Information Resource (https://www.Arabidopsis.oro/) (Tian et al 2004).…”

“…Pepper (Capsicum annuum L.) is an economically important veoetable and has tremendous value for providino food, spice, colorino aoent, pharmaceuticals and ornamental products (Kim et al 2014;Qin et al 2014). In 2013, the total pepper production of the world already reached 34.9 million tons, makino it the second laroest Solanaceae crop after tomato (Kim et al 2014).…”

“…In 2013, the total pepper production of the world already reached 34.9 million tons, makino it the second laroest Solanaceae crop after tomato (Kim et al 2014). The accomplishment of whole pepper oenome sequencino project in 2014 provides a platform for us to conduct a oenome-wide analysis for an entire oene family and explore the rioht oene which is critical for pepper orowth and development (Kim et al 2014;Qin et al 2014). By far, transcription factor families, such as WRKY, Dof, SBP-Box and Hsp70 have been characterized in pepper (Guo et al 2016; Guo et al 2015b; Wu et al 2016).…”