(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Eukaryota: NE > Viridiplantae: NE > Streptophyta: NE > Streptophytina: NE > Embryophyta: NE > Tracheophyta: NE > Euphyllophyta: NE > Spermatophyta: NE > Magnoliophyta: NE > Mesangiospermae: NE > eudicotyledons: NE > Gunneridae: NE > Pentapetalae: NE > asterids: NE > lamiids: NE > Solanales: NE > Solanaceae: NE > Solanoideae: NE > Capsiceae: NE > Capsicum: NE > Capsicum annuum: NE
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MIAFPQSDLRWAIHSAASLPSFSAVSSPQQRRRPLCTNGSAGGSGSRTTP KPSVCTADELHYVPLPNNEWKLALWRYLPSPQGSRRNHPLLLLSGVGTNA IGYDLAPGSSFARYMSGQGFDTWILEVRGAGLSAKNSQVELKESLQGELE GISEELLGSTGAVSGLRDAAQVSAITSQLTEFGRALGNIVDGSQQPITQL TGLHNRFSITLEDFWKQLQLIGKYNWDFDHYLEEDMPTAMDYIRNQSRPE DGKLLAIGHSMGGILLYAMLSQDGYRGKCSELASVITLGSSLDYTTSRSS LKMLIPFVDPAKAVNLPVVPVGALLAAIYPLASYPPYLLSWLNPQISAQN MMHPELFERLVLKNFCTIPAKLLSQLSTAFEKGGLRNRSGTFFYKDHLHK SNVPLLALAGDKDLICPPEAVYETVKLIPENLATYKVFGEPRGPHYAHYD LVGGRMAYYQVYPRIIEFLSRHDTS
BACKGROUND: Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. RESULTS: We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. CONCLUSIONS: Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.
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 approximately 0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of approximately 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.
Capsicum annuum (Capsicum pepper) phospholipase A1, CaPLA1