| Lineage-specific genes,a set of genes with no detectable coding-sequence similarity in the genomes of other lineages,are often associated with species-specific traits and adaptive evolution.Solanum is a large and important genus of flowering plants,which includes many plants of economic,ornamental and officinal importance,and steroidal glycoalkaloids are mainly produced by most species of this genus.Potato(Solanum tuberosum)is the most important non-grain food crop in the world and is the core of global food security and economic development.The study of lineage-specific genes in potato can help reveal the mechanisms of special traits of potatoes or Solanum plants,and it provides a distinct frame on crop genetic improvement and resistance breeding.It also sets the stage for investigating genes with unknown function.Based on local alignment search,2521 potato-specific genes and 3331 Solanumspecific genes were identified in a doubled-monoploid potato,S.tuberosum group Phureja DM1-3 516 R44(hereafter referred to as DM).1361 potato-specific genes and 1687 Solanum-specific genes were found in a diploid wild potato,S.commersonii(hereafter referred to as CMM).1023 potato-specific genes and 617 Solanum-specific genes were detected in M6,a diploid inbred clone of S.chacoense.Moreover,26 and 22 single-copy orthologous groups restricted to the 3 kinds of potatoes and Solanum lineage separately were identified by comparative analysis.On average,lineage-specific genes have shorter gene lengths,longer intron lengths,shorter protein lengths,higher GC contents,fewer exons and a higher percentage of singleexon genes compared to evolutionarily conserved genes in DM.The numbers of both the potato-specific genes and the Solanum-specific genes on each chromosome are positively correlated with the lengths of chromosomes of DM and CMM,but the numbers of the lineage-specific genes show preferential distribution on certain chromosomes in M6 genome.Contrary to the evolutionarily conserved genes,the lineage-specific genes,especially the Solanum-specific genes,are mainly located near the centromere of each chromosome in DM genome,which may lead to the decrease of their transcription levels.Expression profiling indicated that the transcript support of lineage-specific genes was significantly less than that of the evolutionarily conserved genes,and most of them exhibited distinct temporal and spatial expression patterns and/or related to biotic/abiotic stress or different phytohormones.GO and KEGG enrichment analysis showed that lineage-specific genes were mainly enriched in the term of “binding” and the pathway of aromatic amino acids biosynthesis.Subcellular localization showed the proteins of selected 10 lineage-specific genes were at least located in nucleus,and 3 of them had transcriptional activation activity in yeast.These results suggest that lineage-specific genes may function through transcriptional regulation and may play an important role in environmental adaption by participating in secondary metabolic pathways.We luckily found that transient overexpression of PGSC0003DMG400046242,a Solanum-specific gene with transcriptional activation activity in yeast,can lead to plant hypersensitive cell death in Nicotiana benthamiana,implying that its function might be related to the immune response.Overall,this study identified lineage-specific genes in 3 different species of potato,and systematically analyzed their characteristics,expression patterns and potential functions.Finally,the function of PGSC0003DMG400046242 was preliminarily explored.It provides valuable clues for future functional analysis of special characters of Solanum plants such as potato that may be related to lineage-specific genes,and it is also of great significance for researches on biodiversity and environmental adaptability. |
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