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Positively Selected Orthologous Genes Identified in Sesame (Sesamum indicum) by Deep Resequencing
( Jie Yu ),( Myeong-hyeon Min ),( Sang-ho Chu ),( Kyu-won Kim ),( Yong-jin Park ) 한국육종학회 2019 Plant Breeding and Biotechnology Vol.7 No.1
Sesame (Sesamum indicum L.) is the queen of oil seed crops and is cultivated widely in tropical and subtropical areas. The availability of the sesame genome sequence presents unprecedented opportunities for studying its genetics, genomics, and evolution. In this report, we conducted a genome resequencing-based identification of sesame orthologs; in total, 26,379 coding sequences (CDSs) were isolated. Using a reciprocal best hit, we ultimately identified a total of 639 orthologs sets after one-to-one orthologs extraction across seven Pentapetalae plant species. These orthologs were considered to be the most credible between the two species, and in sesame. Furthermore, we performed a branch model-based maximum likelihood estimation of dN/dS of the orthologs, resulting in the identification of 198 evolutionarily accelerated orthologs and 66 positively selected genes (P-value and FDR < 0.05). An enrichment analysis and protein interaction network suggested 19 genes with important functions of the orthologs specific in sesame development and domestication. The method we used here provides a case study for identifying orthologous genes between sesame and other plants species that are distributed in equilibrium phylogenetically, which can be used in other plants.
( Jun Sang Ham ),( Woori Kwak ),( Oun Ki Chang ),( Gi Sung Han ),( Seok Geun Jeong ),( Kuk Hwan Seol ),( Hyoun Wook Kim ),( Geun Ho Kang ),( Beom Young Park ),( Hyun Jeong Lee ),( Jong Geun Kim ),( Ky 한국미생물 · 생명공학회 2013 Journal of microbiology and biotechnology Vol.23 No.7
Using a newly constructed de novo assembly pipeline, finished genome level assembly had been conducted for the probiotic candidate strain E. faecalis KACC 91532 isolated from a stool samples of Korean neonates. Our gene prediction identified 3,061 genes in the assembled genome of the strain. Among these, nine genes were specific only for the E. faecalis KACC 91532, compared with all of the four known reference genomes (EF62, D32, V583, OG1RF). We identified genes related to phenotypic characters and detected E. faecalis KACC 91532-specific evolutionarily accelerated genes using dN/dS analysis. From these results, we found the potential risk of KACC 91532 as a useful probiotic strain and identified some candidate genetic variations that could affect the function of enzymes.
정재훈,김권도,유동안,이찬호,강정선,조경진,강대경,곽우리,윤숙희,손화선,김희발,조서애 한국유전학회 2018 Genes & Genomics Vol.40 No.2
Lactobacillus plantarum is one of the widely-used probiotics and there have been a large number of advanced researches on the effectiveness of this species. However, the difference between previously reported plantarum strains, and the source of genomic variation among the strains were not clearly specified. In order to understand further on the molecular basis of L. plantarum on Korean traditional fermentation, we isolated the L. plantarum GB-LP4 from Korean fermented vegetable and conducted whole genome assembly. With comparative genomics approach, we identified the candidate genes that are expected to have undergone evolutionary acceleration. These genes have been reported to associate with the maintaining homeostasis, which are generally known to overcome instability in external environment including low pH or high osmotic pressure. Here, our results provide an evolutionary relationship between L. plantarum species and elucidate the candidate genes that play a pivotal role in evolutionary acceleration of GB-LP4 in high osmolarity environment. This study may provide guidance for further studies on L. plantarum.