Retrotransposons- a Major Driving Force in Plant Genome Evolution and a Useful Tool for Genome Analysis

Jun Zou,Huihui Gong,Tae-Jin Yang,Jinling Meng 한국작물학회 2009 Journal of crop science and biotechnology Vol.12 No.1

As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to the unforeseen transposition activities. Regulation of transposition is relatively complex and three factors such as maintaining structure for none- or cis- or trans-acting transposition, control by host genome and induction by biotic and abiotic stress may contribute altering its transposition activity. The important roles of retrotransposons to modify genome size, remodel genome structure, and displace gene functions in the plant genome have been proven by a growing number of research studies up to now, which indicates that retrotransposons are a great driving force in genome evolution. For this review, we summarized the latest theoretic and practical research progress on plant retrotransposons for their distribution, regulation of activity, the impact on the architecture of plant genomes, and put forward the future prospects. As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to the unforeseen transposition activities. Regulation of transposition is relatively complex and three factors such as maintaining structure for none- or cis- or trans-acting transposition, control by host genome and induction by biotic and abiotic stress may contribute altering its transposition activity. The important roles of retrotransposons to modify genome size, remodel genome structure, and displace gene functions in the plant genome have been proven by a growing number of research studies up to now, which indicates that retrotransposons are a great driving force in genome evolution. For this review, we summarized the latest theoretic and practical research progress on plant retrotransposons for their distribution, regulation of activity, the impact on the architecture of plant genomes, and put forward the future prospects.

Genome Sequencing and Genome-Wide Identification of Carbohydrate-Active Enzymes (CAZymes) in the White Rot Fungus Flammulina fennae

이창수,공원식,박영진 한국미생물·생명공학회 2018 한국미생물·생명공학회지 Vol.46 No.3

Whole-genome sequencing of the wood-rotting fungus, Flammulina fennae, was carried out to identify carbohydrate- active enzymes (CAZymes). De novo genome assembly (31 kmer) of short reads by next-generation sequencing revealed a total genome length of 32,423,623 base pairs (39% GC). A total of 11,591 gene models in the assembled genome sequence of F. fennae were predicted by ab initio gene prediction using the AUGUSTUS tool. In a genome-wide comparison, 6,715 orthologous groups shared at least one gene with F. fennae and 10,667 (92%) of 11,591 genes for F. fennae proteins had orthologs among the Dikarya. Additionally, F. fennae contained 23 species-specific genes, of which 16 were paralogous. CAZyme identification and annotation revealed 513 CAZymes, including 82 auxiliary activities, 220 glycoside hydrolases, 85 glycosyltransferases, 20 polysaccharide lyases, 57 carbohydrate esterases, and 45 carbohydrate binding-modules in the F. fennae genome. The genome information of F. fennae increases the understanding of this basidiomycete fungus. CAZyme gene information will be useful for detailed studies of lignocellulosic biomass degradation for biotechnological and industrial applications.

Genome Sequencing and Genome-Wide Identification of Carbohydrate-Active Enzymes (CAZymes) in the White Rot Fungus Flammulina fennae

( Chang-soo Lee ),( Won-sik Kong ),( Young-jin Park ) 한국미생물생명공학회(구 한국산업미생물학회) 2018 한국미생물·생명공학회지 Vol.46 No.3

Whole-genome sequencing of the wood-rotting fungus, Flammulina fennae, was carried out to identify carbohydrate- active enzymes (CAZymes). De novo genome assembly (31 kmer) of short reads by next-generation sequencing revealed a total genome length of 32,423,623 base pairs (39% GC). A total of 11,591 gene models in the assembled genome sequence of F. fennae were predicted by ab initio gene prediction using the AUGUSTUS tool. In a genome-wide comparison, 6,715 orthologous groups shared at least one gene with F. fennae and 10,667 (92%) of 11,591 genes for F. fennae proteins had orthologs among the Dikarya. Additionally, F. fennae contained 23 species-specific genes, of which 16 were paralogous. CAZyme identification and annotation revealed 513 CAZymes, including 82 auxiliary activities, 220 glycoside hydrolases, 85 glycosyltransferases, 20 polysaccharide lyases, 57 carbohydrate esterases, and 45 carbohydrate binding-modules in the F. fennae genome. The genome information of F. fennae increases the understanding of this basidiomycete fungus. CAZyme gene information will be useful for detailed studies of lignocellulosic biomass degradation for biotechnological and industrial applications.

Genome Sequencing and Genome-Wide Identification of Carbohydrate-Active Enzymes (CAZymes) in the White Rot Fungus Flammulina fennae

Lee, Chang-Soo,Kong, Won-Sik,Park, Young-Jin The Korean Society for Microbiology and Biotechnol 2018 한국미생물·생명공학회지 Vol.46 No.3

Whole-genome sequencing of the wood-rotting fungus, Flammulina fennae, was carried out to identify carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) of short reads by next-generation sequencing revealed a total genome length of 32,423,623 base pairs (39% GC). A total of 11,591 gene models in the assembled genome sequence of F. fennae were predicted by ab initio gene prediction using the AUGUSTUS tool. In a genome-wide comparison, 6,715 orthologous groups shared at least one gene with F. fennae and 10,667 (92%) of 11,591 genes for F. fennae proteins had orthologs among the Dikarya. Additionally, F. fennae contained 23 species-specific genes, of which 16 were paralogous. CAZyme identification and annotation revealed 513 CAZymes, including 82 auxiliary activities, 220 glycoside hydrolases, 85 glycosyltransferases, 20 polysaccharide lyases, 57 carbohydrate esterases, and 45 carbohydrate binding-modules in the F. fennae genome. The genome information of F. fennae increases the understanding of this basidiomycete fungus. CAZyme gene information will be useful for detailed studies of lignocellulosic biomass degradation for biotechnological and industrial applications.

Retrotransposons - a Major Driving Force in Plant Genome Evolution and a Useful Tool for Genome Analysis

Zou, Jun,Gong, Huihui,Yang, Tae-Jin,Meng, Jinling 한국작물학회 2009 Journal of crop science and biotechnology Vol.12 No.1

As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to unforeseen transposition activities. Regulation of transposition is relatively complex and three factors such as maintaining structure for none- or cis- or trans-acting transposition, being controlled by the host genome and induction by biotic and abiotic stress may contribute altering its transposition activity. The important roles of retrotransposons to modify genome size, remodel genome structure, and displace gene functions in the plant genome have been proven by a growing number of research studies till date, which indicates that retrotransposons are important driving force in genome evolution. For this review, we summarized the latest theoretic and practical research progresses on plant retrotransposons for their distribution, regulation of activity, the impact on the architecture of plant genomes, and put forward the future prospects.

No excessive mutations in transcription activator-like effector nuclease-mediated α-1,3-galactosyltransferase knockout Yucatan miniature pigs

Choi, Kimyung,Shim, Joohyun,Ko, Nayoung,Park, Joonghoon Asian Australasian Association of Animal Productio 2020 Animal Bioscience Vol.33 No.2

Objective: Specific genomic sites can be recognized and permanently modified by genome editing. The discovery of endonucleases has advanced genome editing in pigs, attenuating xenograft rejection and cross-species disease transmission. However, off-target mutagenesis caused by these nucleases is a major barrier to putative clinical applications. Furthermore, off-target mutagenesis by genome editing has not yet been addressed in pigs. Methods: Here, we generated genetically inheritable α-1,3-galactosyltransferase (GGTA1) knockout Yucatan miniature pigs by combining transcription activator-like effector nuclease (TALEN) and nuclear transfer. For precise estimation of genomic mutations induced by TALEN in GGTA1 knockout pigs, we obtained the whole-genome sequence of the donor cells for use as an internal control genome. Results: In-depth whole-genome sequencing analysis demonstrated that TALEN-mediated GGTA1 knockout pigs had a comparable mutation rate to homologous recombination-treated pigs and wild-type strain controls. RNA sequencing analysis associated with genomic mutations revealed that TALEN-induced off-target mutations had no discernable effect on RNA transcript abundance. Conclusion: Therefore, TALEN appears to be a precise and safe tool for generating genomeedited pigs, and the TALEN-mediated GGTA1 knockout Yucatan miniature pigs produced in this study can serve as a safe and effective organ and tissue resource for clinical applications.

T-DNA 돌연변이를 이용한 벼 기능 유전체 연구

류학승,류나연,정기홍,안진흥,전종성 한국식물생명공학회 2010 JOURNAL OF PLANT BIOTECHNOLOGY Vol.37 No.2

Rice (Oryza sativa) is a major cereal crop that has been developed as a monocot model species. In past decades rice researchers have established valuable resources for functional genomics in rice, such as complete genome sequencing, high-density genetic maps, a full length cDNA database, genome-wide transcriptome data, and a large number of mutants. Of these, rice mutant lines are very important to definitively determine functions of genes associated with valuable agronomic traits. In this review we summarize the progress of functional genomics approaches in rice using T-DNA mutants. 주요 작물인 벼 (Oryza sativa)는 단자엽 모델식물이다. 현재까지 벼 연구자들은 전체 염기서열 분석을 완료하였으며, 고밀도 유전자 지도 작성, 전장 cDNA 유전자 은행구축, 게놈 규모의 유전자 발현 정보 및 대량의 돌연변이 집단을 육성하는 등 기능 유전체 연구를 위한 중요한 재료를 확립하였다. 특히 벼 돌연변이 라인은 유용 농업형질 유전자들의 기능을 최종적으로 규명하는데 매우 중요하게 사용되고 있다. 본 종설에서는 벼 T-DNA 돌연변이를 사용한 기능 유전체 연구에 대한 최근의 현황을 요약하고자 하였다.

A One-Step System for Convenient and Flexible Assembly of Transcription Activator-Like Effector Nucleases (TALENs)

Zhao, Jinlong,Sun, Wenye,Liang, Jing,Jiang, Jing,Wu, Zhao Korean Society for Molecular and Cellular Biology 2016 Molecules and cells Vol.39 No.9

Transcription activator-like effector nucleases (TALENs) are powerful tools for targeted genome editing in diverse cell types and organisms. However, the highly identical TALE repeat sequences make it challenging to assemble TALEs using conventional cloning approaches, and multiple repeats in one plasmid are easily catalyzed for homologous recombination in bacteria. Although the methods for TALE assembly are constantly improving, these methods are not convenient because of laborious assembly steps or large module libraries, limiting their broad utility. To overcome the barrier of multiple assembly steps, we report a one-step system for the convenient and flexible assembly of a 180 TALE module library. This study is the first demonstration to ligate 9 mono-/dimer modules and one circular TALEN backbone vector in a one step process, generating 9.5 to 18.5 repeat sequences with an overall assembly rate higher than 50%. This system makes TALEN assembly much simpler than the conventional cloning of two DNA fragments because this strategy combines digestion and ligation into one step using circular vectors and different modules to avoid gel extraction. Therefore, this system provides a convenient tool for the application of TALEN-mediated genome editing in scientific studies and clinical trials.

Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus <i>Flammulina elastica</i>

Park, Young-Jin,Jeong, Yong-Un,Kong, Won-Sik MDPI 2018 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.19 No.8

<P>Next-generation sequencing (NGS) of the <I>Flammulina elastica</I> (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one <I>F. elastica</I> protein. Among the 12,536 predicted genes, <I>F. elastica</I> contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from <I>F. elastica</I> genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the <I>F. elastica</I> genome. Although the CAZyme repertoire of <I>F. elastica</I> was similar to those of other fungal species, the total number of GTs in <I>F. elastica</I> was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in <I>F. elastica</I>, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.</P>

T-DNA 돌연변이를 이용한 벼 기능 유전체 연구

류학승,류나연,정기홍,안진흥,전종성,Ryu, Hak-Seung,Ryoo, Na-Yeon,Jung, Ki-Hong,An, Gynheung,Jeon, Jong-Seong 한국식물생명공학회 2010 식물생명공학회지 Vol.37 No.2

Rice (Oryza sativa) is a major cereal crop that has been developed as a monocot model species. In past decades rice researchers have established valuable resources for functional genomics in rice, such as complete genome sequencing, high-density genetic maps, a full length cDNA database, genome-wide transcriptome data, and a large number of mutants. Of these, rice mutant lines are very important to definitively determine functions of genes associated with valuable agronomic traits. In this review we summarize the progress of functional genomics approaches in rice using T-DNA mutants.