De novo gene set assembly of the transcriptome of diploid, oilseed-crop species Perilla citriodora

• 발행기관: (사)한국식물생명공학회
• 저자명: Ji-Eun Kim Junkyoung Choe Woo Kyung Lee Sangmi Kim Myoung Hee Lee Tae-Ho Kim Sung-Hwan Jo Jeong Hee
• 간행물 정보: 『Journal of Plant Biotechnology』43권 3호, 293~301쪽, 전체 9쪽
• 주제분류: 농수해양 > 기타농수해양
• 파일형태: PDF
• 발행일자: 2016.09.30

영문 초록

High-quality gene sets are necessary for functional research of genes. Although Perilla is a commonly cultivated oil crop and vegetable crop in Southeast Asia, the quality of its available gene set is insufficient. To construct a high-quality Perilla gene set, we sequenced mRNAs extracted from different tissues of Perilla citriodora, the wild species (2n = 20) of Perilla. To make a high-quality gene set for P. citriodora, we compared the quality of assemblies produced by Velvet and Trinity, the two well-known de novo assemblers, and improved the de novo assembly pipeline by optimizing k-mers and removing redundant sequences. We then selected representative transcripts for loci according to several criteria. The improved assembly yielded a total of 86,396 transcripts and 38,413 representative transcripts. We evaluated the assembled transcripts by comparing them to 638 homologous Arabidopsis genes involved in fatty acid and TAG biosynthesis pathways. High proportions of full-length genes and transcripts in the assembled transcripts matched known genes in other species, indicating that the P. citriodora gene set can be applied in future functional studies. Our study provides a reference P. citriodora gene set for further studies. It will serve as valuable genetic resource to elucidate the molecular basis of various metabolisms.

목차

Introduction

Materials and Methods

Results and Discussion

Conclusions

Acknowledgements

References

키워드

Perilla citriodora Transcriptome de novo assembly gene set fatty acid biosynthesis TAG(triacylglyceride) biosynthesis metabolic pathway oilseed crop