Organellar genome assembly methods and comparative analysis of horticultural plants. Issue 1 (10th January 2018)

• Record Type: Journal Article
• Authors: Wang, Xuelin; Cheng, Feng; Rohlsen, Dekai; Bi, Changwei; Wang, Chunyan; Xu, Yiqing; Wei, Suyun; Ye, Qiaolin; Yin, Tongming; Ye, Ning
• Is Part Of: Horticulture research. Volume 5:Issue 1(2018)
• Publication Date: 2018-01-10
• Subjects: Genome -- Genome assembly algorithms -- Next-generation sequencing; Horticulture -- Research -- Periodicals; 635.072
• DOI: 10.1038/s41438-017-0002-1
• Languages: English
• ISSNs: 2052-7276

Abstract

Abstract: Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants. In this paper, we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing (NGS) data. Sequencing reads were first assembled by Newbler, Amos, and Minimus software with default parameters. The remaining gaps were then filled through BLASTN search and PCR. The complete DNA sequence was corrected based on Illumina sequencing data using BWA (Burrows–Wheeler Alignment tool) software. The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation. Using this procedure, the complete mitochondrial and chloroplast genomes of an ornamental plant, Salix suchowensis, and a fruit tree, Ziziphus jujuba, were identified. This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants. Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome. In addition, a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA. Our study will provide an important reference for organellar genome assembly in other horticultural plants. Furthermore, phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants. Genetics: Innovative DNA assembly method for mitochondrial and chloroplast genomes: A new method makes it easier to assemble the DNA sequences of mitochondrial and chloroplast genomes for horticultural plants. Most strategies for assembling the genomes of chloroplasts (which conduct photosynthesis) and mitochondria (which supply cellular energy) require the isolation of organellar DNA from total DNA. However, using bioinformatics software, a team led by Tongming Yin and Ning Ye from Nanjing Forestry University, China, identified a way to pull out all the DNA sequence reads for these organelles from complete next-generation sequencing data, without the need for specialized sample preparation. As a proof-of-principle, the researchers used the protocol to decode the mitochondrial and chloroplast genomes of the ornamental plant Salix suchowensis and the fruit tree Ziziphus jujube . Comparative analyses of mitochondrial and chloroplast genomes assembled in this way could reveal new insights into plant evolutionary relationships.