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.
Highlights
Horticultural plants, which are grown for aesthetic value or as food in a home garden, can improve mental and physical health[1]
A total of 573,141 raw reads were obtained with a mean length of 360 bp
The sequencing of S. suchowensis was performed on the Roche 454 and Illumina HiSeq 2000 systems
Summary
Horticultural plants, which are grown for aesthetic value or as food in a home garden, can improve mental and physical health[1]. Chloroplasts and mitochondria are the necessary organelles forming the powerhouse of the cell. Chloroplasts conduct photosynthesis, and mitochondria indirectly supply energy. Wang et al Horticulture Research (2018)5:3 coding sequence extension and a large repetitive section[7], the lengths of the published mitochondrial genomes of angiosperms, especially horticultural plants, vary in size[8,9], ranging from 258 kb in Raphanus sativus[10] to 983 kb in Cucurbita pepo[11]. Sequence data of plant organellar genomes are accumulating at a very rapid pace. Over 1193 chloroplast and 199 mitochondrial genome sequences of land plants are included in the NCBI GenBank Organelle Genome Resources Only 39 organellar genomes of horticultural plants are present in the database
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