Organellar genome assembly methods and comparative analysis of horticultural plants

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.

The complete chloroplast genome sequence of pomegranate ‘Bhagwa’

“…As important resources for both basic research and crop breeding, the nuclear genome of P. granatum has been determined (Yuan et al 2018). Compared to the nuclear genome, chloroplast (cp) genome is a low-cost and efficient way to get valuable information for understanding the evolutionary history of plants due to its relatively small size, predominantly uniparental inheritance, and near absence of recombination (Gitzendanner et al 2018;Wang et al 2018). In some cases, high-copy numbers of the cp genome may be found in the whole genome sequencing data of plants, which makes it possible to obtain complete cp genome using whole genome sequencing data (Twyford and Ness 2017).…”

PACVr: Plastome Assembly Coverage Visualization in R

“…Despite the development of assembly algorithms customized for plastid genomes, the plastome assembly process remains imperfect and often requires the verification, if not manual correction, of the assembly product. Concomitant with the surge in plastid genome sequencing, many new algorithms and pipelines specifically designed for the assembly of plastid genomes have been developed (Ankenbrand et al, 2018;Dierckxsens et al, 2017;Izan et al, 2017;McKain and Wilson, 2017;Coissac, 2017;Gruenstaeudl et al, 2018;Jian et al, 2018;Wang et al, 2018). Most of these tools allow a more accurate and targeted assembly of the plastid genome than generic assembly software, but in many cases some form of manual intervention or post-processing of the assembly results remains necessary (Izan et al, 2017;Gruenstaeudl et al, 2018).…”

The complete mitochondrial genome of an important root crop cassava (Manihot esculenta)

“…The genomic DNA was isolated from fresh young leaves as described previously (Zhang et al 1995) and deposited in CIAT (International Center for Tropical Agriculture). In this study, we assembled the complete mt DNA sequence of M. esculenta into a freeof-gap genome of 682,840 bp according to the reference (Bi et al 2016;Wang et al 2018). The GC content is 44.47%, which is a widespread value in higher plants.…”