Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos

Abstract

Background The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. However, the phylogenetic relationships based on large-scale chloroplast genomes (CpGenomes) were elusive. Moreover, most of the chloroplast DNA sequencing methods cannot meet the requirements of large-scale CpGenome sequencing, which greatly limits and impedes the in-depth research of plant genetics and evolution. Results To develop a set of bamboo probes, we used 99 high-quality CpGenomes with 6 bamboo CpGenomes as representative species for the probe design, and assembled 15 M unique sequences as the final pan-chloroplast genome. A total of 180,519 probes for chloroplast DNA fragments were designed and synthesized by a novel hybridization-based targeted enrichment approach. Another 468 CpGenomes were selected as test data to verify the quality of the newly synthesized probes and the efficiency of the probes for chloroplast capture. We then successfully applied the probes to synthesize, enrich, and assemble 358 non-redundant CpGenomes of woody bamboo in China. Evaluation analysis showed the probes may be applicable to chloroplasts in Magnoliales, Pinales, Poales et al. Moreover, we reconstructed a phylogenetic tree of 412 bamboos (358 in-house and 54 published), supporting a non-monophyletic lineage of the genus Phyllostachys. Additionally, we shared our data by uploading a dataset of bamboo CpGenome into CNGB (https://db.cngb.org/search/project/CNP0000502/) to enrich resources and promote the development of bamboo phylogenetics. Conclusions The development of the CpGenome enrichment pipeline and its performance on bamboos recommended an inexpensive, high-throughput, time-saving and efficient CpGenome sequencing strategy, which can be applied to facilitate the phylogenetics analysis of most green plants.

Comparative analyses of chloroplast genomes in ‘Red Fuji’ apples: low rate of chloroplast genome mutations

“…In addition, the moderate cp genome size is easy to sequence, and there is good collinearity between the cp genomes of various plant groups, making it convenient for comparative analysis ( Alzahrani, 2021 ). Therefore, the cp genome has a significant impact on the development of phylogenetic genomics ( Wang et al, 2021 ). The number of cp genomes that have been sequenced has increased exponentially owing to the development of sequencing technology ( Liu et al, 2012 ) The cp genome has been successfully used to analyze the phylogenetic relationships between numerous difficult species and study the structural characteristics, variation, and evolution of plants ( Yagi & Shiina, 2014 ).…”

Nanopore Sequencing Technology as an Emerging Tool for Diversity Studies of Plant Organellar Genomes

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