Abstract
BackgroundThe 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.ResultsTo 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.ConclusionsThe 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.
Highlights
The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology
Development of universal chloroplast probes for bamboos From the 3654 CpGenomes collected from NCBI, 567 high-quality CpGenomes were selected for probe development and divided into two datasets, with 99 CpGenomes for probe design and 468 CpGenomes for probe evaluation
We recommend a universal probe-based CpGenome enrichment pipeline, which successfully applied to bamboo CpGenomes, and 358 woody bamboo CpGenomes were acquired
Summary
The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. The phylogenetic relationships based on large-scale chloroplast genomes (CpGenomes) were elusive. 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. The subfamily Bambusoideae belongs to the grass family Poaceae and exhibits substantial phenotypic diversity, with 1642 species in 125 genera, three tribes, and 15 subtribes, which have been classified into ~ 75 clades [1]. As one of the most ecologically and industrially valuable tribes of Bambusoideae, woody bamboos were used for furniture, paper, fiber textiles, and fuel [2]. The phylogenetic relationships based on more massive amounts of woody bamboos remain elusive due to the lack of extensive and high-quality genomic resources
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