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Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos.
Wang, Jiongliang; Mu, Weixue; Yang, Ting; Song, Yue; Hou, Yin Guang; Wang, Yu; Gao, Zhimin; Liu, Xin; Liu, Huan; Zhao, Hansheng.
Afiliación
  • Wang J; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, China.
  • Mu W; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.
  • Yang T; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
  • Song Y; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
  • Hou YG; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
  • Wang Y; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, China.
  • Gao Z; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.
  • Liu X; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, China.
  • Liu H; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.
  • Zhao H; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, China.
BMC Plant Biol ; 21(1): 76, 2021 Feb 05.
Article en En | MEDLINE | ID: mdl-33546593
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Filogenia / Sondas de ADN / Cloroplastos / Poaceae Idioma: En Revista: BMC Plant Biol Asunto de la revista: BOTANICA Año: 2021 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Filogenia / Sondas de ADN / Cloroplastos / Poaceae Idioma: En Revista: BMC Plant Biol Asunto de la revista: BOTANICA Año: 2021 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido