A novel in-situ-process technique constructs whole circular cpDNA library

• Published in: Plant methods 2024-01, Vol.20 (1), p.2-2, Article 2
• Main Authors: Zhou, Qiang, Ding, Xianlong, Wang, Hongjie, Farooq, Zunaira, Wang, Liang, Yang, Shouping
• Format: Article
• Language: English
• Subjects: BAC library; Bioinformatics; Chloroplast; Chloroplast DNA; Chloroplasts; Circular cpDNA; Cloning; Deoxyribonucleic acid; DNA; Ethylenediaminetetraacetic acid; Evolution; Evolutionary biology; Functional analysis; Gene mapping; Gene sequencing; Genomes; Genomic libraries; Genomics; Humidity; In-situ lysis; In-situ substitute/ligation; In-situ-process; Leaves; Light; Lysis; Methodology; Methods; Molecular weight; Nucleotide sequence; Phylogeny; Physical mapping; Plants; Substitutes
• ISSN: 1746-4811; 1746-4811
• DOI: 10.1186/s13007-023-01126-7

The chloroplast genome (cp genome) is directly related to the study and analysis of molecular phylogeny and evolution of plants in the phylogenomics era. The cp genome, whereas, is highly plastic and exists as a heterogeneous mixture of sizes and physical conformations. It is advantageous to purify/enrich the circular chloroplast DNA (cpDNA) to reduce sequence complexity in cp genome research. Large-insert, ordered DNA libraries are more practical for genomics research than conventional, unordered ones. From this, a technique of constructing the ordered BAC library with the goal-insert cpDNA fragment is developed in this paper. This novel in-situ-process technique will efficiently extract circular cpDNA from crops and construct a high-quality cpDNA library. The protocol combines the in-situ chloroplast lysis for the high-purity circular cpDNA with the in-situ substitute/ligation for the high-quality cpDNA library. Individually, a series of original buffers/solutions and optimized procedures for chloroplast lysis in-situ is different than bacterial lysis in-situ; the in-situ substitute/ligation that reacts on the MCE membrane is suitable for constructing the goal-insert, ordered cpDNA library while preventing the large-insert cpDNA fragment breakage. The goal-insert, ordered cpDNA library is arrayed on the microtiter plate by three colonies with the definite cpDNA fragment that are homologous-corresponds to the whole circular cpDNA of the chloroplast. The novel in-situ-process technique amply furtherance of research in genome-wide functional analysis and characterization of chloroplasts, such as genome sequencing, bioinformatics analysis, cloning, physical mapping, molecular phylogeny and evolution.