{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T17:09:24Z","timestamp":1790096964608,"version":"4.0.1"},"reference-count":42,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T00:00:00Z","timestamp":1789862400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing","id":[{"id":"https:\/\/ror.org\/014pqvh89","id-type":"ROR","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/014pqvh89","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Chinese Academy of Agricultural Sciences Innovation Project","award":["CAAS-ASTIP-IVFCAAS"],"award-info":[{"award-number":["CAAS-ASTIP-IVFCAAS"]}],"id":[{"id":"https:\/\/ror.org\/0313jb750","id-type":"ROR","asserted-by":"crossref"}]},{"award":["CAAS-ASTIP-IVFCAAS"],"award-info":[{"award-number":["CAAS-ASTIP-IVFCAAS"]}],"id":[{"id":"https:\/\/ror.org\/0313jb750","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Common bean (Phaseolus vulgaris L.) is an economically important grain legume for the human diet and sustainable agricultural development. Snap bean, a vegetable-type common bean cultivated for edible immature pods, serves as a crucial dietary source of essential vitamins, minerals and proteins. However, its evolutionary and domestication history remains poorly characterized. Here, we assembled and characterized the complete chloroplast genome of snap bean using PacBio HiFi sequencing technology. The chloroplast genome formed a single circular molecule of 150,248 bp, consisting of a pair of inverted repeat regions, a large single-copy region, and a small single-copy region. A total of 75 protein-coding genes, 37 tRNA genes, and 8 rRNA genes were annotated. Phylogenomics revealed that snap bean has the closest relationship with dry common bean, grouping with lima bean; Phaseolus is phylogenetically nearest to Vigna. Comparative plastid genomics identified variants in accD, rpoC2, matK, and other coding genes. Nucleotide diversity analysis detected several highly variable hotspot regions, including accD, trnY-psbD, ndhH, and ycf1-rps15, which are promising informative plastid markers for phylogeny and population genetics. These findings deepen our understanding of legume chloroplast evolution and lay genomic foundations for common bean phylogenetic research and genetic breeding improvement.<\/jats:p>","DOI":"10.3390\/ijms27188393","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T13:32:12Z","timestamp":1790083932000},"page":"8393","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Chloroplast Genome Sequence of Snap Bean (Phaseolus vulgaris L.) and Comparative Analyses with Other Legume Chloroplast Genomes"],"prefix":"10.3390","volume":"27","author":[{"given":"Zhiyuan","family":"Liu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Jiawei","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Zhaosheng","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Helong","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Hongbing","family":"She","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8919-2747","authenticated-orcid":false,"given":"Wei","family":"Qian","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Pathania, A., Sharma, S.K., and Sharma, P.N. 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