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The chloroplast phylogenetic haplotype network clustered individuals per species instead of S\n                    <jats:sub>H<\/jats:sub>\n                    factors. However, for the first time, it allowed the molecular validation of\n                    <jats:italic>Coffea arabica<\/jats:italic>\n                    as the maternal parent of the spontaneous hybrid \u201cH\u00edbrido de Timor\u201d. Individual reads were also aligned on the\n                    <jats:italic>C. arabica<\/jats:italic>\n                    reference genome to relate S\n                    <jats:sub>H<\/jats:sub>\n                    factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the S\n                    <jats:sub>H<\/jats:sub>\n                    9 factor, due to specific DNA variants linked to chromosome 7c (from\n                    <jats:italic>C. canephora<\/jats:italic>\n                    -derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in S\n                    <jats:sub>H<\/jats:sub>\n                    9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the S\n                    <jats:sub>H<\/jats:sub>\n                    profile. This study introduces an unexplored strategy for identifying protein\/genes associated with S\n                    <jats:sub>H<\/jats:sub>\n                    factors and candidate targets of\n                    <jats:italic>H. vastatrix<\/jats:italic>\n                    effectors, thereby creating new perspectives for coffee breeding programs.\n                  <\/jats:p>","DOI":"10.1038\/s41598-023-41950-4","type":"journal-article","created":{"date-parts":[[2023,9,25]],"date-time":"2023-09-25T07:02:49Z","timestamp":1695625369000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["The chloroplast protein HCF164 is predicted to be associated with Coffea SH9 resistance factor against Hemileia vastatrix"],"prefix":"10.1038","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9676-1036","authenticated-orcid":false,"given":"Leonor","family":"Guerra-Guimar\u00e3es","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7799-0183","authenticated-orcid":false,"given":"Carla","family":"Pinheiro","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8753-4950","authenticated-orcid":false,"given":"Ana Sofia F.","family":"Oliveira","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9425-2326","authenticated-orcid":false,"given":"Andrea","family":"Mira-Jover","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8807-567X","authenticated-orcid":false,"given":"Javier","family":"Valverde","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6927-8938","authenticated-orcid":false,"given":"Fernanda A. de F.","family":"Guedes","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9324-3030","authenticated-orcid":false,"given":"Herlander","family":"Azevedo","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9507-3311","authenticated-orcid":false,"given":"Vitor","family":"V\u00e1rzea","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2505-8116","authenticated-orcid":false,"given":"Antonio Jes\u00fas","family":"Mu\u00f1oz Pajares","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,9,25]]},"reference":[{"key":"41950_CR1","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1111\/mpp.12512","volume":"18","author":"P Talhinhas","year":"2017","unstructured":"Talhinhas, P. et al. The coffee leaf rust pathogen Hemileia vastatrix: One and a half centuries around the tropics. Mol. Plant Pathol. 18, 1039. https:\/\/doi.org\/10.1111\/mpp.12512 (2017).","journal-title":"Mol. Plant Pathol."},{"key":"41950_CR2","doi-asserted-by":"publisher","first-page":"16209","DOI":"10.1038\/nplants.2016.209","volume":"3","author":"Z Mehrabi","year":"2017","unstructured":"Mehrabi, Z. & Lashermes, P. Protecting the origins of coffee to safeguard its future. Nat. Plants 3, 16209. https:\/\/doi.org\/10.1038\/nplants.2016.209 (2017).","journal-title":"Nat. Plants"},{"key":"41950_CR3","unstructured":"International Coffee Organization. Coffee Market Report, accessed 08 February 2023; www.ico.org\/documents\/cy2022-23\/cmr-0123-e.pdf (2023)."},{"key":"41950_CR4","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1007\/s004380050965","volume":"261","author":"P Lashermes","year":"1999","unstructured":"Lashermes, P. et al. 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