{"id":5203,"date":"2025-12-22T09:31:35","date_gmt":"2025-12-22T02:31:35","guid":{"rendered":"https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/?p=5203"},"modified":"2026-03-30T14:12:15","modified_gmt":"2026-03-30T07:12:15","slug":"revisiting-chloroplast-genomic-landscape-and-annotation-towards-comparative-chloroplast-genomes-of-rhamnaceae","status":"publish","type":"post","link":"https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/en\/revisiting-chloroplast-genomic-landscape-and-annotation-towards-comparative-chloroplast-genomes-of-rhamnaceae\/","title":{"rendered":"Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae"},"content":{"rendered":"\t<div class=\"img has-hover x md-x lg-x y md-y lg-y\" id=\"image_1723189329\">\n\t\t\t\t\t\t\t\t<div class=\"img-inner dark\" >\n\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"766\" height=\"800\" src=\"https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/wp-content\/uploads\/2025\/12\/12870_2023_4074_Fig1_HTML-766x800.jpg\" class=\"attachment-large size-large\" alt=\"\" srcset=\"https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/wp-content\/uploads\/2025\/12\/12870_2023_4074_Fig1_HTML-766x800.jpg 766w, https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/wp-content\/uploads\/2025\/12\/12870_2023_4074_Fig1_HTML-383x400.jpg 383w, https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/wp-content\/uploads\/2025\/12\/12870_2023_4074_Fig1_HTML-768x802.jpg 768w, https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/wp-content\/uploads\/2025\/12\/12870_2023_4074_Fig1_HTML.jpg 777w\" sizes=\"auto, (max-width: 766px) 100vw, 766px\" \/>\t\t\t\t\t\t\n\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t\n<style>\n#image_1723189329 {\n  width: 100%;\n}\n<\/style>\n\t<\/div>\n\t\n<p>Kwanjeera Wanichthanarak, Intawat Nookaew, Phongthana Pasookhush, Thidathip Wongsurawat, Piroon Jenjaroenpun, Namkhang Leeratsuwan, Songsak Wattanachaisaereekul, <strong>Wonnop Visessanguan<\/strong>, Yongyut Sirivatanauksorn, Narong Nuntasaen, Chutima Kuhakarn, Vichai Reutrakul, Pravech Ajawatanawong, <strong>Sakda Khoomrung<\/strong><\/p>\n<h2 class=\"title\">Abstract<\/h2>\n<div id=\"eng-abstract\" class=\"abstract-content selected\">\n<div class=\"title\">\n<p>Background: Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family Rhamnaceae. The current Rhamnaceae phylogenetic tree is from 13 out of 24 Rhamnaceae chloroplast genomes, and only one chloroplast genome of the genus Ventilago is available. Hence, the phylogenetic relationships in Rhamnaceae remain incomplete, and more representative species are needed.<\/p>\n<p>Results: The complete chloroplast genome of Ventilago harmandiana Pierre was outlined using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the final genome were confirmed with PCR amplifications and investigation of coverage depth. Sanger sequencing was used to correct for differences in lengths and nucleotide bases between inverted repeats because of the homopolymers. The phylogenetic trees reconstructed using prevalent methods for phylogenetic inference were topologically similar. The clustering based on codon usage was congruent with the molecular phylogenetic tree. The groups of genera in each tribe were in accordance with tribal classification based on molecular markers. We resolved the phylogenetic relationships among six Hovenia species, three Rhamnus species, and two Ventilago species. Our reconstructed tree provides the most complete and reliable low-level taxonomy to date for the family Rhamnaceae. Similar to other higher plants, the RNA editing mostly resulted in converting serine to leucine. Besides, most genes were subjected to purifying selection. Annotation anomalies, including indel calling errors, unaligned open reading frames of the same gene, inconsistent prediction of intergenic regions, and misannotated genes, were identified in the published chloroplast genomes used in this study. These could be a result of the usual imperfections in computational tools, and\/or existing errors in reference genomes. Importantly, these are points of concern with regards to utilizing published chloroplast genomes for comparative genomic analysis.<\/p>\n<p>Conclusions: In summary, we successfully demonstrated the use of comprehensive genomic data, including DNA and amino acid sequences, to build a reliable and high-resolution phylogenetic tree for the family Rhamnaceae. Additionally, our study indicates that the revision of genome annotation before comparative genomic analyses is necessary to prevent the propagation of errors and complications in downstream analysis and interpretation.<\/p>\n<p><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36707785\/\">https:\/\/pubmed.ncbi.nlm.nih.gov\/36707785\/<\/a><\/p>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Kwanjeera Wanichthanarak, Intawat Nookaew, Phongthana Pasookhush, Thidathip Wongsurawat, Piroon Jenjaroenpun, Namkhang Leeratsuwan, Songsak Wattanachaisaereekul, Wonnop Visessanguan, Yongyut Sirivatanauksorn, Narong Nuntasaen, Chutima Kuhakarn, Vichai Reutrakul, Pravech Ajawatanawong, Sakda Khoomrung Abstract Background: Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family [&#8230;]\n","protected":false},"author":6,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[18],"tags":[],"class_list":["post-5203","post","type-post","status-publish","format-standard","hentry","category-research-innovation-en"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.0 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae - \u0e20\u0e32\u0e04\u0e27\u0e34\u0e0a\u0e32\u0e0a\u0e35\u0e27\u0e40\u0e04\u0e21\u0e35 \u0e04\u0e13\u0e30\u0e41\u0e1e\u0e17\u0e22\u0e28\u0e32\u0e2a\u0e15\u0e23\u0e4c\u0e28\u0e34\u0e23\u0e34\u0e23\u0e32\u0e0a\u0e1e\u0e22\u0e32\u0e1a\u0e32\u0e25 \u0e21\u0e2b\u0e32\u0e27\u0e34\u0e17\u0e22\u0e32\u0e25\u0e31\u0e22\u0e21\u0e2b\u0e34\u0e14\u0e25<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/en\/revisiting-chloroplast-genomic-landscape-and-annotation-towards-comparative-chloroplast-genomes-of-rhamnaceae\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae - \u0e20\u0e32\u0e04\u0e27\u0e34\u0e0a\u0e32\u0e0a\u0e35\u0e27\u0e40\u0e04\u0e21\u0e35 \u0e04\u0e13\u0e30\u0e41\u0e1e\u0e17\u0e22\u0e28\u0e32\u0e2a\u0e15\u0e23\u0e4c\u0e28\u0e34\u0e23\u0e34\u0e23\u0e32\u0e0a\u0e1e\u0e22\u0e32\u0e1a\u0e32\u0e25 \u0e21\u0e2b\u0e32\u0e27\u0e34\u0e17\u0e22\u0e32\u0e25\u0e31\u0e22\u0e21\u0e2b\u0e34\u0e14\u0e25\" \/>\n<meta property=\"og:description\" content=\"Kwanjeera Wanichthanarak, Intawat Nookaew, Phongthana Pasookhush, Thidathip Wongsurawat, Piroon Jenjaroenpun, Namkhang Leeratsuwan, Songsak Wattanachaisaereekul, Wonnop Visessanguan, Yongyut Sirivatanauksorn, Narong Nuntasaen, Chutima Kuhakarn, Vichai Reutrakul, Pravech Ajawatanawong, Sakda Khoomrung Abstract Background: Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family [...]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/en\/revisiting-chloroplast-genomic-landscape-and-annotation-towards-comparative-chloroplast-genomes-of-rhamnaceae\/\" \/>\n<meta property=\"og:site_name\" content=\"\u0e20\u0e32\u0e04\u0e27\u0e34\u0e0a\u0e32\u0e0a\u0e35\u0e27\u0e40\u0e04\u0e21\u0e35 \u0e04\u0e13\u0e30\u0e41\u0e1e\u0e17\u0e22\u0e28\u0e32\u0e2a\u0e15\u0e23\u0e4c\u0e28\u0e34\u0e23\u0e34\u0e23\u0e32\u0e0a\u0e1e\u0e22\u0e32\u0e1a\u0e32\u0e25 \u0e21\u0e2b\u0e32\u0e27\u0e34\u0e17\u0e22\u0e32\u0e25\u0e31\u0e22\u0e21\u0e2b\u0e34\u0e14\u0e25\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/SIBBprogram\/\" \/>\n<meta property=\"article:published_time\" content=\"2025-12-22T02:31:35+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2026-03-30T07:12:15+00:00\" \/>\n<meta name=\"author\" content=\"Poorintra Sakuna\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Poorintra Sakuna\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/www2.si.mahidol.ac.th\\\/department\\\/biochemistry\\\/en\\\/revisiting-chloroplast-genomic-landscape-and-annotation-towards-comparative-chloroplast-genomes-of-rhamnaceae\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/www2.si.mahidol.ac.th\\\/department\\\/biochemistry\\\/en\\\/revisiting-chloroplast-genomic-landscape-and-annotation-towards-comparative-chloroplast-genomes-of-rhamnaceae\\\/\"},\"author\":{\"name\":\"Poorintra Sakuna\",\"@id\":\"https:\\\/\\\/www2.si.mahidol.ac.th\\\/department\\\/biochemistry\\\/en\\\/#\\\/schema\\\/person\\\/75170c4a414d080cfd0b7428b2e0d11a\"},\"headline\":\"Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae\",\"datePublished\":\"2025-12-22T02:31:35+00:00\",\"dateModified\":\"2026-03-30T07:12:15+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/www2.si.mahidol.ac.th\\\/department\\\/biochemistry\\\/en\\\/revisiting-chloroplast-genomic-landscape-and-annotation-towards-comparative-chloroplast-genomes-of-rhamnaceae\\\/\"},\"wordCount\":399,\"publisher\":{\"@id\":\"https:\\\/\\\/www2.si.mahidol.ac.th\\\/department\\\/biochemistry\\\/en\\\/#organization\"},\"articleSection\":[\"Research Innovation\"],\"inLanguage\":\"en-US\"},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/www2.si.mahidol.ac.th\\\/department\\\/biochemistry\\\/en\\\/revisiting-chloroplast-genomic-landscape-and-annotation-towards-comparative-chloroplast-genomes-of-rhamnaceae\\\/\",\"url\":\"https:\\\/\\\/www2.si.mahidol.ac.th\\\/department\\\/biochemistry\\\/en\\\/revisiting-chloroplast-genomic-landscape-and-annotation-towards-comparative-chloroplast-genomes-of-rhamnaceae\\\/\",\"name\":\"Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae - 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