---
title: "Reference-guided genomics of seven Indonesian rice cultivars reveals conserved gene space and cand"
id: "biorxiv-21-reference-guided-comparative-genomics-of-seven-indonesian-rice-cultivars"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-21-reference-guided-comparative-genomics-of-seven-indonesian-rice-cultivars"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.08.26.747264v1?rss=1"
published_at: "2026-08-29T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Reference-guided genomics of seven Indonesian rice cultivars reveals conserved gene space and cand
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-21-reference-guided-comparative-genomics-of-seven-indonesian-rice-cultivars
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.08.26.747264v1?rss=1)
- **Published At:** 2026-08-29T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The study generated 95.40 Gb of **PacBio HiFi** sequence from seven Indonesian rice cultivars and produced cultivar-specific consensus genomes using the telomere-to-telomere Nipponbare reference AGIS1.0. - Sequencing coverage per cultivar ranged from 27.92x to 41.58x; consensus genome sizes spanned 387.93–390.54 Mb. - Assemblies achieved high completeness with **BUSCO** scores of approximately 98.3–98.5%. - Protein prediction and clustering with **OrthoFinder** assigned 99.1% of predicted proteins into 40,737 orthogroups; 27,514 orthogroups were present across all seven cultivars, indicating a highly conserved predicted gene space in this reference-guided framework. - Targeted locus-by-cultivar analysis recovered 278 of 280 cultivar-by-locus combinations covering 40 genes or gene-family entries linked to grain pigmentation, nitrogen and amino-acid metabolism, and starch properties. - Comparative predicted protein analyses prioritized several candidate genes for follow-up: **ANS1**, **SBE2b**, **SSIIa/ALK**, **Wx/GBSSI**, **OsAAP6/qPC1**, and **SSI**. - Among 269 AGIS1.0-anchored promoter comparisons, 159 passed quality-control criteria; 110 comparisons were flagged for gene-model, boundary, synteny, or structural concerns. - The flagged promoter comparisons contributed over 90% of alignment-derived sequence variation, underscoring the need for stringent quality control when interpreting promoter divergence. - The resulting reference-guided genomic resources provide a standardized framework for assessing sequence variation in Indonesian rice germplasm and prioritize coding and regulatory candidates for functional validation and genomics-assisted improvement.
## Clinical Analysis & Structured Key Points
Reference-guided comparative genomics of seven Indonesian rice cultivars identifies conserved gene space and trait-associated sequence candidates | bioRxiv Skip to main content New Results Reference-guided comparative genomics of seven Indonesian rice cultivars identifies conserved gene space and trait-associated sequence candidates View ORCID Profile Yekti Asih Purwestri , View ORCID Profile Adhityo Wicaksono , View ORCID Profile Siti Nurbaiti , View ORCID Profile Nada Tazkia Purba , View ORCID Profile Dewi Retnaningati , View ORCID Profile Ratih Restiani , Nirma Kumalasari , View ORCID Profile Tri Rini Nuringtyas , View ORCID Profile Valentina Dwi Suci Handayani doi: https://doi.org/10.64898/2026.08.26.747264 Yekti Asih Purwestri Universitas Gadjah Mada Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Yekti Asih Purwestri For correspondence: yekti{at}ugm.ac.id Adhityo Wicaksono Universitas Gadjah Mada Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Adhityo Wicaksono Siti Nurbaiti Universitas Gadjah Mada Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Siti Nurbaiti Nada Tazkia Purba Universitas Gadjah Mada Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Nada Tazkia Purba Dewi Retnaningati Universitas Gadjah Mada Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Dewi Retnaningati Ratih Restiani Universitas Gadjah Mada Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Ratih Restiani Nirma Kumalasari Universitas Gadjah Mada Find this author on Google Scholar Find this author on PubMed Search for this author on this site Tri Rini Nuringtyas Universitas Gadjah Mada Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Tri Rini Nuringtyas Valentina Dwi Suci Handayani Universitas Gadjah Mada Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Valentina Dwi Suci Handayani Abstract Info/History Metrics Supplementary material Preview PDF Abstract Indonesian rice cultivars represent valuable genetic resources, yet many remain poorly characterized at the genomic level. Here, we generated 95.40 Gb of PacBio HiFi sequence data from seven Indonesian rice cultivars and constructed cultivar-specific consensus genomes using the telomere-to-telomere Nipponbare reference AGIS1.0. Sequencing coverage ranged from 27.92x to 41.58x, and the resulting consensus genomes spanned 387.93-390.54 Mb, with BUSCO completeness of approximately 98.3-98.5%. OrthoFinder assigned 99.1% of predicted proteins to 40,737 orthogroups, including 27,514 core orthogroups represented across all seven cultivars, indicating a highly conserved predicted gene space within the reference-guided framework. Targeted analysis recovered 278 of 280 cultivar-by-locus combinations representing 40 genes or gene family entries associated with grain pigmentation, nitrogen and amino-acid metabolism, and starch properties. Comparative predicted protein analysis prioritized ANS1, SBE2b, SSIIa/ALK, Wx/GBSSI, OsAAP6/qPC1, and SSI as candidates for further investigation. Among 269 completed AGIS1.0-anchored promoter comparisons, 159 passed quality-control criteria, whereas 110 were flagged for gene-model, boundary, synteny, or structural concerns. Notably, these flagged comparisons accounted for more than 90% of the alignment-derived sequence variation, emphasizing the importance of rigorous quality control when interpreting apparent promoter divergence. Collectively, these reference-guided genomic resources provide a standardized framework for investigating sequence variation in Indonesian rice germplasm and prioritize testable coding and regulatory candidates for functional validation and future genomics-assisted crop improvement. Competing Interest Statement The authors have declared no competing interest. Funder Information Declared Lembaga Pengelola Dana Pendidikan , 4301/B3/DT.03.08/2025 , 10107/UN1.P/Dit-Keu/HK.08.00/2025 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . Back to top Previous Next Posted August 29, 2026. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. 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Share Reference-guided comparative genomics of seven Indonesian rice cultivars identifies conserved gene space and trait-associated sequence candidates Yekti Asih Purwestri , Adhityo Wicaksono , Siti Nurbaiti , Nada Tazkia Purba , Dewi Retnaningati , Ratih Restiani , Nirma Kumalasari , Tri Rini Nuringtyas , Valentina Dwi Suci Handayani bioRxiv 2026.08.26.747264; doi: https://doi.org/10.64898/2026.08.26.747264 Share This Article: Copy Citation Tools Reference-guided comparative genomics of seven Indonesian rice cultivars identifies conserved gene space and trait-associated sequence candidates Yekti Asih Purwestri , Adhityo Wicaksono , Siti Nurbaiti , Nada Tazkia Purba , Dewi Retnaningati , Ratih Restiani , Nirma Kumalasari , Tri Rini Nuringtyas , Valentina Dwi Suci Handayani bioRxiv 2026.08.26.747264; doi: https://doi.org/10.64898/2026.08.26.747264 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Genomics Subject Areas All Articles Animal Behavior and Cognition (7945) Biochemistry (18565) Bioengineering (14718) Bioinformatics (43981) Biophysics (22375) Cancer Biology (19499) Cell Biology (26670) Clinical Trials (138) Developmental Biology (13855) Ecology (20805) Epidemiology (2067) Evolutionary Biology (25250) Genetics (16067) Genomics (23351) Immunology (18528) Microbiology (42092) Molecular Biology (17885) Neuroscience (92579) Paleontology (691) Pathology (2958) Pharmacology and Toxicology (5051) Physiology (8029) Plant Biology (15846) Scientific Communication and Education (2090) Synthetic Biology (4523) Systems Biology (10156) Zoology (2368)
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