دورية أكاديمية

A consensus genome of sika deer (Cervus nippon) and transcriptome analysis provided novel insights on the regulation mechanism of transcript factor in antler development

التفاصيل البيبلوغرافية
العنوان: A consensus genome of sika deer (Cervus nippon) and transcriptome analysis provided novel insights on the regulation mechanism of transcript factor in antler development
المؤلفون: Qianghui Wang, Ruobing Han, Haihua Xing, Heping Li
المصدر: BMC Genomics, Vol 25, Iss 1, Pp 1-13 (2024)
بيانات النشر: BMC, 2024.
سنة النشر: 2024
المجموعة: LCC:Biotechnology
LCC:Genetics
مصطلحات موضوعية: Sika deer, Consensus genome, Chromosome evolution, TFs, Antler development, Biotechnology, TP248.13-248.65, Genetics, QH426-470
الوصف: Abstract Background Sika deer (Cervus nippon) holds significance among cervids, with three genomes recently published. However, these genomes still contain hundreds of gaps and display significant discrepancies in continuity and accuracy. This poses challenges to functional genomics research and the selection of an appropriate reference genome. Thus, obtaining a high-quality reference genome is imperative to delve into functional genomics effectively. Findings Here we report a high-quality consensus genome of male sika deer. All 34 chromosomes are assembled into single-contig pseudomolecules without any gaps, which is the most complete assembly. The genome size is 2.7G with 23,284 protein-coding genes. Comparative genomics analysis found that the genomes of sika deer and red deer are highly conserved, an approximately 2.4G collinear regions with up to 99% sequence similarity. Meanwhile, we observed the fusion of red deer's Chr23 and Chr4 during evolution, forming sika deer's Chr1. Additionally, we identified 607 transcription factors (TFs) that are involved in the regulation of antler development, including RUNX2, SOX6, SOX8, SOX9, PAX8, SIX2, SIX4, SIX6, SPI1, NFAC1, KLHL8, ZN710, JDP2, and TWST2, based on this consensus reference genome. Conclusions Our results indicated that we acquired a high-quality consensus reference genome. That provided valuable resources for understanding functional genomics. In addition, discovered the genetic basis of sika-red hybrid fertility and identified 607 significant TFs that impact antler development.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 1471-2164
Relation: https://doaj.org/toc/1471-2164
DOI: 10.1186/s12864-024-10522-9
URL الوصول: https://doaj.org/article/a836b0418dde4b0cac882dc872af43d8
رقم الأكسشن: edsdoj.836b0418dde4b0cac882dc872af43d8
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:14712164
DOI:10.1186/s12864-024-10522-9