Insights from the first chromosome-level genome assembly of the alpine gentian Gentiana straminea Maxim.

IF 3.9 2区生物学 Q1 GENETICS & HEREDITY DNA Research Pub Date : 2024-10-01 DOI:10.1093/dnares/dsae022

Gyab Ala Kelsang, Lianghong Ni, Zhili Zhao

{"title":"Insights from the first chromosome-level genome assembly of the alpine gentian Gentiana straminea Maxim.","authors":"Gyab Ala Kelsang, Lianghong Ni, Zhili Zhao","doi":"10.1093/dnares/dsae022","DOIUrl":null,"url":null,"abstract":"<p><p>Gentiana straminea Maxim. is a perennial herb and mainly distributed in the Qinghai-Tibetan Plateau. To adapt to the extreme environment, it has developed particular morphological, physiological, and genetic structures. Also, rich in iridoids, it is one of the original plants of traditional Chinese herb 'Qinjiao'. Herein, we present its first chromosome-level genome sequence assembly and compare it with the genomes of other Gentiana species to facilitate the analysis of genomic characteristics. The assembled genome size of G. straminea was 1.25 Gb, with a contig N50 of 7.5 Mb. A total of 96.08% of the genome sequences was anchored on 13 pseudochromosomes, with a scaffold N50 of 92.70 Mb. A total of 54,310 protein-coding genes were predicted, 80.25% of which were functionally annotated. Comparative genomic analyses indicated that G. straminea experienced two whole-genome duplication events after the γ whole-genome triplication with other eudicots, and it diverged from other Gentiana species at ~3.2 Mya. A total of 142 enzyme-coding genes related to iridoid biosynthesis were identified in its genome. Additionally, we identified differences in the number and expression patterns of iridoid biosynthetic pathway genes in G. straminea compared with two other Gentiana species by integrating whole-genome sequence and transcriptomic analyses.</p>","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9000,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11375616/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"DNA Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/dnares/dsae022","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}

引用次数: 0

Abstract

Gentiana straminea Maxim. is a perennial herb and mainly distributed in the Qinghai-Tibetan Plateau. To adapt to the extreme environment, it has developed particular morphological, physiological, and genetic structures. Also, rich in iridoids, it is one of the original plants of traditional Chinese herb 'Qinjiao'. Herein, we present its first chromosome-level genome sequence assembly and compare it with the genomes of other Gentiana species to facilitate the analysis of genomic characteristics. The assembled genome size of G. straminea was 1.25 Gb, with a contig N50 of 7.5 Mb. A total of 96.08% of the genome sequences was anchored on 13 pseudochromosomes, with a scaffold N50 of 92.70 Mb. A total of 54,310 protein-coding genes were predicted, 80.25% of which were functionally annotated. Comparative genomic analyses indicated that G. straminea experienced two whole-genome duplication events after the γ whole-genome triplication with other eudicots, and it diverged from other Gentiana species at ~3.2 Mya. A total of 142 enzyme-coding genes related to iridoid biosynthesis were identified in its genome. Additionally, we identified differences in the number and expression patterns of iridoid biosynthetic pathway genes in G. straminea compared with two other Gentiana species by integrating whole-genome sequence and transcriptomic analyses.

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

高山龙胆 Gentiana straminea Maxim 首次染色体级基因组组装的启示。(Gentiana straminea基因组组装的启示）。

龙胆草（Gentiana straminea Maxim.）是一种多年生草本植物，主要分布在青藏高原。为了适应极端的环境，它形成了特殊的形态、生理和遗传结构。此外，它还富含鸢尾素，是传统中草药 "秦艽 "的原植物之一。在此，我们首次对其进行了染色体水平的基因组序列组装，并将其与其他龙胆属植物的基因组进行了比较，以便于分析其基因组特征。G. straminea的基因组大小为1.25 Gb，等位基因N50为7.5 Mb。共有 96.08% 的基因组序列锚定在 13 个假染色体上，支架 N50 为 92.70 Mb。共预测出 54,310 个编码蛋白质的基因，其中 80.25% 的基因已进行了功能注释。基因组比较分析表明，G. straminea 在与其他裸子植物经历了γ全基因组三重复制之后，又经历了两次全基因组复制事件，并在约 3.2 Mya 时与其他 Gentiana 物种分化。在其基因组中总共发现了 142 个与铱类生物合成相关的酶编码基因。此外，通过整合全基因组序列和转录组分析，我们发现了 G. straminea 与其他两个 Gentiana 物种在铱类生物合成途径基因的数量和表达模式上的差异。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊

DNA Research 生物-遗传学

CiteScore

6.00

自引率

4.90%

发文量

审稿时长

4.5 months

期刊介绍： DNA Research is an internationally peer-reviewed journal which aims at publishing papers of highest quality in broad aspects of DNA and genome-related research. Emphasis will be made on the following subjects: 1) Sequencing and characterization of genomes/important genomic regions, 2) Comprehensive analysis of the functions of genes, gene families and genomes, 3) Techniques and equipments useful for structural and functional analysis of genes, gene families and genomes, 4) Computer algorithms and/or their applications relevant to structural and functional analysis of genes and genomes. The journal also welcomes novel findings in other scientific disciplines related to genomes.