• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

一份用于测序你最喜欢的植物基因组的指南。

A guide to sequence your favorite plant genomes.

作者信息

Li Fay-Wei, Harkess Alex

机构信息

Boyce Thompson Institute Ithaca New York 14853 USA.

Plant Biology Section Cornell University Ithaca New York 14853 USA.

出版信息

Appl Plant Sci. 2018 Mar 30;6(3):e1030. doi: 10.1002/aps3.1030. eCollection 2018 Mar.

DOI:10.1002/aps3.1030
PMID:29732260
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5895188/
Abstract

With the rapid development of sequencing technology and the plummeting cost, assembling whole genomes from non-model plants will soon become routine for plant systematists and evolutionary biologists. Here we summarize and compare several of the latest genome sequencing and assembly approaches, offering a practical guide on how to approach a genome project. We also highlight certain precautions that need to be taken before investing time and money into a genome project.

摘要

随着测序技术的迅速发展和成本的大幅下降，从非模式植物中组装全基因组对于植物分类学家和进化生物学家来说很快将成为常规操作。在此，我们总结并比较了几种最新的基因组测序和组装方法，提供了关于如何开展基因组项目的实用指南。我们还强调了在投入时间和资金开展基因组项目之前需要采取的某些预防措施。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcd5/5895188/af59adab49e2/APS3-6-e1030-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcd5/5895188/2e29a9408c48/APS3-6-e1030-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcd5/5895188/af59adab49e2/APS3-6-e1030-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcd5/5895188/2e29a9408c48/APS3-6-e1030-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fcd5/5895188/af59adab49e2/APS3-6-e1030-g002.jpg

相似文献

1
A guide to sequence your favorite plant genomes.一份用于测序你最喜欢的植物基因组的指南。
Appl Plant Sci. 2018 Mar 30;6(3):e1030. doi: 10.1002/aps3.1030. eCollection 2018 Mar.
2
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.简而言之：使用Illumina、Nanopore和PacBio测序技术对病毒组进行基准测试。
Microb Genom. 2024 Feb;10(2). doi: 10.1099/mgen.0.001198.
3
Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information.利用 Hi-C 图谱信息对 PromethION 和 PacBio 测序的韩国参考基因组 KOREF 进行染色体水平组装比较。
Gigascience. 2019 Dec 1;8(12). doi: 10.1093/gigascience/giz125.
4
PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Two-Chromosome Genome.PacBio技术而非Illumina技术能够实现对高GC含量、复杂的双染色体基因组的快速、准确且完整的封闭。
Front Microbiol. 2017 Aug 2;8:1448. doi: 10.3389/fmicb.2017.01448. eCollection 2017.
5
Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing.我们可以使用它吗？从头组装和基于参考的纳米孔数据在植物质体测序中的应用。
PLoS One. 2020 Mar 24;15(3):e0226234. doi: 10.1371/journal.pone.0226234. eCollection 2020.
6
Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis.我们到了吗？使用脆弱的灰鲭鲨（Carcharhinus falciformis）对低覆盖度纳米孔长读测序进行线粒体基因组组装的基准测试。
BMC Genomics. 2022 Apr 22;23(1):320. doi: 10.1186/s12864-022-08482-z.
7
A critical comparison of technologies for a plant genome sequencing project.植物基因组测序项目技术的关键比较
Gigascience. 2019 Mar 1;8(3). doi: 10.1093/gigascience/giy163.
8
Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data.双核体中单倍型的物理分离允许使用 Hi-C 数据对 Nanopore 和 HiFi 组装的相位准确性进行基准测试。
Genome Biol. 2022 Mar 25;23(1):84. doi: 10.1186/s13059-022-02658-2.
9
Comparison of De Novo Assembly Strategies for Bacterial Genomes.细菌基因组从头组装策略比较。
Int J Mol Sci. 2021 Jul 17;22(14):7668. doi: 10.3390/ijms22147668.
10
Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data.细胞器_PBA，一种用于从PacBio DNA测序数据组装叶绿体和线粒体基因组的流程。
BMC Genomics. 2017 Jan 7;18(1):49. doi: 10.1186/s12864-016-3412-9.

引用本文的文献

1
Ionic liquid-assisted seed genomic DNA extraction for advanced sequencing applications.用于高级测序应用的离子液体辅助种子基因组DNA提取
Plant Methods. 2025 Jul 16;21(1):97. doi: 10.1186/s13007-025-01417-1.
2
Expression-based machine learning models for predicting plant tissue identity.用于预测植物组织身份的基于表达的机器学习模型。
Appl Plant Sci. 2024 Oct 19;13(1):e11621. doi: 10.1002/aps3.11621. eCollection 2025 Jan-Feb.
3
Development of genomic and genetic resources facilitating molecular genetic studies on untapped Myanmar rice germplasms.

本文引用的文献

1
A critical comparison of technologies for a plant genome sequencing project.植物基因组测序项目技术的关键比较
Gigascience. 2019 Mar 1;8(3). doi: 10.1093/gigascience/giy163.
2
10KP: A phylodiverse genome sequencing plan.10KP：一个系统发育多样化的基因组测序计划。
Gigascience. 2018 Mar 1;7(3):1-9. doi: 10.1093/gigascience/giy013.
3
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell.利用单个纳米孔流动槽实现高连续性拟南芥基因组组装。
开发基因组和遗传资源，以促进对未开发的缅甸水稻种质进行分子遗传学研究。
Breed Sci. 2024 Apr;74(2):124-137. doi: 10.1270/jsbbs.23077. Epub 2024 Mar 22.
4
LocoGSE, a sequence-based genome size estimator for plants.LocoGSE，一种基于序列的植物基因组大小估计工具。
Front Plant Sci. 2024 Mar 14;15:1328966. doi: 10.3389/fpls.2024.1328966. eCollection 2024.
5
The Plant DNA C-Values Database: A One-Stop Shop for Plant Genome Size Data.植物 DNA C 值数据库：植物基因组大小数据的一站式资源。
Methods Mol Biol. 2023;2703:111-122. doi: 10.1007/978-1-0716-3389-2_9.
6
Nanopore sequencing technology and its applications.纳米孔测序技术及其应用。
MedComm (2020). 2023 Jul 10;4(4):e316. doi: 10.1002/mco2.316. eCollection 2023 Aug.
7
Balancing read length and sequencing depth: Optimizing Nanopore long-read sequencing for monocots with an emphasis on the Liliales.平衡读长与测序深度：优化针对单子叶植物（重点为百合目）的纳米孔长读长测序
Appl Plant Sci. 2023 Jun 6;11(3):e11524. doi: 10.1002/aps3.11524. eCollection 2023 May-Jun.
8
Modified CTAB protocols for high-molecular-weight DNA extractions from ferns.用于从蕨类植物中提取高分子量DNA的改良十六烷基三甲基溴化铵（CTAB）方案。
Appl Plant Sci. 2023 Jun 14;11(3):e11526. doi: 10.1002/aps3.11526. eCollection 2023 May-Jun.
9
Improvements in the sequencing and assembly of plant genomes.植物基因组测序与组装的改进。
GigaByte. 2021 Jun 10;2021:gigabyte24. doi: 10.46471/gigabyte.24. eCollection 2021.
10
Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding.无间隙植物基因组时代：测序和作图技术的创新变革基因组学与育种。
Curr Opin Biotechnol. 2023 Feb;79:102886. doi: 10.1016/j.copbio.2022.102886. Epub 2023 Jan 12.
Nat Commun. 2018 Feb 7;9(1):541. doi: 10.1038/s41467-018-03016-2.
4
The asparagus genome sheds light on the origin and evolution of a young Y chromosome.芦笋基因组揭示了年轻 Y 染色体的起源和进化。
Nat Commun. 2017 Nov 2;8(1):1279. doi: 10.1038/s41467-017-01064-8.
5
The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.首个六倍体普通小麦基因组的近完整组装。
Gigascience. 2017 Nov 1;6(11):1-7. doi: 10.1093/gigascience/gix097.
6
De Novo Assembly of a New Accession Using Nanopore Sequencing.使用纳米孔测序从头组装一个新的访问号。
Plant Cell. 2017 Oct;29(10):2336-2348. doi: 10.1105/tpc.17.00521. Epub 2017 Oct 12.
7
Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution.单分子测序和基于 Hi-C 的邻近引导组装苋菜（Amaranthus hypochondriacus）染色体提供了对基因组进化的见解。
BMC Biol. 2017 Aug 31;15(1):74. doi: 10.1186/s12915-017-0412-4.
8
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.BGISEQ-500与Illumina HiSeq2500测序平台在古基因组测序方面的比较性能
Gigascience. 2017 Aug 1;6(8):1-13. doi: 10.1093/gigascience/gix049.
9
Improved maize reference genome with single-molecule technologies.利用单分子技术改进玉米参考基因组。
Nature. 2017 Jun 22;546(7659):524-527. doi: 10.1038/nature22971. Epub 2017 Jun 12.
10
Is There an Upper Limit to Genome Size?基因组大小是否存在上限？
Trends Plant Sci. 2017 Jul;22(7):567-573. doi: 10.1016/j.tplants.2017.04.005. Epub 2017 May 12.