使用PacBio长读测序,对临灭绝的加勒比山脉星珊瑚 (Orbicella faveolata) 的基因组和转录组进行了注释
Benjamin D Young1,2, Olivia M Williamson3, Nicholas S Kron3
1Cooperative Institute of Marine and Atmospheric Science, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA. benjamindouglasyoung1993@gmail.com.
BMC genomics
|February 29, 2024
概括
用长时间读取的测序创建了临灭绝的加勒比星珊瑚Orbicella faveolata的新的de novo基因组组件. 这种改进的基因组资源将有助于保护这个重要的礁石建造珊瑚的保护工作.
科学领域:
- 海洋生物学 海洋生物学
- 基因组学就是基因组学.
- 保护科学 保护科学
背景情况:
- 长期阅读的测序技术正在推动对未经研究的生物体进行新的基因组组装.
- 石珊瑚,如Orbicella faveolata,对珊瑚礁生态系统至关重要,但需要更好的基因组资源.
研究的目的:
- 为临灭绝的加勒比星珊瑚,Orbicella faveolata.生成一个高质量的de novo基因组组合.
- 提供一个改进的基因组资源,用于保护和'omics研究这个物种.
主要方法:
- 用PacBio循环共识 (HiFi) 长读测序来进行基因组组.
- 用长读RNA测序 (ISO-seq) 和现有的短读RNA-seq数据进行基因注释.
- 进行了端粒重复分析以确定假定染色体.
主要成果:
- 新的O. faveolata基因组组件与以前的短读组件相比,显著提高了连续性和BUSCO (基准测试通用单拷贝正义词) 的完整性.
- 组装展示了与其他珊瑚长读基因组相比的质量指标.
- 确定了32172个编码蛋白质的基因,并通过端粒重复分析提出了假定染色体.
结论:
- 这种高质量的基因组组件代表了O. faveolata研究的重大进步.
- 该资源将促进种群基因组学和其他'omics研究,以支持对这个临灭绝的珊瑚物种的保护战略.
- 该研究强调了长读测序对非模型生物在海洋保护中的有用性.
相关概念视频
RNA-seq
10.0K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.0K
Genome Annotation and Assembly
18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
Next-generation Sequencing
88.8K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
88.8K
Ribosome Profiling
3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K
lncRNA - Long Non-coding RNAs
2.8K
2.8K


