干旱区生态环境知识资源中心(Arid): Analysis of High-Throughput Transcriptome Sequencing of Orychophragmus violaceus Seedlings

Arid

DOI	10.15244/pjoes/146557
	Analysis of High-Throughput Transcriptome Sequencing of Orychophragmus violaceus Seedlings
	Hang, Hongtao
通讯作者	Hang, HT
来源期刊	POLISH JOURNAL OF ENVIRONMENTAL STUDIES
ISSN	1230-1485
EISSN	2083-5906
出版年	2022
卷号	31 期号:4 页码:3561-3571
英文摘要	In order to obtain the genetic basis of transcriptome data of Orychophragmus violaceus seedlings, the transcriptome of Orychophragmus violaceus was paired-end sequenced by Illumina Novaseq 6000 platform, a total of 59174171 clean reads (17.75 Gb clean bases) were obtained, and 110919 unigenes were obtained after assembly by de novo, with the longest and shortest length of 15030, 301 bp and an average length of 784 bp. The N50 was 947 bp and the N90 was 396 bp. These unigenes were compared among seven public databases including Non-redundant protein sequences (NR), Nucleotide (NT), Swiss-prot protein database (Swiss-Prot), Protein family (Pfam), Eu-karyotic ortholog groups (KOG), Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG), as a result of 75369 (67.94%), 69004 (62.21%), 62258 (56.12%), 56068 (50.54%), 27796 (25.05%), 56066 (50.54%), 32897 (29.65%) unigenes were annotated respectively. These annotation results showed that Orychophragmus violaceus had most homologous sequences with 13610 unigenes with Quercus suber. The GO annotations showed that 56066 unigenes were annotated with 219038, which were divided into 3 categories and 43 functional groups. The KOG annotations showed that 27796 unigenes were annotated and grouped into 25 functional categories. The KEGG annotations showed that 32897 unigenes were involved in 34 types of metabolic pathways and 305 metabolic pathway branches. A total of 18118 SSR sites and 112584 CDS sequences were detected according to analyzing the coding sequences and microsatellite. Base on the high-throughput transcriptome sequencing of Orychophragmus violaceus, with a large number of functional genes are excavated, which provide certain basic data support for the subsequent development of bioinformatics analysis such as molecular markers and functional metabolic pathways.
英文关键词	Orychophragmus violaceus adaptable plant high-throughput sequencing function annotation bioinformation analysis
类型	Article
语种	英语
开放获取类型	gold
收录类别	SCI-E
WOS记录号	WOS:000836393000002
WOS关键词	KARST ROCKY DESERTIFICATION ; RESTORATION ; BIODIVERSITY ; CHINA
WOS类目	Environmental Sciences
WOS研究方向	Environmental Sciences & Ecology
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/394057
推荐引用方式 GB/T 7714	Hang, Hongtao. Analysis of High-Throughput Transcriptome Sequencing of Orychophragmus violaceus Seedlings[J],2022,31(4):3561-3571.
APA	Hang, Hongtao.(2022).Analysis of High-Throughput Transcriptome Sequencing of Orychophragmus violaceus Seedlings.POLISH JOURNAL OF ENVIRONMENTAL STUDIES,31(4),3561-3571.
MLA	Hang, Hongtao."Analysis of High-Throughput Transcriptome Sequencing of Orychophragmus violaceus Seedlings".POLISH JOURNAL OF ENVIRONMENTAL STUDIES 31.4(2022):3561-3571.

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