Genome Sequencing and Bioinformatics Analysis of Gelidibacter sp. PG-2

doi:10.13560/j.cnki.biotech.bull.1985.2022-0919

Abstract

Abstract:

Gelidibacter sp. PG-2 is a carotenoid-producing strain, and genome-wide sequencing was conducted in order to further study its carotenoid-producing mechanisms. After the carotenoids were extracted from PG-2, qualitative analysis was performed by LC-MS/MS, the content was calculated by liquid UV full wavelength scanning, and the metabolic pathways of carotenoid-producing in this strain were predicted based on the results of whole genome sequencing. The results showed that the carotenoids produced by PG-2 were zeaxanthin with a content of 185.81 μg/g of dry weight, the whole genome size of PG-2 was 3 850 413 bp, the GC content was 37.91%, the total rRNA was 5, the total tRNA was 37, and the sRNA was 19, which were annotated in COG, GO and KEGG databases to genes 3 401, 1 797 and 1 495, respectively. The strain PG-2 contained three core genes associated with carotenoid production, crtI, crtZ, and lcyB, and their metabolic pathways were predicted. GenBank accession number JAMJTV000000000 was obtained after Genome Framework Sequencing Data submitted to NCBI. The above results demonstrate that the strain PG-2 has the ability to produce carotenoids, and it is speculated that its carotenoid production is related to the genes crtI, crtZ and lcyB.

Key words: Gelidibacter sp., whole genome sequencing, liquid UV full wavelength scans, carotenoids

ZHANG Zhi-xia, LI Tian-pei, ZENG Hong, ZHU Xi-xian, YANG Tian-xiong, MA Si-nan, HUANG Lei. Genome Sequencing and Bioinformatics Analysis of Gelidibacter sp. PG-2[J]. Biotechnology Bulletin, 2023, 39(3): 290-300.

Figures/Tables 13

References 38

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名称Name	数据 Data
原始碱基对Raw bases/bp	1 218 127 570
过滤碱基对Clean bases/bp	1 174 477 731
最长支架 Longest scaffold/bp	519 035
总长度 Total length/bp	3 850 413
GC含量 GC/%	37.91
N50/bp	257 421
基因数目 Gene number	4 262
总长 Total length/bp	3 850 413
GC含量（基因区域）GC%（gene region）	38.65
rRNA	5
16sRNA	2
23sRNA	1
5sRNA	2
tRNA	37
sRNA	19
基因组岛数目 gene iland No.	9
CRISPR-Cas 数目CRISPR-Cas No.	30

名称Name	数据 Data
原始碱基对Raw bases/bp	1 218 127 570
过滤碱基对Clean bases/bp	1 174 477 731
最长支架 Longest scaffold/bp	519 035
总长度 Total length/bp	3 850 413
GC含量 GC/%	37.91
N50/bp	257 421
基因数目 Gene number	4 262
总长 Total length/bp	3 850 413
GC含量（基因区域）GC%（gene region）	38.65
rRNA	5
16sRNA	2
23sRNA	1
5sRNA	2
tRNA	37
sRNA	19
基因组岛数目 gene iland No.	9
CRISPR-Cas 数目CRISPR-Cas No.	30

基因 Gene	酶 Enzyme	菌名 Bacterial name	最大分 Max score	总分 Total score	覆盖率 Query cover/%	百分比同一性 Percent identity/%	长度 Length/aa	登录号 Accession
crtI	八氢番茄红素脱氢酶家族 Phytoene desaturase family protein	Gelidibacter japonicus Bio 7-1	1 008	1 008	100	98.38	495	WP_163516639.1
lcyB	番茄红素环化酶 Lycopene cyclase family protein	Gelidibacter japonicus Bio 7-1	704	704	100	98.70	384	WP_163516633.1
crtZ	甾醇去饱和酶家族蛋白 Sterol desaturase family protein	Gelidibacter japonicus Bio 7-1	226	226	100	99.17	149	WP_163516635.1

基因 Gene	酶 Enzyme	菌名 Bacterial name	最大分 Max score	总分 Total score	覆盖率 Query cover/%	百分比同一性 Percent identity/%	长度 Length/aa	登录号 Accession
crtI	八氢番茄红素脱氢酶家族 Phytoene desaturase family protein	Gelidibacter japonicus Bio 7-1	1 008	1 008	100	98.38	495	WP_163516639.1
lcyB	番茄红素环化酶 Lycopene cyclase family protein	Gelidibacter japonicus Bio 7-1	704	704	100	98.70	384	WP_163516633.1
crtZ	甾醇去饱和酶家族蛋白 Sterol desaturase family protein	Gelidibacter japonicus Bio 7-1	226	226	100	99.17	149	WP_163516635.1