De Novo Hybrid Assembled Draft Genome of ICommiphora wightii/I Bhandari Reveals Key Enzymes Involved in Phytosterol Biosynthesis
Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a...
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| Veröffentlicht in: | Life (Basel, Switzerland) Switzerland), 2023-02, Vol.13 (3) |
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| creator | Banerjee, Rudra Prasad Tiwari, Gopal Ji Joshi, Babita Jena, Satya Narayan Sidhu, Om Prakash Meena, Baleshwar Rana, Tikam S Barik, Saroj K |
| description | Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which is useful for treating atherosclerosis, arthritis, high cholesterol, acne, and obesity. For enhanced guggulsterone yield, key genes involved in its biosynthesis pathway need to be predicted, for which the genome sequence of the species is a pre-requisite. Therefore, we assembled the first-ever hybrid draft genome of C. wightii with a genome size of 1.03 Gb and 107,221 contigs using Illumina and PacBio platforms. The N50 and L50 values in this assembled genome were ~74 Kb and 3486 bp, respectively with a guanine–cytosine (GC) content of 35.6% and 98.7%. The Benchmarking Universal Single Copy Ortholog (BUSCO) value indicated good integrity of assembly. Analysis predicted the presence of 31,187 genes and 342.35 Mb repeat elements in the genome. The comparative genome analysis of C. wightii with relevant orthogroups predicted a few key genes associated with phytosterol biosynthesis and secondary metabolism pathways. The assembled draft genome and the predicted genes should help the future variety development program with improved guggulsterone contents in C. wightii. |
| doi_str_mv | 10.3390/life13030662 |
| format | Article |
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Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which is useful for treating atherosclerosis, arthritis, high cholesterol, acne, and obesity. For enhanced guggulsterone yield, key genes involved in its biosynthesis pathway need to be predicted, for which the genome sequence of the species is a pre-requisite. Therefore, we assembled the first-ever hybrid draft genome of C. wightii with a genome size of 1.03 Gb and 107,221 contigs using Illumina and PacBio platforms. The N50 and L50 values in this assembled genome were ~74 Kb and 3486 bp, respectively with a guanine–cytosine (GC) content of 35.6% and 98.7%. The Benchmarking Universal Single Copy Ortholog (BUSCO) value indicated good integrity of assembly. Analysis predicted the presence of 31,187 genes and 342.35 Mb repeat elements in the genome. The comparative genome analysis of C. wightii with relevant orthogroups predicted a few key genes associated with phytosterol biosynthesis and secondary metabolism pathways. The assembled draft genome and the predicted genes should help the future variety development program with improved guggulsterone contents in C. wightii.</description><identifier>ISSN: 2075-1729</identifier><identifier>EISSN: 2075-1729</identifier><identifier>DOI: 10.3390/life13030662</identifier><language>eng</language><publisher>MDPI AG</publisher><subject>Analysis ; Biosynthesis ; Biotechnology industry ; Chemical properties ; Cholesterol ; DNA sequencing ; Enzymes ; Genes ; Genetic aspects ; Genomes ; Genomics ; Identification and classification ; Medicinal plants ; Medicine, Botanic ; Medicine, Herbal ; Metabolites ; Methods ; Nucleotide sequencing ; Physiological aspects ; Phytosterols ; Pyrimidines</subject><ispartof>Life (Basel, Switzerland), 2023-02, Vol.13 (3)</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,860,27901,27902</link.rule.ids></links><search><creatorcontrib>Banerjee, Rudra Prasad</creatorcontrib><creatorcontrib>Tiwari, Gopal Ji</creatorcontrib><creatorcontrib>Joshi, Babita</creatorcontrib><creatorcontrib>Jena, Satya Narayan</creatorcontrib><creatorcontrib>Sidhu, Om Prakash</creatorcontrib><creatorcontrib>Meena, Baleshwar</creatorcontrib><creatorcontrib>Rana, Tikam S</creatorcontrib><creatorcontrib>Barik, Saroj K</creatorcontrib><title>De Novo Hybrid Assembled Draft Genome of ICommiphora wightii/I Bhandari Reveals Key Enzymes Involved in Phytosterol Biosynthesis</title><title>Life (Basel, Switzerland)</title><description>Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which is useful for treating atherosclerosis, arthritis, high cholesterol, acne, and obesity. For enhanced guggulsterone yield, key genes involved in its biosynthesis pathway need to be predicted, for which the genome sequence of the species is a pre-requisite. Therefore, we assembled the first-ever hybrid draft genome of C. wightii with a genome size of 1.03 Gb and 107,221 contigs using Illumina and PacBio platforms. The N50 and L50 values in this assembled genome were ~74 Kb and 3486 bp, respectively with a guanine–cytosine (GC) content of 35.6% and 98.7%. The Benchmarking Universal Single Copy Ortholog (BUSCO) value indicated good integrity of assembly. Analysis predicted the presence of 31,187 genes and 342.35 Mb repeat elements in the genome. The comparative genome analysis of C. wightii with relevant orthogroups predicted a few key genes associated with phytosterol biosynthesis and secondary metabolism pathways. The assembled draft genome and the predicted genes should help the future variety development program with improved guggulsterone contents in C. wightii.</description><subject>Analysis</subject><subject>Biosynthesis</subject><subject>Biotechnology industry</subject><subject>Chemical properties</subject><subject>Cholesterol</subject><subject>DNA sequencing</subject><subject>Enzymes</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Identification and classification</subject><subject>Medicinal plants</subject><subject>Medicine, Botanic</subject><subject>Medicine, Herbal</subject><subject>Metabolites</subject><subject>Methods</subject><subject>Nucleotide sequencing</subject><subject>Physiological aspects</subject><subject>Phytosterols</subject><subject>Pyrimidines</subject><issn>2075-1729</issn><issn>2075-1729</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNptkD1PwzAQhiMEEhV04wdYYmJIa-fDjsd-0UZUgArMlROfE6MkRnEIhImfjiUYWom74U6n53mH87wrgidhyPG00gpIiENMaXDijQLMYp-wgJ8e7Ofe2NpX7IrGhCbRyPteAro3vUGbIWu1RDNroc4qkGjZCtWhNTSmBmQUShemrvVbaVqBPnRRdlpPUzQvRSNFq9EOehCVRXcwoFXzNdRgUdr0pupdlm7QYzl0xnbQmgrNtbFD05Vgtb30zpTzYPw3L7yX29XzYuNvH9bpYrb1C4IJ9bkKGOeYSiZFKDOIQhokeSxYhFUSQhBwECSBhEdMMh4whSmWTEQqJzLLRBJeeNe_uYWoYK8bZbpW5LW2-X7GYuxeyCl11OQfyrWEWuemAaXd_Ui4ORIc08FnV4h3a_fp0-6Q_QH_in_9</recordid><startdate>20230201</startdate><enddate>20230201</enddate><creator>Banerjee, Rudra Prasad</creator><creator>Tiwari, Gopal Ji</creator><creator>Joshi, Babita</creator><creator>Jena, Satya Narayan</creator><creator>Sidhu, Om Prakash</creator><creator>Meena, Baleshwar</creator><creator>Rana, Tikam S</creator><creator>Barik, Saroj K</creator><general>MDPI AG</general><scope>ISR</scope></search><sort><creationdate>20230201</creationdate><title>De Novo Hybrid Assembled Draft Genome of ICommiphora wightii/I Bhandari Reveals Key Enzymes Involved in Phytosterol Biosynthesis</title><author>Banerjee, Rudra Prasad ; Tiwari, Gopal Ji ; Joshi, Babita ; Jena, Satya Narayan ; Sidhu, Om Prakash ; Meena, Baleshwar ; Rana, Tikam S ; Barik, Saroj K</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-g1016-9f279906d7da3dbe43628c5a740f83e229ea18e8947d7927f060d7a4fc1dbba83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Analysis</topic><topic>Biosynthesis</topic><topic>Biotechnology industry</topic><topic>Chemical properties</topic><topic>Cholesterol</topic><topic>DNA sequencing</topic><topic>Enzymes</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Identification and classification</topic><topic>Medicinal plants</topic><topic>Medicine, Botanic</topic><topic>Medicine, Herbal</topic><topic>Metabolites</topic><topic>Methods</topic><topic>Nucleotide sequencing</topic><topic>Physiological aspects</topic><topic>Phytosterols</topic><topic>Pyrimidines</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Banerjee, Rudra Prasad</creatorcontrib><creatorcontrib>Tiwari, Gopal Ji</creatorcontrib><creatorcontrib>Joshi, Babita</creatorcontrib><creatorcontrib>Jena, Satya Narayan</creatorcontrib><creatorcontrib>Sidhu, Om Prakash</creatorcontrib><creatorcontrib>Meena, Baleshwar</creatorcontrib><creatorcontrib>Rana, Tikam S</creatorcontrib><creatorcontrib>Barik, Saroj K</creatorcontrib><collection>Gale In Context: Science</collection><jtitle>Life (Basel, Switzerland)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Banerjee, Rudra Prasad</au><au>Tiwari, Gopal Ji</au><au>Joshi, Babita</au><au>Jena, Satya Narayan</au><au>Sidhu, Om Prakash</au><au>Meena, Baleshwar</au><au>Rana, Tikam S</au><au>Barik, Saroj K</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>De Novo Hybrid Assembled Draft Genome of ICommiphora wightii/I Bhandari Reveals Key Enzymes Involved in Phytosterol Biosynthesis</atitle><jtitle>Life (Basel, Switzerland)</jtitle><date>2023-02-01</date><risdate>2023</risdate><volume>13</volume><issue>3</issue><issn>2075-1729</issn><eissn>2075-1729</eissn><abstract>Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which is useful for treating atherosclerosis, arthritis, high cholesterol, acne, and obesity. For enhanced guggulsterone yield, key genes involved in its biosynthesis pathway need to be predicted, for which the genome sequence of the species is a pre-requisite. Therefore, we assembled the first-ever hybrid draft genome of C. wightii with a genome size of 1.03 Gb and 107,221 contigs using Illumina and PacBio platforms. The N50 and L50 values in this assembled genome were ~74 Kb and 3486 bp, respectively with a guanine–cytosine (GC) content of 35.6% and 98.7%. The Benchmarking Universal Single Copy Ortholog (BUSCO) value indicated good integrity of assembly. Analysis predicted the presence of 31,187 genes and 342.35 Mb repeat elements in the genome. The comparative genome analysis of C. wightii with relevant orthogroups predicted a few key genes associated with phytosterol biosynthesis and secondary metabolism pathways. The assembled draft genome and the predicted genes should help the future variety development program with improved guggulsterone contents in C. wightii.</abstract><pub>MDPI AG</pub><doi>10.3390/life13030662</doi></addata></record> |
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| source | MDPI - Multidisciplinary Digital Publishing Institute; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access |
| subjects | Analysis Biosynthesis Biotechnology industry Chemical properties Cholesterol DNA sequencing Enzymes Genes Genetic aspects Genomes Genomics Identification and classification Medicinal plants Medicine, Botanic Medicine, Herbal Metabolites Methods Nucleotide sequencing Physiological aspects Phytosterols Pyrimidines |
| title | De Novo Hybrid Assembled Draft Genome of ICommiphora wightii/I Bhandari Reveals Key Enzymes Involved in Phytosterol Biosynthesis |
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