The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway

Yannan Fan; Sunil Kumar Sahu; Ting Yang; Weixue Mu; Jinpu Wei; Le Cheng; Jinlong Yang; Jie Liu; Yuxian Zhao; Michael Lisby; Huan Liu

doi:10.1016/j.ygeno.2021.09.007

The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway

Yannan Fan, Sunil Kumar Sahu, Ting Yang, Weixue Mu, Jinpu Wei, Le Cheng, Jinlong Yang, Jie Liu, Yuxian Zhao, Michael Lisby, Huan Liu^*

^*Corresponding author af dette arbejde

Functional genomics

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

18 Citationer (Scopus)

Abstract

Clausena lansium (Lour.) Skeels (Rutaceae), recognized as wampee, is a widely distributed fruit tree which is utilized as a folk-medicine for treatment of several common diseases. However, the genomic information about this medicinally important species is still lacking. Therefore, we assembled the first genome of Clausena genus with a total length of 310.51 Mb and scaffold N50 of 2.24 Mb by using 10× Genomics technology. Further annotation revealed a total of 34,419 protein-coding genes, while repetitive elements covered 39.08% (121.36 Mb) of the genome. The Clausena and Citrus genus were found to diverge around 22 MYA, and also shared an ancient whole-genome triplication event with Vitis. Furthermore, multi-tissue transcriptomic analysis enabled the identification of genes involved in the synthesis of carbazole alkaloids. Altogether, these findings provided new insights into the genome evolution of Wampee species and highlighted the possible role of key genes involved in the carbazole alkaloids biosynthetic pathway.

Originalsprog	Engelsk
Tidsskrift	Genomics
Vol/bind	113
Udgave nummer	6
Sider (fra-til)	3696-3704
Antal sider	9
ISSN	0888-7543
DOI	https://doi.org/10.1016/j.ygeno.2021.09.007
Status	Udgivet - 2021

Bibliografisk note

Funding Information:
This work was financially supported by research funding from the National Key R&D Program of China (No. 2019YFC1711000 ), Shenzhen Municipal Government of China (No. JCYJ20170817145512476 ), and Major Science and Technology Projects of Yunnan Province (Digitalization, development and application of biotic resource, 202002AA100007 ). This work is part of the 10KP project and the NMPA Key Laboratory for Rapid Testing Technology of Drugs .

Funding Information:
This work was financially supported by research funding from the National Key R&D Program of China (No. 2019YFC1711000), Shenzhen Municipal Government of China (No. JCYJ20170817145512476), and Major Science and Technology Projects of Yunnan Province (Digitalization, development and application of biotic resource, 202002AA100007). This work is part of the 10KP project and the NMPA Key Laboratory for Rapid Testing Technology of Drugs.

Publisher Copyright:
© 2021

Adgang til dokumentet

10.1016/j.ygeno.2021.09.007

Citationsformater

The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway. / Fan, Yannan; Sahu, Sunil Kumar; Yang, Ting; Mu, Weixue; Wei, Jinpu; Cheng, Le; Yang, Jinlong; Liu, Jie; Zhao, Yuxian; Lisby, Michael ; Liu, Huan.

I: Genomics, Bind 113, Nr. 6, 2021, s. 3696-3704.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

@article{fb822e11a4ea498e80212bd424c57da9,

title = "The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway",

abstract = "Clausena lansium (Lour.) Skeels (Rutaceae), recognized as wampee, is a widely distributed fruit tree which is utilized as a folk-medicine for treatment of several common diseases. However, the genomic information about this medicinally important species is still lacking. Therefore, we assembled the first genome of Clausena genus with a total length of 310.51 Mb and scaffold N50 of 2.24 Mb by using 10× Genomics technology. Further annotation revealed a total of 34,419 protein-coding genes, while repetitive elements covered 39.08% (121.36 Mb) of the genome. The Clausena and Citrus genus were found to diverge around 22 MYA, and also shared an ancient whole-genome triplication event with Vitis. Furthermore, multi-tissue transcriptomic analysis enabled the identification of genes involved in the synthesis of carbazole alkaloids. Altogether, these findings provided new insights into the genome evolution of Wampee species and highlighted the possible role of key genes involved in the carbazole alkaloids biosynthetic pathway.",

keywords = "Carbazole alkaloids, Clausena, Evolution, Genome assembly, Wampee",

author = "Yannan Fan and Sahu, {Sunil Kumar} and Ting Yang and Weixue Mu and Jinpu Wei and Le Cheng and Jinlong Yang and Jie Liu and Yuxian Zhao and Michael Lisby and Huan Liu",

note = "Publisher Copyright: {\textcopyright} 2021",

year = "2021",

doi = "10.1016/j.ygeno.2021.09.007",

language = "English",

volume = "113",

pages = "3696--3704",

journal = "Genomics",

issn = "0888-7543",

publisher = "Academic Press",

number = "6",

}

TY - JOUR

T1 - The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway

AU - Fan, Yannan

AU - Sahu, Sunil Kumar

AU - Yang, Ting

AU - Mu, Weixue

AU - Wei, Jinpu

AU - Cheng, Le

AU - Yang, Jinlong

AU - Liu, Jie

AU - Zhao, Yuxian

AU - Lisby, Michael

AU - Liu, Huan

PY - 2021

Y1 - 2021

N2 - Clausena lansium (Lour.) Skeels (Rutaceae), recognized as wampee, is a widely distributed fruit tree which is utilized as a folk-medicine for treatment of several common diseases. However, the genomic information about this medicinally important species is still lacking. Therefore, we assembled the first genome of Clausena genus with a total length of 310.51 Mb and scaffold N50 of 2.24 Mb by using 10× Genomics technology. Further annotation revealed a total of 34,419 protein-coding genes, while repetitive elements covered 39.08% (121.36 Mb) of the genome. The Clausena and Citrus genus were found to diverge around 22 MYA, and also shared an ancient whole-genome triplication event with Vitis. Furthermore, multi-tissue transcriptomic analysis enabled the identification of genes involved in the synthesis of carbazole alkaloids. Altogether, these findings provided new insights into the genome evolution of Wampee species and highlighted the possible role of key genes involved in the carbazole alkaloids biosynthetic pathway.

AB - Clausena lansium (Lour.) Skeels (Rutaceae), recognized as wampee, is a widely distributed fruit tree which is utilized as a folk-medicine for treatment of several common diseases. However, the genomic information about this medicinally important species is still lacking. Therefore, we assembled the first genome of Clausena genus with a total length of 310.51 Mb and scaffold N50 of 2.24 Mb by using 10× Genomics technology. Further annotation revealed a total of 34,419 protein-coding genes, while repetitive elements covered 39.08% (121.36 Mb) of the genome. The Clausena and Citrus genus were found to diverge around 22 MYA, and also shared an ancient whole-genome triplication event with Vitis. Furthermore, multi-tissue transcriptomic analysis enabled the identification of genes involved in the synthesis of carbazole alkaloids. Altogether, these findings provided new insights into the genome evolution of Wampee species and highlighted the possible role of key genes involved in the carbazole alkaloids biosynthetic pathway.

KW - Carbazole alkaloids

KW - Clausena

KW - Evolution

KW - Genome assembly

KW - Wampee

U2 - 10.1016/j.ygeno.2021.09.007

DO - 10.1016/j.ygeno.2021.09.007

M3 - Journal article

C2 - 34520805

AN - SCOPUS:85114940052

VL - 113

SP - 3696

EP - 3704

JO - Genomics

JF - Genomics

SN - 0888-7543

IS - 6

ER -