Chromosome-scale genome assembly of oil-tea tree Camellia crapnelliana

被引：4

作者：

Zhang, Fen ^{[1
,2
]}

Feng, Li-ying ^{[1
,2
]}

Lin, Pei-fan ^{[1
,2
]}

Jia, Ju-jin ^{[1
,2
]}

Gao, Li-zhi ^{[1
,2
]}

机构：

[1] Hainan Univ, Engn Res Ctr Selecting & Breeding New Trop Crop Va, Minist Educ, Haikou 570228, Peoples R China

[2] Hainan Univ, Trop Biodivers & Genom Res Ctr, Haikou 570228, Peoples R China

来源：

SCIENTIFIC DATA | 2024年 / 11卷 / 01期

关键词：

PROVIDES INSIGHTS; EVOLUTION; IDENTIFICATION; ALIGNMENT; PROGRAM; PLANT; PERSPECTIVE; ANNOTATION; METABOLISM; PREDICTION;

D O I：

10.1038/s41597-024-03459-x

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Camellia crapnelliana Tutch., belonging to the Theaceae family, is an excellent landscape tree species with high ornamental values. It is particularly an important woody oil-bearing plant species with high ecological, economic, and medicinal values. Here, we first report the chromosome-scale reference genome of C. crapnelliana with integrated technologies of SMRT, Hi-C and Illumina sequencing platforms. The genome assembly had a total length of similar to 2.94 Gb with contig N50 of similar to 67.5 Mb, and similar to 96.34% of contigs were assigned to 15 chromosomes. In total, we predicted 37,390 protein-coding genes, similar to 99.00% of which could be functionally annotated. The chromosome-scale genome of C. crapnelliana will become valuable resources for understanding the genetic basis of the fatty acid biosynthesis, and greatly facilitate the exploration and conservation of C. crapnelliana.

引用

页数：8

共 87 条

[1]

[Anonymous], 2024, National Genomics Data Center Genome Warehouse

[2]

[Anonymous], 2024, NCBI Sequence Read Archive

[3]

[Anonymous], 2024, NCBI Sequence Read Archive

[4]

[Anonymous], 2024, NCBI GenBank

[5] The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution [J].

Badouin, Helene ;

Gouzy, Jerome ;

Grassa, Christopher J. ;

Murat, Florent ;

Staton, S. Evan ;

Cottret, Ludovic ;

Lelandais-Briere, Christine ;

Owens, Gregory L. ;

Carrere, Sebastien ;

Mayjonade, Baptiste ;

Legrand, Ludovic ;

Gill, Navdeep ;

Kane, Nolan C. ;

Bowers, John E. ;

Hubner, Sariel ;

Bellec, Arnaud ;

Berard, Aurelie ;

Berges, Helene ;

Blanchet, Nicolas ;

Boniface, Marie-Claude ;

Brunel, Dominique ;

Catrice, Olivier ;

Chaidir, Nadia ;

Claudel, Clotilde ;

Donnadieu, Cecile ;

Faraut, Thomas ;

Fievet, Ghislain ;

Helmstetter, Nicolas ;

King, Matthew ;

Knapp, Steven J. ;

Lai, Zhao ;

Le Paslier, Marie-Christine ;

Lippi, Yannick ;

Lorenzon, Lolita ;

Mandel, Jennifer R. ;

Marage, Gwenola ;

Marchand, Gwenaelle ;

Marquand, Elodie ;

Bret-Mestries, Emmanuelle ;

Morien, Evan ;

Nambeesan, Savithri ;

Thuy Nguyen ;

Pegot-Espagnet, Prune ;

Pouilly, Nicolas ;

Raftis, Frances ;

Sallet, Erika ;

Schiex, Thomas ;

Thomas, Justine ;

Vandecasteele, Celine ;

Vares, Didier .

NATURE, 2017, 546 (7656) :148-+

[6] UniProt: the universal protein knowledgebase in 2021 [J].

Bateman, Alex ;

Martin, Maria-Jesus ;

Orchard, Sandra ;

Magrane, Michele ;

Agivetova, Rahat ;

Ahmad, Shadab ;

Alpi, Emanuele ;

Bowler-Barnett, Emily H. ;

Britto, Ramona ;

Bursteinas, Borisas ;

Bye-A-Jee, Hema ;

Coetzee, Ray ;

Cukura, Austra ;

Da Silva, Alan ;

Denny, Paul ;

Dogan, Tunca ;

Ebenezer, ThankGod ;

Fan, Jun ;

Castro, Leyla Garcia ;

Garmiri, Penelope ;

Georghiou, George ;

Gonzales, Leonardo ;

Hatton-Ellis, Emma ;

Hussein, Abdulrahman ;

Ignatchenko, Alexandr ;

Insana, Giuseppe ;

Ishtiaq, Rizwan ;

Jokinen, Petteri ;

Joshi, Vishal ;

Jyothi, Dushyanth ;

Lock, Antonia ;

Lopez, Rodrigo ;

Luciani, Aurelien ;

Luo, Jie ;

Lussi, Yvonne ;

Mac-Dougall, Alistair ;

Madeira, Fabio ;

Mahmoudy, Mahdi ;

Menchi, Manuela ;

Mishra, Alok ;

Moulang, Katie ;

Nightingale, Andrew ;

Oliveira, Carla Susana ;

Pundir, Sangya ;

Qi, Guoying ;

Raj, Shriya ;

Rice, Daniel ;

Lopez, Milagros Rodriguez ;

Saidi, Rabie ;

Sampson, Joseph .

NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D480-D489

[7] MISA-web: a web server for microsatellite prediction [J].

Beier, Sebastian ;

Thiel, Thomas ;

Muench, Thomas ;

Scholz, Uwe ;

Mascher, Martin .

BIOINFORMATICS, 2017, 33 (16) :2583-2585

[8] Tandem repeats finder: a program to analyze DNA sequences [J].

Benson, G .

NUCLEIC ACIDS RESEARCH, 1999, 27 (02) :573-580

[9] The InterPro protein families and domains database: 20 years on [J].

Blum, Matthias ;

Chang, Hsin-Yu ;

Chuguransky, Sara ;

Grego, Tiago ;

Kandasaamy, Swaathi ;

Mitchell, Alex ;

Nuka, Gift ;

Paysan-Lafosse, Typhaine ;

Qureshi, Matloob ;

Raj, Shriya ;

Richardson, Lorna ;

Salazar, Gustavo A. ;

Williams, Lowri ;

Bork, Peer ;

Bridge, Alan ;

Gough, Julian ;

Haft, Daniel H. ;

Letunic, Ivica ;

Marchler-Bauer, Aron ;

Mi, Huaiyu ;

Natale, Darren A. ;

Necci, Marco ;

Orengo, Christine A. ;

Pandurangan, Arun P. ;

Rivoire, Catherine ;

Sigrist, Christian J. A. ;

Sillitoe, Ian ;

Thanki, Narmada ;

Thomas, Paul D. ;

Tosatto, Silvio C. E. ;

Wu, Cathy H. ;

Bateman, Alex ;

Finn, Robert D. .

NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D344-D354

[10] BLAST: a more efficient report with usability improvements [J].

Boratyn, Grzegorz M. ;

Camacho, Christiam ;

Cooper, Peter S. ;

Coulouris, George ;

Fong, Amelia ;

Ma, Ning ;

Madden, Thomas L. ;

Matten, Wayne T. ;

McGinnis, Scott D. ;

Merezhuk, Yuri ;

Raytselis, Yan ;

Sayers, Eric W. ;

Tao, Tao ;

Ye, Jian ;

Zaretskaya, Irena .

NUCLEIC ACIDS RESEARCH, 2013, 41 (W1) :W29-W33

← 1 2 3 4 5 6 7 8 9 →