Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of <i>Brassica campestris</i> (syn. <i>Brassica rapa</i>) ssp. <i>chinensis</i>
The availability of a high-quality genome sequence of <i>Brassica campestris</i> ssp. <i>chinensis</i> NHCC001 has paved the way for deep mining of genome data. We used the <i>B. campestris</i> NHCC001 draft genome to develop a comprehensive database, known as the...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-04-01
|
| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/11/8/1005 |
| _version_ | 1827627092388347904 |
|---|---|
| author | Zhidong Li Ying Li Tongkun Liu Changwei Zhang Dong Xiao Xilin Hou |
| author_facet | Zhidong Li Ying Li Tongkun Liu Changwei Zhang Dong Xiao Xilin Hou |
| author_sort | Zhidong Li |
| collection | DOAJ |
| description | The availability of a high-quality genome sequence of <i>Brassica campestris</i> ssp. <i>chinensis</i> NHCC001 has paved the way for deep mining of genome data. We used the <i>B. campestris</i> NHCC001 draft genome to develop a comprehensive database, known as the non-heading Chinese cabbage database, which provides access to the <i>B. campestris</i> NHCC001 genome data. The database provides 127,347 SSR, from which 382,041 pairs of primers were designed. NHCCDB contains information on 105,360 genes, which were further classified into 63 transcription factor families. Furthermore, NHCCDB provides eight kinds of tools for biological or sequencing data analyses, including sequence alignment tools, functional genomics tools, comparative genomics tools, motif analysis tools, genome browser, primer design, and SSR analysis tools. In addition, eight kinds of graphs, including a box plot, Venn diagram, corrplot, Q-Q plot, Manhattan plot, seqLogo, volcano plot, and a heatmap, can be generated rapidly using NHCCDB. We have incorporated a search system for efficient mining of transcription factors and genes, along with an embedded data submit function in NHCCDB. We believe that the NHCCDB database will be a useful platform for non-heading Chinese cabbage research and breeding. |
| first_indexed | 2024-03-09T13:07:37Z |
| format | Article |
| id | doaj.art-69a0fbf953c84bb9ae524ea59a7c2905 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T13:07:37Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-69a0fbf953c84bb9ae524ea59a7c29052023-11-30T21:46:03ZengMDPI AGPlants2223-77472022-04-01118100510.3390/plants11081005Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of <i>Brassica campestris</i> (syn. <i>Brassica rapa</i>) ssp. <i>chinensis</i>Zhidong Li0Ying Li1Tongkun Liu2Changwei Zhang3Dong Xiao4Xilin Hou5State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing Suman Plasma Engineering Research Institute, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing Suman Plasma Engineering Research Institute, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing Suman Plasma Engineering Research Institute, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing Suman Plasma Engineering Research Institute, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing Suman Plasma Engineering Research Institute, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing Suman Plasma Engineering Research Institute, Nanjing 210095, ChinaThe availability of a high-quality genome sequence of <i>Brassica campestris</i> ssp. <i>chinensis</i> NHCC001 has paved the way for deep mining of genome data. We used the <i>B. campestris</i> NHCC001 draft genome to develop a comprehensive database, known as the non-heading Chinese cabbage database, which provides access to the <i>B. campestris</i> NHCC001 genome data. The database provides 127,347 SSR, from which 382,041 pairs of primers were designed. NHCCDB contains information on 105,360 genes, which were further classified into 63 transcription factor families. Furthermore, NHCCDB provides eight kinds of tools for biological or sequencing data analyses, including sequence alignment tools, functional genomics tools, comparative genomics tools, motif analysis tools, genome browser, primer design, and SSR analysis tools. In addition, eight kinds of graphs, including a box plot, Venn diagram, corrplot, Q-Q plot, Manhattan plot, seqLogo, volcano plot, and a heatmap, can be generated rapidly using NHCCDB. We have incorporated a search system for efficient mining of transcription factors and genes, along with an embedded data submit function in NHCCDB. We believe that the NHCCDB database will be a useful platform for non-heading Chinese cabbage research and breeding.https://www.mdpi.com/2223-7747/11/8/1005<i>Brassica campestris</i>non-heading Chinese cabbagewhole-genome sequencegenome database |
| spellingShingle | Zhidong Li Ying Li Tongkun Liu Changwei Zhang Dong Xiao Xilin Hou Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of <i>Brassica campestris</i> (syn. <i>Brassica rapa</i>) ssp. <i>chinensis</i> Plants <i>Brassica campestris</i> non-heading Chinese cabbage whole-genome sequence genome database |
| title | Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of <i>Brassica campestris</i> (syn. <i>Brassica rapa</i>) ssp. <i>chinensis</i> |
| title_full | Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of <i>Brassica campestris</i> (syn. <i>Brassica rapa</i>) ssp. <i>chinensis</i> |
| title_fullStr | Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of <i>Brassica campestris</i> (syn. <i>Brassica rapa</i>) ssp. <i>chinensis</i> |
| title_full_unstemmed | Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of <i>Brassica campestris</i> (syn. <i>Brassica rapa</i>) ssp. <i>chinensis</i> |
| title_short | Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of <i>Brassica campestris</i> (syn. <i>Brassica rapa</i>) ssp. <i>chinensis</i> |
| title_sort | non heading chinese cabbage database an open access platform for the genomics of i brassica campestris i syn i brassica rapa i ssp i chinensis i |
| topic | <i>Brassica campestris</i> non-heading Chinese cabbage whole-genome sequence genome database |
| url | https://www.mdpi.com/2223-7747/11/8/1005 |
| work_keys_str_mv | AT zhidongli nonheadingchinesecabbagedatabaseanopenaccessplatformforthegenomicsofibrassicacampestrisisynibrassicarapaisspichinensisi AT yingli nonheadingchinesecabbagedatabaseanopenaccessplatformforthegenomicsofibrassicacampestrisisynibrassicarapaisspichinensisi AT tongkunliu nonheadingchinesecabbagedatabaseanopenaccessplatformforthegenomicsofibrassicacampestrisisynibrassicarapaisspichinensisi AT changweizhang nonheadingchinesecabbagedatabaseanopenaccessplatformforthegenomicsofibrassicacampestrisisynibrassicarapaisspichinensisi AT dongxiao nonheadingchinesecabbagedatabaseanopenaccessplatformforthegenomicsofibrassicacampestrisisynibrassicarapaisspichinensisi AT xilinhou nonheadingchinesecabbagedatabaseanopenaccessplatformforthegenomicsofibrassicacampestrisisynibrassicarapaisspichinensisi |