Vanilla planifolia
Overview
The vanilla planifolia, commonly known as vanilla, is a perennial vine belonging to the genus Vanilla in the family Orchidaceae. Vanilla is considered the second most valuable spice for its rich vanillin content, which makes it a key source of vanilla flavoring. The scientific name for vanilla was first established in 1808. Unfortunately, due to the decreasing population of the species and the conversion of its natural habitat for other purposes, the IUCN has classified vanilla as an endangered species.
Geographical Distribution
Vanilla is native to the Neotropics, spanning from southern Mexico to Central America, Colombia, and northern Brazil, typically found within the range of 27° latitude and at elevations of up to 700m above sea level. Commercial production of vanilla is primarily concentrated in tropical coastal regions such as Mexico, Madagascar, Comoros Islands, Réunion, Indonesia, etc. Some smaller-scale cultivation also takes place in Seychelles, Mauritius, Puerto Rico, Sri Lanka, Tahiti, Tonga, Uganda, India, etc.
Since the successful introduction of the fragrant orchid from Indonesia in 1960, vanilla cultivation has expanded to Fujian, Hainan, and Yunnan provinces in China. It is widely cultivated for use as a spice.
Application
- Edible use: Fresh vanilla pods contain over 200 aromatic compounds, and after processing, they are primarily used as flavoring agents in the food industry, as well as in the production of perfumes and pharmaceuticals. Vanilla is renowned as the "king of food spices".
- Medicinal use: In terms of medicinal value, vanilla is mainly used for the treatment of diseases such as epilepsy and hypothermia.
- Horticultural use: The vanilla orchid has erect and neatly arranged leaves, with a deep green and glossy color. It exhibits a graceful posture and vigorous growth, demonstrating strong adaptability and high shade tolerance. It is an excellent shade-loving foliage plant for indoor greening and decoration.
Genome sequencing
The "Daphna" species is considered the predominant commercial type of vanilla. The reference genome project is led by Elo Life Systems, Inc. and the Center for Tropical Research and Education, Department of Horticultural Sciences, University of Florida, USA. Hasing et al. conducted the reassembly of the phased diploid reference genome of V. planifolia "Daphna" using a combination of long reads from Oxford Nanopore Technologies (ONT) and short reads from Illumina. This approach resulted in the generation of highly contiguous pseudochromosomes. The final assembled genome had a length of 1480.9 Mb.
V. planifolia CR0040 is a traditional vanilla cultivar from Reunion Island. The genome was completed under the leadership of the UMR AGAP Institute of the University of Montpellier in 2022. The reference genome was obtained by using a combination of PacBio, Oxford Nanopore Technology, Illumina and other sequencing technologies. Best results are obtained using only high quality HiFi long reads. Contigs from the HiFi read assembly were constructed with optical maps, resulting in a phased assembly of 3.4 Gb, which is approximately 83% of the expected genome size. Using the published Daphna chromosome as a reference, one-third of the assembly could be anchored to 14 chromosomes. The assembly yielded 2,453 contigs with a contig N50 of 924 kb and a scaffold N50 of 1.2 Mb, predicting 59128 protein-coding genes.
Reference
1.梁淑云,吴刚,杨逢春,等. 香荚兰属种质研究与利用现状[J]. 热带农业科学,2009,29(1):54-58. DOI:10.3969/j.issn.1009-2196.2009.01.015.
2.赵青云. 起源于热带雨林的香料之王:香荚兰[J]. 生命世界,2021(9):16-19.
3.韦霄,里雨桐,秦惠珍,等. 香荚兰化学成分及栽培技术研究进展[J]. 广西科学院学报,2022,38(2):118-124. DOI:10.13657/j.cnki.gxkxyxb.20220622.003.
4.李瑞丽,田数,郭春生,等. 基于感官导向的香荚兰特征风味物质分析及重构[J]. 食品科学,2023,44(4):217-223. DOI:10.7506/spkx1002-6630-20220421-270.
5.Hasing T, Tang H, Brym M, Khazi F, Huang T, Chambers AH. A phased Vanilla planifolia genome enables genetic improvement of flavour and production. Nat Food. 2020;1(12):811-819. [OpenLBID: OLB-PM-37128067]
6.Piet Q, Droc G, Marande W, et al. A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly. Plant Commun. 2022;3(5):100330. [OpenLBID: OLB-PM-35617961]