Overview

The pineapple, a herbaceous plant in the Bromeliadaceae family, is one of the most famous tropical fruits and is widely grown in the tropics. Pineapple is one of the "four famous fruits in the south of the Five Ridges" in China, for the highly adaptable, barren, drought-resistant and pests-resistant plant is an important pioneer crop in newly reclaimed hills. Pineapple is also very easy to cultivate, with remarkable high yield and high productivity for intercropping. In southeast hilly area of China, it is chosen for the development of rural economy and the enrichment of farmers.

Geographical Distribution

Pineapple is native to the Amazon basin of Brazil and Paraguay in South America. It was spread to Central America and Northern South America about 1600 AD. The pineapple's sprouts were resistant to storage and transportation, so it rapidly spread to tropical and subtropical regions of the world in a short time, and it were introduced into southern China between the late 16th or 17th centuries.

Pineapple are cultivated in more than 60 countries and regions around the world. In addition to China, it is mainly cultivated in Thailand, the United States, Brazil, Mexico, Philippines and Malaysia. Pineapple cultivation in China has a history of more than 400 years, mainly concentrated in Taiwan, Guangdong, Guangxi, Fujian, Hainan and other provinces, with a small amount cultivated in Yunnan and southern Guizhou.

Application

• Edible use: The edible part of pineapple consists mainly of the fleshy, enlarged inflorescence axis and the flowers arranged in a spiral pattern around the periphery, which are richly flavoured, sweet and sour, crisp and juicy. In addition to fresh food, pineapple fruit is often used to make cans, which is popular for its ability to retain its original flavour.
• Health care: pineapple is mild, sweet, slightly sour and astringent. It has the ability to quench heat and thirst, eliminate diarrhoea, tonify the spleen and stomach, strengthen the vital energy and so on. It contains a substance called Bromelains which is able to break down proteins and help digestion. In addition, the sugar and enzyme have a certain diuretic effect, which is beneficial to nephritis and hypertension, and also has auxiliary curative effect on bronchitis.
• Industrial raw materials: The fiber of pineapple leaves are very tough thus can be used for fabric, rope making, netting and papermaking.

Genome sequencing

The pineapple variety F153, which has been cultivated by Del Monte for 80 years, was subjected to sequencing and assembly by Fujian Agriculture and Forestry University. The sequencing approach involved the use of 400× Illumina reads, 2× Moleculo synthetic long reads, 1× 454 reads, 5× PacBio single-molecule long reads, and 9,400 BACs. The resulting assembly had a total span of 382 Mb, representing 72.6% of the estimated 526 Mb pineapple genome. The contig N50 was 126.5 kb, while the scaffold N50 was 11.8 Mb. Gene annotation analysis identified 27,024 gene models, with 89% of them categorized as complete.

The pineapple CB5 reference genome was completed under the leadership of Fujian Agriculture and Forestry University. The reference genome was generated by the PacBio RSII platform with 26.9 Gb of reads, and approximately 100× Illumina short reads. The initial assembly with CANU resulted in 809.6 Mb of assembled sequence. Flow cytometry estimated the genome size of CB5 to be approximately 591 Mb. To address heterozygosity, the researchers developed a new algorithm called Pseudohaploid, which identifies and filters out heterozygotes based on whole-genome comparisons. The final assembly yielded 513 Mb, with a contig N50 of 427 kb and 92.6% completeness. High-throughput chromatin conformation capture (Hi-C) was used to correct and scaffold the contigs, resulting in 25 pseudochromosomes that covered 456 Mb (88.8%) of the genome. A total of 29,412 putative protein-coding gene models were annotated.

In the improved F153 genome assembly (referred to as F153 v.7), the misassembled linkage groups were corrected. Specifically, LG01 was separated into AccChr1 and AccChr24, while LG24 and LG25 were linked together to form AccChr25.

Reference

1.中国科学院中国植物志委员会. 中国植物志.第13卷[M]. 科学出版社, 1980.

2.Ming R, VanBuren R, Wai CM, et al. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet. 2015;47(12):1435-1442. [OpenLBID: OLB-PM-26523774]

3.Chen LY, VanBuren R, Paris M, et al. The bracteatus pineapple genome and domestication of clonally propagated crops. Nat Genet. 2019;51(10):1549-1558. [OpenLBID: OLB-PM-31570895]