Improved high-quality genome assembly and annotation of pineapple (Ananas comosus) cultivar md2 revealed extensive haplotype diversity and diversified frs/frf gene family
Yow, Ashley (North Carolina State University. Department of Horticultural Science)
Bostan, Hamed (North Carolina State University. Plants for Human Health Institute)
Castanera, Raúl (Centre de Recerca en Agrigenòmica)
Ruggieri, Valentino (Biomeets Consulting (Barcelona))
Mengist, Mengist F. (North Carolina State University. Plants for Human Health Institute)
Curaba, Julien (North Carolina State University. Plants for Human Health Institute)
Young, Roberto (Standard Fruit de Honduras. Research Department of Dole)
Gillitt, Nicholas (David H. Murdock Research Institute)
Iorizzo, Massimo (North Carolina State University. Plants for Human Health Institute)

Data:	2022
Resum:	Pineapple (Ananas comosus (L. ) Merr. ) is the second most important tropical fruit crop globally, and 'MD2' is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26. 6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161. 6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple.
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	PineappleMD2 ; Ananas comosus ; Improved assembly ; Haplotype diversity ; FHY3/FAR1 genes ; FRS/FRF genes
Publicat a:	Genes, Vol. 13, Issue 1 (January 2022) , art. 52, ISSN 2073-4425

DOI: 10.3390/genes13010052
PMID: 35052394

20 p, 3.6 MB

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