The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales

Abstract

Summary Celery (Apium graveolens L. 2n = 2x = 22), a member of the Apiaceae family, is among the most important and globally grown vegetables. Here, we report a high‐quality genome sequence assembly, anchored to 11 chromosomes, with total length of 3.33 Gb and N50 scaffold length of 289.78 Mb. Most (92.91%) of the genome is composed of repetitive sequences, with 62.12% of 31 326 annotated genes confined to the terminal 20% of chromosomes. Simultaneous bursts of shared long‐terminal repeats (LTRs) in different Apiaceae plants suggest inter‐specific exchanges. Two ancestral polyploidizations were inferred, one shared by Apiales taxa and the other confined to Apiaceae. We reconstructed 8 Apiales proto‐chromosomes, inferring their evolutionary trajectories from the eudicot common ancestor to extant plants. Transcriptome sequencing in three tissues (roots, leaves and petioles), and varieties with different‐coloured petioles, revealed 4 and 2 key genes in pathways regulating anthocyanin and coumarin biosynthesis, respectively. A remarkable paucity of NBS disease‐resistant genes in celery (62) and other Apiales was explained by extensive loss and limited production of these genes during the last ~10 million years, raising questions about their biotic defence mechanisms and motivating research into effects of chemicals, for example coumarins, that give off distinctive odours. Celery genome sequencing and annotation facilitates further research into important gene functions and breeding, and comparative genomic analyses in Apiales.

Integrative genome, transcriptome, microRNA, and degradome analysis of water dropwort (Oenanthe javanica) in response to water stress

“…The average contig N50 length was 13,040 bp, while the scaffold N50 length was 23,281 bp. In Apiaceae, the genome sizes of carrot, coriander, and celery were 421.5 Mb, 2118.31 Mb, and 3.33 Gb 33 – 35 , respectively. A total of 42,270 genes were identified in the genome of O. javanica , of which 93.92% of genes were functionally annotated.…”

“…The dynamic evolution process of gene families was constructed using CAFÉ version 3.1 with a probabilistic graphical model 35 . The evolutionary timescale was directly retrieved from http://www.timetree.org 64 and used to construct a primary phylogenetic tree.…”

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

“…= not specified). Of these, four genomes are finely assembled into pseudomolecules (i.e., chromosomes, Apium graveolens [98], Daucus carota [76], Centella asiatica [99] and Coriandrum sativum [100]); whereas the others (Angelica gigas, Oenanthe javanica, Bupleurum falcatum and Foeniculum vulgare) were incomplete and/or assembled at the scaffold level [46,96,97,101]. While the latter were obtained exclusively through short reads sequencing, the first four resulted from a combination of second-and third-generation sequencing platforms, proving to be the most suitable approach for obtaining fully assembled, highly accurate genome sequences.…”

“…The same species are inflorescence-rich in secondary metabolites, while another RNA-seq analysis was aimed at the identification of genes involved in terpenoid and brassinosteroid accumulation [118]. Coumarins and coumarin-derived compounds (e.g., furanocoumarins) play a repulsive and toxic role against certain insect larvae, and the key genes involved in their biosynthesis have been greatly investigated in Pastinaca sativa [119], Angelica dahurica [120] and Apium graveolens [98]. In particular, Munakata et al identified two different prenyltransferases (PT1 and PT2) responsible for the synthesis of the two furanocoumarin isomers (linear and angular) in P. sativa [119]; whilst Zhao et al and Song et al elucidated the seven enzymes leading to coumarin production in A. dahurica and A. graveolens, respectively [98,120].…”

“…Coumarins and coumarin-derived compounds (e.g., furanocoumarins) play a repulsive and toxic role against certain insect larvae, and the key genes involved in their biosynthesis have been greatly investigated in Pastinaca sativa [119], Angelica dahurica [120] and Apium graveolens [98]. In particular, Munakata et al identified two different prenyltransferases (PT1 and PT2) responsible for the synthesis of the two furanocoumarin isomers (linear and angular) in P. sativa [119]; whilst Zhao et al and Song et al elucidated the seven enzymes leading to coumarin production in A. dahurica and A. graveolens, respectively [98,120]. Among the triterpene saponins employed in traditional medicine, saikosaponins and asiaticoside are particularly abundant in Bupleurum chinense [121] and Centella asiatica [122,123], and the main enzymes involved in their synthesis are currently under study.…”