Search

SUMMARY: Cryptotaenia japonica, a traditional medicinal and edible vegetable crops, is well‐known for its attractive flavors and health care functions. As a member of the Apiaceae family, the evolutionary trajectory and biological properties of C. japonica are not clearly understood. Here, we first reported a high‐quality genome of C. japonica with a total length of 427 Mb and N50 length 50.76 Mb, was anchored into 10 chromosomes, which confirmed by chromosome (cytogenetic) analysis. Comparative genomic analysis revealed C. japonica exhibited low genetic redundancy, contained a higher percentage of single‐cope gene families. The homoeologous blocks, Ks, and collinearity were analyzed among Apiaceae species contributed to the evidence that C. japonica lacked recent species‐specific WGD. Through comparative genomic and transcriptomic analyses of Apiaceae species, we revealed the genetic basis of the production of anthocyanins. Several structural genes encoding enzymes and transcription factor genes of the anthocyanin biosynthesis pathway in different species were also identified. The CjANSa, CjDFRb, and CjF3H gene might be the target of Cjaponica_2.2062 (bHLH) and Cjaponica_1.3743 (MYB). Our findings provided a high‐quality reference genome of C. japonica and offered new insights into Apiaceae evolution and biology. Significance Statement: Our results indicated how the genome of C. japonica provided a useful model for studying evolutionary trajectory and biological properties in Apiaceae species. Our findings are helpful for enriching genome research of Apiaceae family. [ABSTRACT FROM AUTHOR]

VQ motif-containing proteins play crucial roles in plant growth, development, and stress responses. However, no information of VQ motif-containing proteins has been studied at the microevolutionary level in species of Fragaria. In this study, a total of 19, 21, 23, 23, 23, and 25 genes containing the VQ motif were identified from the genomes of F. nipponica, F. iinumae, F. orientalis, F. vesca, F. nubicola, and F. x ananassa, respectively. We classified the VQ genes into 15 clades with grapevine VQ genes, which indicated that at least 15 ancient VQ genes existed before the divergence of the six studied species of Fragaria. Phylogenetic analysis indicated that 28 gene duplication events have occurred in the evolutionary process of the six species of Fragaria. Structural analysis showed that most of the VQ genes have no introns and that VQ proteins in each clade have a similar motif composition. The majority of gene pairs had [K.sub.a]/[K.sub.s] ratios less than 1, which illustrated that most of the VQ genes underwent purifying selection in the six species of Fragaria. Four types of cis-elements in promoters of VQ genes were detected, which is an important basis for further studies about plant stress responses. Furthermore, the expression analysis of FvVQ genes indicated that these genes are expressed differentially in the examined organs and tissues. The identification of VQ genes and the analysis of VQ gene duplication and polyploidization events in the six species of Fragaria provide important information on the evolutionary fate of VQ genes during the divergence of the six species of Fragaria. Key words: VQ gene family, Fragaria, cis-acting elements, gene duplication. Les proteines contenant des motifs VQ jouent des roles critiques dans la croissance, le developpement et les reponses aux stress chez les plantes. Cependant, aucune information sur les proteines a motifs VQ n'est disponible au niveau de la micro-evolution chez les especes de Fragaria. Dans ce travail, un total de 19, 21, 23, 23, 23 et 25 genes contenant des motifs VQ ont ete identifies respectivement au sein des genomes des especes suivantes : F. nipponica, F. iinumae, F. orientalis, F. vesca, F. nubicola et F. x ananassa. Les auteurs ont classifie les VQ en 15 clades avec les VQ de la vigne, ce qui indique qu'au moins 15 genes VQ anciens existaient avant la divergence des six especes de Fragaria. Une analyse phylogenetique a indique que 28 duplications geniques etaient survenues au cours de l'evolution de ces six especes du genre Fragaria. Des analyses structurales ont montre que la plupart des genes VQ ne presentent pas d'intron et que les proteines VQ dans chaque clade presentent une composition semblable en matiere de motifs. La majorite des paires de genes affichaient un ratio [K.sub.a]/[K.sub.s] inferieur a un, ce qui indique que la plupart des genes VQ auraient subi une selection purificatrice chez les six especes de Fragaria. Quatre types d'elements en cis au sein des promoteurs des genes VQ ont ete detectes, une assise importante pour de futures etudes sur les reponses aux stress. De plus, une analyse de l'expression des genes FvVQ a indique que ces genes sont exprimes differentiellement au sein des organes et tissus examines. L'identification de genes VQ et l'analyse de leur duplication ainsi que des evenements de polyploidisation chez les six especes de Fragaria fournissent des informations importantes sur le sort evolutif des genes VQ au cours de la divergence des six especes du genre Fragaria. [Traduit par la Redaction] Mots-cles : famille de genes VQ, Fragaria, elements en cis, duplications geniques., Introduction Plants have evolved a large number of complex mechanisms in response to developmental cues and to external stimuli to survive adverse environmental conditions (Fujita et al. 2006). Transcription factors [...]

Abstract: The ABA/water stress/ripening-induced (ASR) gene family exists universally in higher plants, and many ASR genes are up-regulated during periods of environmental stress and fruit ripening. Although a considerable amount [...]