Complete genome sequence of the carrot black rot pathogen Alternaria radicina isolate CBR2.

Black rot, caused by Alternaria radicina, seriously endangers carrots throughout the growing season, affecting both leaves and fleshy roots. In this study, we sequenced and assembled the genome of the A. radicina isolate CBR2. The genome was 34.6 Mb in size and consisted of 6 scaffolds. The sequence information provided in this genome will be used as a reference for further comparative genomics analysis of Alternaria species and will contribute to disease control in carrot production.

First Report of Black Rot of Carrot Caused by Alternaria carotiincultae in China.

China is the world's largest producer and exporter of carrot (Daucus carota L. var. sativa), a well-known and nutritious root vegetable. In the spring seasons of 2021-2023, dark brown lesions were observed on field-grown and cold-stored carrot roots in the Xiamen City, Fujian Province, China. Although just discovered in recent years, the disease has expanded from the initial point to the most planting area in there, and causing over 20% yield loss in the most severely affected fields. This disease symptom is consistent with black rot, a carrot disease found globally and caused by the fungal pathogen Alternaria radicina (Saude et al. 2006). Small pieces of symptomatic roots (3 to 5 mm) from diseased carrot roots were surface disinfested with 75% alcohol for 3 minutes and 10% sodium hypochlorite solution for 8 minutes, and then rinsed in sterile distilled water and cultured on potato dextrose agar (PDA) medium at 28°C with a 12-h dark/light photoperiod. By tissue isolation and single-spore culture, six isolates were obtained from the disease plants in the past three years, and used for morphological and molecular analyses. Unexpectedly, the morphological characteristics of conidia of the six isolates, shape (long and ellipsoid), size (27 to 60 × 17 to 21 µm, n =50), and color (dark olive-brown) were similar to those of A. radicina, but with more transverse septae (Figure 1, Trivedi et al. 2010). Meanwhile, compared to A. radicina, the colony's margin was highly uniform and smooth, without an accumulation of yellow pigment and with fewer dendritic rhizomycin crystals at the bottom of agar media. These characteristics were similar to those of Alternaria carotiincultae, but not to those of A. radicina (Park et al. 2008). Genomic DNA of the six isolates was extracted and further molecular identification was performed. The EF-1α gene was amplified using EF-1/EF-2 primer pairs and sequenced (O'Donnell et al. 1998.). The EF-1α gene sequences of the six isolates were compared using DNAMAN 5.2.9 software. They were found to be 100% identical, and the sequences has been deposited in GenBank under accession number OR449062. BLAST analysis of the amplicon revealed 100% nucleotide sequence identity with the A. carotiincultae strain YZU 151039 (GenBank accession No. MK279390), while 2bp difference between the sequences of A. radicina strains present in GenBank. Pathogenicity tests of the isolate were carried on the unwounded carrots (5 roots each, with three replications). These tap roots were surface disinfected with 75% alcohol and disinfected by immersion in 0.75% sodium hypochlorite solution for 10 minutes, then immediately rinsed with sterile water and dried with sterile filter paper. Mycelial plugs (6 mm diameter) were taken from the margin of a vigorously growing colony and inoculated into the sterilized carrot roots. Another group of sterilised tap roots inoculated with sterile agar plugs were used as negative control. All the roots were incubated in the dark at 25°C with 80% humidity. After 2 days, colonies were observed on the surface of the roots that had been inoculated with the mycelial plugs. After 7 days, the inoculated tap roots showed symptoms of black rot with dark brown sunken lesions as the diseased plants in the field. However, no disease was observed on the control roots. Following the previous method, a strain was re-isolated from the inoculated carrot roots and again identified as A. carotiincultae, thus fulfilling Koch's postulates, and confirming that A. carotiincultae is the pathogen causing dark brown lesions of carrots. To our knowledge, this is the first report of A. carotiincultae causing carrot black rot in China. Attention should be paid to the damage caused by this pathogen during the production and storage stages of carrots, and strategies should be developed to prevent its spread.

Draft Genome Sequence of Carrot Alternaria Leaf Blight Pathogen Alternaria dauci.

The fungal genus Alternaria, which causes a variety of crop diseases, is widely distributed in the world. Alternaria leaf blight, caused by Alternaria dauci, is one of the most common and destructive diseases in carrot. The infection of A. dauci leads to dramatic decay on both foliage and taproot in severe cases, which results in significant yield losses. In this study, we sequenced and assembled the genome of A. dauci isolate CALB1, which isolated from the major carrot producing areas of China. A total of 65 contigs were assembled, and the estimated genome size was 34.9 Mb. The draft genome of A. dauci can be used for comparative genomic analysis of Alternaria species and provide genetic information for further research on plant-pathogen interactions.

Genome-wide identification and characterization profile of phosphatidy ethanolamine-binding protein family genes in carrot.

Members of the family of Phosphatidy Ethanolamine-Binding Protein (PEBP) have been shown to be key regulators of the transition of plants from vegetative to reproductive phases. Here, a total of 12 PEBP proteins were identified in the carrot (Daucus carota L.) genome and classified into FT-like (4), TFL1-like (6), and MFT-like 2) subfamilies, that had different lengths (110-267 aa) and were distributed unevenly across seven chromosomes. Moreover, 13 and 31 PEBP proteins were identified in other two Apiaceae species, celery (Apium graveolens L.) and coriander (Coriandrum sativum L.). The phylogenetic and evolutionary results of these PEBP family proteins were obtained based on the protein sequences. In the three Apiaceae species, purifying selection was the main evolutionary force, and WGD, segmental duplication, and dispersed duplication have played key roles in the PEBP family expansion. The expression analysis showed that carrot PEBP genes exhibited relatively broad expression patterns across various tissues. In the period of bolting to flowering, the carrot FT-like subfamily genes were upregulated as positive regulators, and TFL1-like subfamily genes remained at lower expression levels as inhibitors. More interestingly, the members of carrot FT-like genes had different temporal-spatial expression characteristics, suggesting that they have different regulatory functions in the carrot reproductive phase. In summary, this study contributes to our understanding of the PEBP family proteins and provides a foundation for exploring the mechanism of carrot bolting and flowering for the breeding of cultivars with bolting resistance.