Characterization of the complete chloroplast genome of leek Allium porrum L. (Amaryllidaceae)

The complete chloroplast genome sequence of Allium porrum was determined by Illumina single-end sequencing. The complete plastid genome was 152,732 bp in length containing a large single copy (LSC) of 81,744 bp and a small single copy (SSC) of 17,910 bp, which were separated by a pair of 26,524 bp inverted repeats (IRs). A total of 133 genes were annotated, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 7 pseudogenes. The overall GC contents of the plastid genome were 36.7%. Unlike A. sativum and A. obliquum in the leek, plastome infA gene is absent, and rpl23 gene is a pseudogene due to a 4 bp deletion and the formation of a premature stop codon

Genome-Wide Identification and Expression of Chitinase Class I Genes in Garlic (Allium sativum L.) Cultivars Resistant and Susceptible to Fusarium proliferatum

Vegetables of the Allium genus are prone to infection by Fusarium fungi. Chitinases of the GH19 family are pathogenesis-related proteins inhibiting fungal growth through the hydrolysis of cell wall chitin; however, the information on garlic (Allium sativum L.) chitinases is limited. In the present study, we identified seven class I chitinase genes, AsCHI1–7, in the A. sativum cv. Ershuizao genome, which may have a conserved function in the garlic defense against Fusarium attack. The AsCHI1–7 promoters contained jasmonic acid-, salicylic acid-, gibberellins-, abscisic acid-, auxin-, ethylene-, and stress-responsive elements associated with defense against pathogens. The expression of AsCHI2, AsCHI3, and AsCHI7 genes was constitutive in Fusarium-resistant and -susceptible garlic cultivars and was mostly induced at the early stage of F. proliferatum infection. In roots, AsCHI2 and AsCHI3 mRNA levels were increased in the susceptible and decreased in the resistant cultivar, whereas in cloves, AsCHI7 and AsCHI5 expression was decreased in the susceptible but increased in the resistant plants, suggesting that these genes are involved in the garlic response to Fusarium proliferatum attack. Our results provide insights into the role of chitinases in garlic and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections

<i>Thaumatin-like Protein</i> (<i>TLP</i>) Genes in Garlic (<i>Allium sativum</i> L.): Genome-Wide Identification, Characterization, and Expression in Response to <i>Fusarium proliferatum</i> Infection

Plant antifungal proteins include the pathogenesis-related (PR)-5 family of fungi- and other stress-responsive thaumatin-like proteins (TLPs). However, the information on the TLPs of garlic (Allium sativum L.), which is often infected with soil Fusarium fungi, is very limited. In the present study, we identified 32 TLP homologs in the A. sativum cv. Ershuizao genome, which may function in the defense against Fusarium attack. The promoters of A. sativumTLP (AsTLP) genes contained cis-acting elements associated with hormone signaling and response to various types of stress, including those caused by fungal pathogens and their elicitors. The expression of AsTLP genes in Fusarium-resistant and -susceptible garlic cultivars was differently regulated by F. proliferatum infection. Thus, in the roots the mRNA levels of AsTLP7–9 and 21 genes were increased in resistant and decreased in susceptible A. sativum cultivars, suggesting the involvement of these genes in the garlic response to F. proliferatum attack. Our results provide insights into the role of TLPs in garlic and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections

Genome-Wide Identification, Expression, and Response to <i>Fusarium</i> Infection of the <i>SWEET</i> Gene Family in Garlic (<i>Allium sativum</i> L.)

Proteins of the SWEET (Sugar Will Eventually be Exported Transporters) family play an important role in plant development, adaptation, and stress response by functioning as transmembrane uniporters of soluble sugars. However, the information on the SWEET family in the plants of the Allium genus, which includes many crop species, is lacking. In this study, we performed a genome-wide analysis of garlic (Allium sativum L.) and identified 27 genes putatively encoding clade I–IV SWEET proteins. The promoters of the A. sativum (As) SWEET genes contained hormone- and stress-sensitive elements associated with plant response to phytopathogens. AsSWEET genes had distinct expression patterns in garlic organs. The expression levels and dynamics of clade III AsSWEET3, AsSWEET9, and AsSWEET11 genes significantly differed between Fusarium-resistant and -susceptible garlic cultivars subjected to F. proliferatum infection, suggesting the role of these genes in the garlic defense against the pathogen. Our results provide insights into the role of SWEET sugar uniporters in A. sativum and may be useful for breeding Fusarium-resistant Allium cultivars

Pathogenesis-Related Genes of PR1, PR2, PR4, and PR5 Families Are Involved in the Response to Fusarium Infection in Garlic (Allium sativum L.)

Plants of the genus Allium developed a diversity of defense mechanisms against pathogenic fungi of the genus Fusarium, including transcriptional activation of pathogenesis-related (PR) genes. However, the information on the regulation of PR factors in garlic (Allium sativum L.) is limited. In the present study, we identified AsPR genes putatively encoding PR1, PR2, PR4, and PR5 proteins in A. sativum cv. Ershuizao, which may be involved in the defense against Fusarium infection. The promoters of the AsPR1–5 genes contained jasmonic acid-, salicylic acid-, gibberellin-, abscisic acid-, auxin-, ethylene-, and stress-responsive elements associated with the response to plant parasites. The expression of AsPR1c, d, g, k, AsPR2b, AsPR5a, c (in roots), and AsPR4a(c), b, and AsPR2c (in stems and cloves) significantly differed between garlic cultivars resistant and susceptible to Fusarium rot, suggesting that it could define the PR protein-mediated protection against Fusarium infection in garlic. Our results provide insights into the role of PR factors in A. sativum and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections

Garlic (<i>Allium sativum</i> L.) Invertase Genes: Genome-Wide Identification and Expression in Response to Abiotic Stresses and Phytohormones

Invertases are involved in plant growth, development, and stress adaptation; however, invertase-encoding genes have not yet been reported in Allium species. In this study, we identified 23 invertase izogenes in garlic (Allium sativum L.): 11 encoding putative neutral/alkaline (AsN/AINV1–11) and 12 acid (6 cell-wall—AsCWINV1–6 and 6 vacuolar—AsVINV1–6) enzymes. Among them, AsN/AINV1, 3, 8–10, AsCWINV2–5, and AsVINV2–6 showed significant transcription in garlic organs (roots, bulbs, pseudostems, leaves, sprouts, and reproductive parts) in a tissue-specific manner, whereas the AsN/AINV4–6, 11, AsCWINV1, 6, and AsVINV1 genes had weak or no detectable expression. Gene promoters contained nine, nine, and sixteen hormone-, stress-, and light-responsive cis-regulatory elements, respectively, and fifteen sites related to transcription factor binding and plant development. Expression analysis revealed that 12 invertase genes strongly transcribed in the roots of A. sativum cv. Ershuizao showed differential expression in the roots and leaves of A. sativum cv. Sarmat exposed to abiotic stresses (low temperature, high salinity, and drought) and phytohormones (abscisic acid and methyl jasmonate), which was significantly correlated with glucose, fructose, and sucrose contents. Our results should further functional analysis of invertases from Allium crops and contribute to the breeding of stress-tolerant varieties

Pretreatment with Chitosan Prevents <i>Fusarium</i> Infection and Induces the Expression of Chitinases and β-1,3-Glucanases in Garlic (<i>Allium sativum</i> L.)

Fusarium infection decreases the yield of garlic (Allium sativum L.); however, the knowledge about garlic response to fungal attack is limited. Chitosan induces plant defense response to stress conditions. Here, we analyzed the effects of chitosan with low (Ch1, 39 kDa) and medium (Ch2, 135 kDa) molecular weight on Fusarium infection in garlic. Ch1 and Ch2 at concentrations 0.125–0.400 mg/mL suppressed the growth of Fusarium proliferatum cultures in vitro. Pretreatment of garlic bulbs with Ch1 or Ch2 prevented disease symptoms after F. proliferatum inoculation, while exerting early inhibitory and late stimulatory effects on chitinase and β-1,3-glucanase activities. Ch1/Ch2 treatment of garlic already infected with F. proliferatum caused transcriptional upregulation of chitinases and β-1,3-glucanases at the early stage, which was maintained at the late stage in Ch2-treated samples, but not in Ch1-treated samples, where transcriptional inhibition was observed. The stimulatory effect of Ch2 pretreatment on the expression of chitinase and endo-β-1,3-glucanase genes was stronger than that of Ch1 pretreatment, suggesting that Ch2 could be more effective than Ch1 in pre-sowing treatment of garlic bulbs. Our results provide insights into the effects of chitosan on the garlic response to Fusarium, suggesting a novel strategy to protect garlic crop against fungal infection

The YABBY

Monotropa hypopitys is a mycoheterotrophic, nonphotosynthetic plant acquiring nutrients from the roots of autotrophic trees through mycorrhizal symbiosis, and, similar to other extant plants, forming asymmetrical lateral organs during development. The members of the YABBY family of transcription factors are important players in the establishment of leaf and leaf-like organ polarity in plants. This is the first report on the identification of YABBY genes in a mycoheterotrophic plant devoid of aboveground vegetative organs. Seven M. hypopitys YABBY members were identified and classified into four clades. By structural analysis of putative encoded proteins, we confirmed the presence of YABBY-defining conserved domains and identified novel clade-specific motifs. Transcriptomic and qRT-PCR analyses of different tissues revealed MhyYABBY transcriptional patterns, which were similar to those of orthologous YABBY genes from other angiosperms. These data should contribute to the understanding of the role of the YABBY genes in the regulation of developmental and physiological processes in achlorophyllous leafless plants

The YABBY Genes of Leaf and Leaf-Like Organ Polarity in Leafless Plant Monotropa hypopitys

Monotropa hypopitys is a mycoheterotrophic, nonphotosynthetic plant acquiring nutrients from the roots of autotrophic trees through mycorrhizal symbiosis, and, similar to other extant plants, forming asymmetrical lateral organs during development. The members of the YABBY family of transcription factors are important players in the establishment of leaf and leaf-like organ polarity in plants. This is the first report on the identification of YABBY genes in a mycoheterotrophic plant devoid of aboveground vegetative organs. Seven M. hypopitys YABBY members were identified and classified into four clades. By structural analysis of putative encoded proteins, we confirmed the presence of YABBY-defining conserved domains and identified novel clade-specific motifs. Transcriptomic and qRT-PCR analyses of different tissues revealed MhyYABBY transcriptional patterns, which were similar to those of orthologous YABBY genes from other angiosperms. These data should contribute to the understanding of the role of the YABBY genes in the regulation of developmental and physiological processes in achlorophyllous leafless plants

De novo transcriptome assembly of the mycoheterotrophic plant Monotropa hypopitys

Monotropa hypopitys (pinesap) is a non-photosynthetic obligately mycoheterotrophic plant of the family Ericaceae. It obtains the carbon and other nutrients from the roots of surrounding autotrophic trees through the associated mycorrhizal fungi. In order to understand the evolutionary changes in the plant genome associated with transition to a heterotrophic lifestyle, we performed de novo transcriptomic analysis of M. hypopitys using next-generation sequencing. We obtained the RNA-Seq data from flowers, flower bracts and roots with haustoria using Illumina HiSeq2500 platform. The raw data obtained in this study can be available in NCBI SRA database with accession number of SRP069226. A total of 10.3 GB raw sequence data were obtained, corresponding to 103,357,809 raw reads. A total of 103,025,683 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 98,349 unigens with an N50 of 1342 bp. Using the TransDecoder program, we predicted 43,505 putative proteins. 38,416 unigenes were annotated in the Swiss-Prot protein sequence database using BLASTX. The obtained transcriptomic data will be useful for further studies of the evolution of plant genomes upon transition to a non-photosynthetic lifestyle and the loss of photosynthesis-related functions