Root-knot nematodes are obligatory sedentary endoparasites that require a plant host to complete their life cycle. To understand the functions of Meloidogyne incognita nematode genes transcribed from eggs and second-stage juveniles (J2), we have constructed a normalized full-length M. incognita cDNA library and analyzed the ESTs using Pendant-Pro Sequence Analysis Suite. The 5,832 M. incognita ESTs formed 3,263 clusters and 2,241 singletons. The sequences ranged from 51 to 1,740 base pairs, and their average size was 699 base pairs. The protein length of M. incognita ESTs ranged from 150 to 299 amino acids. Forty contigs of predicted proteins that were grouped by BLASTP identity values had significant homology to the genes expressed in their organelle structures (cuticle, epidermis, extracellular matrix and muscle). Using the gomerger method of contigs, we could functionally assign GO terms to 2,147 (53.4%) of 4,024 contigs. Following the E.C. numbers method using UniProt database hits, we could functionally classify E.C. numbers to 288 (7.2%) of 4024 contigs. Also, the taxonomy was classified to 2,329 (57.9%) of 4,024 contigs. We could predict transmembrane regions of 4,024 clusters using the TMpred algorithm. Of the 4,024 contigs with transmembrane regions, 1,457 (36.2%) were assigned more than one domain, and 2,567 (63.8%) could not be assigned a transmembrane domain. The M. incognita ESTs will provide a foundation for developing novel target genes for parasite control and contribute to accelerating the research of biologically-related species.
Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.
-Momordica charantia L. is a valuable food and medicinal plant of the gourd family (Cucurbitaceae) that is cultivated in tropical and subtropical regions of the world. Physicochemical properties of M. charantia based on cultivars, parts and growing stage were investigated. Crude protein contents of leaf were 27.5%, 26.9%, and 23.6% in native leaf (NL), cv. Erabu leaf (EL), and cv. Dragon leaf (DL), respectively. In particular, the crude protein content was the highest in leaves. The crude fat content was in the order of developmental stage 1 of cv. Erabu fruit (EF1) and developmental stage 1 of native fruit (NF1) with values of 4.0%, and 3.9%, respectively. There was also high amount of crude fiber in stem of all three cultivars. The crude ash content was in the order of cv. Erabu leaf, cv. Dragon leaf, and developmental stage 3 of native fruit (NF3) with values of 23.2%, 17.4%, and 13.6%, respectively. The major minerals found in M. charantia were K, Ca, and Mg. The potassium contents of developmental stage 3 of native fruit (NF3), developmental stage 3 of cv. Dragon fruit (DF3), cv. Dragon stem (DS), and developmental stage 2 of native fruit (NF2) were 498.37, 339.21, 314.30, and 307.34 ㎎ /100g, respectively, while the calcium contents were decreased of EL, DL, and NL with values of 513.45, 371.69, and 209.43 ㎎/100g, respectively. The calcium content was higher in leaves and stems than fruits. On the otherhand, the highest magnesium content was measured in EL (69.92 ㎎/100g). The highest contents of chlorophyll a, chlorophyll b, and total chlorophyll were found in NL (442.9 ㎎/100g dw), EL (759.6 ㎎/100g dw), and EL (1164.9 ㎎/100g dw), respectively. The vitamin C contents from developmental stage 2 of cv. Erabu fruit (EF2), NF3, developmental stage 3 of cv. Erabu on fruit (EF3), and NF2 were found with values of 2849.9, 2330.5, 1985.1, and 1844.5 ㎎/㎏, respectively, and found to be higher in Korean cultivar and Erabu fruit than in Dragon. The charantin contents of leaf were higher than the fruit found to be 547.71, 506.04 and 395.62 ㎍/g dw in DL, EL and EF2, respectively. According to the results, mineral contents, total chlorophyll and charantin contents of M. charantia were higher in the leaves (EL and DL) than the fruits. And, vitamin C content was the highest in the fruit (EF2 and EF3). Therefore, much more research needs to be undertaken to use of the leaves as well as fruits. The data showed that M. charantia can be considered a good source of nutrient for application in food system.
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