The amino acid sequence of cytochrome c of Fagopyrum esculentum Moench (buckwheat) and Brassica oleracea L. (cauliflower).
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ABSTRACT:
SUBMITTER: Thompson EW
PROVIDER: S-EPMC1177255 | biostudies-other | 1971 Oct
REPOSITORIES: biostudies-other
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Project description:Cauliflower is an important variety of Brassica oleracea and is planted worldwide. Here, the high-quality genome sequence of cauliflower was reported. The assembled cauliflower genome was 584.60 Mb in size, with a contig N50 of 2.11 Mb, and contained 47,772 genes; 56.65% of the genome was composed of repetitive sequences. Among these sequences, long terminal repeats (LTRs) were the most abundant (32.71% of the genome), followed by transposable elements (TEs) (12.62%). Comparative genomic analysis confirmed that after an ancient paleohexaploidy (γ) event, cauliflower underwent two whole-genome duplication (WGD) events shared with Arabidopsis and an additional whole-genome triplication (WGT) event shared with other Brassica species. The present cultivated cauliflower diverged from the ancestral B. oleracea species ~3.0 million years ago (Mya). The speciation of cauliflower (~2.0 Mya) was later than that of B. oleracea L. var. capitata (approximately 2.6 Mya) and other Brassica species (over 2.0 Mya). Chromosome no. 03 of cauliflower shared the most syntenic blocks with the A, B, and C genomes of Brassica species and its eight other chromosomes, implying that chromosome no. 03 might be the most ancient one in the cauliflower genome, which was consistent with the chromosome being inherited from the common ancestor of Brassica species. In addition, 2,718 specific genes, 228 expanded genes, 2 contracted genes, and 1,065 positively selected genes in cauliflower were identified and functionally annotated. These findings provide new insights into the genomic diversity of Brassica species and serve as a valuable reference for molecular breeding of cauliflower.
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Project description:The amino acid sequence of spinach (Spinacea oleracea L., var. Monster Viroflay) cytochrome c was determined on 1mumol of protein. The molecule consists of 111 residues and is homologous with other mitochondrial cytochromes c. Experimental details are given in a supplementary paper that has been deposited as Supplementary Publication SUP 50013, at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973), 131, 5.
| S-EPMC1177464 | biostudies-other
Project description:In agricultural species that are sexually propagated or whose marketable organ is a reproductive structure, management of the flowering process is critical. Inflorescence development in cauliflower is particularly complex, presenting unique challenges for those seeking to predict and manage flowering time. In this study, an integrated physiological and molecular approach was used to clarify the environmental control of cauliflower reproductive development at the molecular level. A functional allele of BoFLC2 was identified for the first time in an annual brassica, along with an allele disrupted by a frameshift mutation (boflc2). In a segregating F? population derived from a cross between late-flowering (BoFLC2) and early-flowering (boflc2) lines, this gene behaved in a dosage-dependent manner and accounted for up to 65% of flowering time variation. Transcription of BoFLC genes was reduced by vernalization, with the floral integrator BoFT responding inversely. Overall expression of BoFT was significantly higher in early-flowering boflc2 lines, supporting the idea that BoFLC2 plays a key role in maintaining the vegetative state. A homologue of Arabidopsis VIN3 was isolated for the first time in a brassica crop species and was up-regulated by two days of vernalization, in contrast to findings in Arabidopsis where prolonged exposure to cold was required to elicit up-regulation. The correlations observed between gene expression and flowering time in controlled-environment experiments were validated with gene expression analyses of cauliflowers grown outdoors under 'natural' vernalizing conditions, indicating potential for transcript levels of flowering genes to form the basis of predictive assays for curd initiation and flowering time.
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Project description:We report the chloroplast (cp) genome sequence of tartary buckwheat (Fagopyrum tataricum) obtained by next-generation sequencing technology and compared this with the previously reported common buckwheat (F. esculentum ssp. ancestrale) cp genome. The cp genome of F. tataricum has a total sequence length of 159,272 bp, which is 327 bp shorter than the common buckwheat cp genome. The cp gene content, order, and orientation are similar to those of common buckwheat, but with some structural variation at tandem and palindromic repeat frequencies and junction areas. A total of seven InDels (around 100 bp) were found within the intergenic sequences and the ycf1 gene. Copy number variation of the 21-bp tandem repeat varied in F. tataricum (four repeats) and F. esculentum (one repeat), and the InDel of the ycf1 gene was 63 bp long. Nucleotide and amino acid have highly conserved coding sequence with about 98% homology and four genes--rpoC2, ycf3, accD, and clpP--have high synonymous (Ks) value. PCR based InDel markers were applied to diverse genetic resources of F. tataricum and F. esculentum, and the amplicon size was identical to that expected in silico. Therefore, these InDel markers are informative biomarkers to practically distinguish raw or processed buckwheat products derived from F. tataricum and F. esculentum.
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Project description:BACKGROUND: Chloroplasts are the green plastids where photosynthesis takes place. The biogenesis of chloroplasts requires the coordinate expression of both nuclear and chloroplast genes and is regulated by developmental and environmental signals. Despite extensive studies of this process, the genetic basis and the regulatory control of chloroplast biogenesis and development remain to be elucidated. RESULTS: Green cauliflower mutant causes ectopic development of chloroplasts in the curd tissue of the plant, turning the otherwise white curd green. To investigate the transcriptional control of chloroplast development, we compared gene expression between green and white curds using the RNA-seq approach. Deep sequencing produced over 15 million reads with lengths of 86 base pairs from each cDNA library. A total of 7,155 genes were found to exhibit at least 3-fold changes in expression between green and white curds. These included light-regulated genes, genes encoding chloroplast constituents, and genes involved in chlorophyll biosynthesis. Moreover, we discovered that the cauliflower ELONGATED HYPOCOTYL5 (BoHY5) was expressed higher in green curds than white curds and that 2616 HY5-targeted genes, including 1600 up-regulated genes and 1016 down-regulated genes, were differently expressed in green in comparison to white curd tissue. All these 1600 up-regulated genes were HY5-targeted genes in the light. CONCLUSIONS: The genome-wide profiling of gene expression by RNA-seq in green curds led to the identification of large numbers of genes associated with chloroplast development, and suggested the role of regulatory genes in the high hierarchy of light signaling pathways in mediating the ectopic chloroplast development in the green curd cauliflower mutant.
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Project description:Black rot caused by Xanthomonas campestris pv. campestris (Xcc) is a very important disease of cauliflower (Brassica oleracea botrytis group) resulting into 10-50% yield losses every year. Since there is a dearth of availability of resistance to black rot disease in B. oleracea (C genome), therefore exploration of A and B genomes was inevitable as they have been reported to be potential reservoirs of gene(s) for resistance to black rot. To utilize these sources, interspecific hybrid and backcross progeny (B1) were generated between cauliflower "Pusa Sharad" and Ethiopian mustard "NPC-9" employing in vitro embryo rescue technique. Direct ovule culture method was better than siliqua culture under different temperature regime periods. Hybridity testing of F1 inter-specific plants was carried out using co-dominant SSR marker and Brassica B and C genome-specific (DB and DC) primers. Meiosis in the di-genomic (BCC) interspecific hybrid of B. oleracea botrytis group (2n = 18, CC) × B. carinata (2n = 4x = 34, BBCC) was higly disorganized and cytological analysis of pollen mother cells revealed chromosomes 2n = 26 at metaphase-I. Fertile giant pollen grain formation was observed frequently in interspecific F1 hybrid and BC1 plants. The F1 inter-specific plants were found to be resistant to Xcc race 1. Segregation distortion was observed in BC1 generation for black rot resistance and different morphological traits. The At1g70610 marker analysis confirmed successful introgression of black rot resistance in interspecific BC1 population. This effort will go a long way in pyramiding gene(s) for resistance against black rot in Cole crops, especially cauliflower and cabbage for developing durable resistance, thus minimize dependency on bactericides.
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Project description:The present study analysed the molecular and agro-morphological diversity in a set of 92 diverse cauliflower genotypes and two each of cabbage and broccoli. Field evaluation of the genotypes was done in randomized block design (RBD) at two locations (i.e. IARI, New Delhi and ICAR-RC-NEH Region, Barapani) during Rabi2019-20. Genotypes showed variation for all the eight observed traits at both locations and, the differences in early and snowball groups were distinct. Pusa Meghna, DC-33-8, Pusa Kartiki and CC-14 were earliest for curd initiation. Genotypes showed higher values for curd traits at Delhi. Molecular diversity was detected with 90 polymorphic simple sequence repeats (SSR). Number of alleles ranged from 1 to 9 with mean value of 2.16 and the highest polymorphic information content (PIC) value was observed for primer BoGMS0742 (0.68) with a mean value of 0.18. Cluster analysis using agro-morphological traits substantiated classification of the genotypes for maturity groups. However, SSR analysis revealed four clusters and with a composite pattern of genotype distribution. STRUCTURE analysis also supported the admixture and four subpopulations. The studyindicates for introgression of genetic fragments across the maturity groups, thereby, potential for use in further genetic improvement and heterosis breeding.
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Project description:Basic helix-loop-helix (bHLH) transcription factors (TFs) are one of the largest TF families in plant species, and they play important roles in plant growth, development and stress responses. The present study systematically identified members of the cauliflower (Brassica oleracea L.) bHLH gene family based on genomic data. Analysis of bHLH family gene numbers, evolution, collinearity, gene structures and motifs indicated that cauliflower contained 256 bHLH family genes distributed on 10 chromosomes. Most of these genes have been localized in the nucleus, and they were divided into 18 subgroups which have been relatively conserved during evolution. Promoter analysis showed that most cis-acting elements were related to MeJA and ABA. Expression analysis suggested that 14 bHLH genes may be involved in the transformation of cauliflower curd from white to purple. An expression analysis of these 14 genes in FQ136 material was performed using qRT-PCR, and 9 bHLH genes (BobHLH1, 14, 58, 61, 63, 84, 231, 239 and 243) showed significantly increased or decreased expression in cauliflower from white to purple, which suggests that these 9 genes play important roles in the accumulation of anthocyanins in cauliflower. The coexpression network of these 9 genes and anthocyanin synthesis-related key genes was analyzed using weighted gene coexpression network analysis (WGCNA). In conclusion, our observations suggested that the bHLH gene family plays an important role in the accumulation of anthocyanins in cauliflower and provide an important theoretical basis for further research on the functions of the bHLH gene family and the molecular mechanism of cauliflower coloration.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-022-01238-9.
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Project description:Inbred lines are important germplasm in cauliflower breeding programs. To understand the genetic diversity and relationships of cauliflower inbred lines, the use of simple sequence repeat (SSR) markers will be of great value for parental line selection and breeding strategy design. In this study, the genetic diversity and relationships of 165 cauliflower inbred lines primarily derived from southeast China were assessed using SSR markers. Forty-three SSR markers were polymorphic across these inbred lines and generated a total of 111 alleles. The mean values of the number of alleles (Na), effective number of alleles (Ne), Shannon's Information index (I), and polymorphism information content (PIC) per locus were 2.581, 1.599, 0.517 and 0.316, respectively. Genetic distance values among all pairs of the inbred lines varied from 0 to 0.67 with an average of 0.30. On the basis of genetic distance data estimated with the SSR markers, the 165 cauliflower inbred lines were classified into four main clusters (from group Ⅰ to group Ⅳ) by cluster analysis and four subpopulations (from POP 1 to POP 4) by structure analysis. The classification patterns of most cauliflower inbred lines were not consistent with their curd maturity, curd solidity or geographic origins. These results based on estimates by the SSR markers, suggested the genetic diversity of the 165 cauliflower inbred lines was relatively narrow. Therefore, pyramiding the valuable genes among different types of the cauliflower inbred lines is important to increase the genetic diversity to obtain desirable hybridization combinations. The information generated in this report will be useful for assessing germplasm and breeding in cauliflower.
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