Additional file 2: of GFF3sort: a novel tool to sort GFF3 files for tabix indexing

The full GFF3 annotation lines used in Fig. 1a and c. It is the gene AT1G01110 extracted from the Arabidopsis thaliana (Araport11) annotation files. It includes three plain-text files: raw.gff3, GNUsort.gff3 (Fig. 1a), and GFF3sort.gff3 (Fig. 1c). (ZIP 2 kb

Additional file 1: of GFF3sort: a novel tool to sort GFF3 files for tabix indexing

Benchmark data. This file displays: 1) the detailed running time of GFF3-to-JSON conversion and the bgzip-tabix process on our test datasets; 2) the detailed running time and 3) memory usage of GFF3sort, GNU sort (v8.4 and v8.28), and GenomeTools on our test datasets. (PDF 720 kb

El Diario de Pontevedra : periódico liberal: Ano XVI Número 4571 - 1899 agosto 8

List of used RNA-seq data. Including 168 RNA-seq analyses for 20 experiment groups of four Gossypium species. (XLSX 36 kb

Additional file 5: of CottonFGD: an integrated functional genomics database for cotton

Snapshots of the profile module. Several snapshots for the gene and transcript profile page are provided. (PDF 1306 kb

Additional file 1: of CottonFGD: an integrated functional genomics database for cotton

List of all used cotton genome assemblies. Including seven cotton assemblies from four Gossypium species. (DOCX 23 kb

Nitric oxide content analysis in the aerial parts and in the roots of ARG-26 and ARG-38 seedlings grown on 1/2 MS medium, 1/2 MS medium with 4×NH4NO3, and 1/2 MS medium lacking nitrogen.

<p>Compared to non-transgenic control plants, the nitric oxide content decreased in the aerial parts and in the roots of ARG-26 and ARG-38 seedlings on all of the various 1/2 MS media compositions. no differences were observed for the aerial parts of the plants. (A) the nitric oxide content in seedlings of transgenic cotton grown on 1/2 MS medium. (B) the nitric oxide content in transgenic cotton seedlings grown on 1/2 MS medium with 4× NH₄NO₃. (C) the nitric oxide content in transgenic cotton seedlings grown on 1/2 MS medium lacking NH₄NO3 and KNO3. ‘FW’ refers to fresh leaf weight. ‘WT’ refers to non-transgenic control plants of wild type cotton. *: P<0.05.</p

Table_2_Anthocyanin gene enrichment in the distal region of cotton chromosome A07: mechanisms of reproductive organ coloration.xlsx

IntroductionThe biosynthesis of secondary metabolites like anthocyanins is often governed by metabolic gene clusters (MGCs) in the plant ancestral genome. However, the existence of gene clusters specifically regulating anthocyanin accumulation in certain organs is not well understood.Methods and resultsIn this study, we identify MGCs linked to the coloration of cotton reproductive organs, such as petals, spots, and fibers. Through genetic analysis and map-based cloning, we pinpointed key genes on chromosome A07, such as PCC/GhTT19, which is involved in anthocyanin transport, and GbBM and GhTT2-3A, which are associated with the regulation of anthocyanin and proanthocyanidin biosynthesis. Our results demonstrate the coordinated control of anthocyanin and proanthocyanidin pathways, highlighting the evolutionary significance of MGCs in plant adaptation. The conservation of these clusters in cotton chromosome A07 across species underscores their importance in reproductive development and color variation. Our study sheds light on the complex biosynthesis and transport mechanisms for plant pigments, emphasizing the role of transcription factors and transport proteins in pigment accumulation.DiscussionThis research offers insights into the genetic basis of color variation in cotton reproductive organs and the potential of MGCs to enhance our comprehension of plant secondary metabolism.</p

Arginase enzyme activity in ARG-26 and ARG-38 transgenic cotton leaves.

<p>Compared with arginase activity of non-transgenic control plants, expression of OsARG increase the total arginase activity in ARG-26 and ARG-38. ‘WT’ refers to non-transgenic control plants of wild type cotton. **: P<0.01.</p

Southern blot analysis of <i>OsARG</i> gene copy number in the genomes of transgenic cotton plants.

<p>The probe was labeled with the radioactive isotope [α-³²P] dCTP. (A) Two copies of <i>OsARG</i> were integrated into the ARG-26 genome. (B) One copy of <i>OsARG</i> was integrated into the ARG-38 genome. The under labels indicate the following samples: M, marker. 1, positive control. 2, negative control. 3, genomic DNA digested using <i>Eco</i>RI. 4, genomic DNA digested using <i>Hind</i>III.</p

Quantitative PCR analysis of OsArg expression in the leaves of ARG-26 and ARG-38 transgenic cotton.

<p>The <i>OsARG</i> gene was detected in ARG-26 and ARG-38 leaves but not in non-transgenic control leaves. ‘WT’ refers to non-transgenic control plants of wild type cotton. **: P<0.01</p