Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication

ArticleProceedings of the National Academy of Sciences. 117(25): 14543-14551. (2020)journal articl

Female flower frequency and GTFL-1 genotype in F₂ population.

<p>For 160 F₂ plants from OHB61-5x OHB95-1A, the frequency of female flowers and GTFL-1 genotype in each plant was investigated, and the scoring results are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087138#pone.0087138.s008" target="_blank">Table S5</a>. The average frequency of female flowers (%) is indicated in the plants for each GTFL-1-genotype: “A” for the homozygotes of the OHB95-1A-type, “G” for the homozygotes of the OHB61-5-type and heterozygotes.</p

Segregation of gynoecy and monoecy in F₂ population from OHB61-5x OHB95-1A.

<p>Segregation of gynoecy and monoecy in F₂ population from OHB61-5x OHB95-1A.</p

Genetic map of putative gynoecious locus (<i>Mcgy</i>).

<p>The genetic distances and location between each RAD-tag marker and the <i>Mcgy</i> locus were calculated from the genotypes of 55 gynoecious F₂ plants. The sequences of alleles in these markers are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087138#pone-0087138-t004" target="_blank">Table 4</a> (GTFL-1, GTFL-2, GTFL-3, GTFL-11, GTFL-13) and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087138#pone.0087138.s005" target="_blank">Table S2</a> (GT1998).</p

Digital Transcriptome Analysis of Putative Sex-Determination Genes in Papaya (<em>Carica papaya</em>)

<div><p>Papaya (<em>Carica papaya</em>) is a trioecious plant species that has male, female and hermaphrodite flowers on different plants. The primitive sex chromosomes genetically determine the sex of the papaya. Although draft sequences of the papaya genome are already available, the genes for sex determination have not been identified, likely due to the complicated structure of its sex-chromosome sequences. To identify the candidate genes for sex determination, we conducted a transcriptome analysis of flower samples from male, female and hermaphrodite plants using high-throughput SuperSAGE for digital gene expression analysis. Among the short sequence tags obtained from the transcripts, 312 unique tags were specifically mapped to the primitive sex chromosome (X or Y^h) sequences. An annotation analysis revealed that retroelements are the most abundant sequences observed in the genes corresponding to these tags. The majority of tags on the sex chromosomes were located on the X chromosome, and only 30 tags were commonly mapped to both the X and Y^h chromosome, implying a loss of many genes on the Y^h chromosome. Nevertheless, candidate Y^h chromosome-specific female determination genes, including a MADS-box gene, were identified. Information on these sex chromosome-specific expressed genes will help elucidating sex determination in the papaya.</p> </div

Summary of RAD-seq analysis of parental lines and bulked F₂ samples using AseI.

<p>Summary of RAD-seq analysis of parental lines and bulked F₂ samples using AseI.</p

RAD-tag markers using AseI, showing linkage to gynoecy in <i>M.charantia</i>.

*<p>SNPs between parental lines in each marker were underlined in the tag sequences.</p>**<p>SNP between OHB61-5 and OHB95-1A in each locus was indicated.</p

Structure and expression analysis of the genes corresponding to the Cp3177 tag, which encodes a putative monodehydroascorbate reductase (MDAR).

<p>A) RT-PCR analysis of the MDAR gene corresponding to the Cp3177 tag. P1 to P6 correspond to the flower samples indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040904#pone-0040904-g001" target="_blank">Figure 1</a>. An actin gene was used as a constitutively expressed control gene <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040904#pone.0040904-Porter1" target="_blank">[32]</a>. B) A list of the polymorphic tags and their counts for the MDAR genes in the Ht-SuperSAGE data. The polymorphic sequences among the tags are underlined. C) The regions flanking the Cp3177 tag on the BAC clones 46O19 (X chromosome) and 90D06 (Y^h chromosome). The arrows indicate the locations of the PCR primers used for amplification. The black regions represent the predicted exons. An insertion of the retroelement sequence was observed in the 90D06 sequence (Y^h chromosome). D) Genomic PCR amplification of the MDAR gene in each sex type. The smaller band was equally amplified in all of the sex types. The larger bands, indicating the insertion of retroelements, were only observed in males and hermaphrodites.</p