Karyotype and genome size comparative analyses among six species of the oilseed-bearing genus Jatropha (Euphorbiaceae)

<div><p>Abstract Jatropha is an important genus of Euphorbiaceae, with species largely used for various purposes, including the manufacturing of soaps and pharmaceutical products and applications in the bioenergetic industry. Although there have been several studies focusing J. curcas in various aspects, the karyotype features of Jatropha species are poorly known. Therefore, we analyzed six Jatropha species through fluorochrome staining (CMA/DAPI), fluorescent in situ hybridization (FISH) with 5S and 45S rDNA probes and genome size estimation by flow cytometry. Our results revealed several chromosome markers by both CMA/DAPI and FISH for the analyzed species. Five Jatropha species (J. curcas, J. gossypiifolia, J. integerrima, J. multifida and J. podagrica) showed four CMA-positive (CMA+) bands associated with the 5S and 45S rDNA sites (one and two pairs, respectively). However, J. mollissima displayed six CMA+/DAPI- bands co-localized with both 5S and 45S rDNA, which showed a FISH superposition. A gradual variation in the genome sizes was observed (2C = 0.64 to 0.86 pg), although an association between evidenced heterochromatin and genome sizes was not found among species. Except for the unique banding pattern of J. mollissima and the pericentromeric heterochromatin of J. curcas and J. podagrica, our data evidenced relatively conserved karyotypes.</p></div

Floral tube length variation-data

Data used to test associations of flower variation with geography, pollinators and climate by means of linear mixed-effect models (LMEs).

Phenotypic RDAs-data

Data used to test associations of phenotypic variation with geography and climate by means of RDA and pRDA

Geographic locations of sampling sites

Geographic coordinates in decimal degrees of the sampling locations

Genetic RDAs-data

Data used to test associations of genetic variation with geography and climate by means of RDA and pRDA

Evidence of genetic differentiation and karyotype evolution of the sedges Cyperus ligularis L. and C. odoratus L. (Cyperaceae)

<div><p>ABSTRACT The taxonomy of Cyperaceae is complex, with genera like Cyperus harboring species complexes. We analyzed the genetic similarity between Cyperus ligularis L. and C. odoratus L. based on DNA fingerprinting and cytogenetics. Significative genetic differentiation (G ST = 0.363) and low gene flow (N m = 0.877) indicated a clear genetic distinction between the two species. Moreover, the clustering analysis showed two distinct genetic groups, suggesting a lack of evidence for hybridization. The phenogram revealed two different lineages, and although all individuals of C. odoratus were collected from plots close to each other, they possessed greater genetic diversity than that observed among individuals of C. ligularis, which were sampled over a wider geographic range. Variation in chromosome number within the two species exhibited the opposite pattern, indicating greater karyotype stability in C. odoratus with 2n = 72 and 2n = 76, while the diploid number for C. ligularis varied from 2n = 66 to 88. The lower genetic variation in C. ligularis may be a result of the founder effect associated with seed dispersion and clonal reproduction. Field observations and analysis of reproductive biology should enrich the understanding of the genetic structure of the investigated populations and their role in successional processes.</p></div

Hierarchical clusterization¹ regarding GO categories [(A) Response to hormones; (B) Response to water], and several contrasts²

<p>¹Gray spots: no expressed unitags; Red: up-regulated unitags; green: down-regulated unitags; black: constitutive expression ². Tolerant accession under stress vs. respective control (I); Sensitive accession under stress vs. respective control (II); and Tolerant accession vs. Sensitive accession, both after root dehydration stress (III). Arrows indicate transcripts mentioned in the discussion.</p

Early Transcriptional Response of Soybean Contrasting Accessions to Root Dehydration

<div><p>Drought is a significant constraint to yield increase in soybean. The early perception of water deprivation is critical for recruitment of genes that promote plant tolerance. DeepSuperSAGE libraries, including one control and a bulk of six stress times imposed (from 25 to 150 min of root dehydration) for drought-tolerant and sensitive soybean accessions, allowed to identify new molecular targets for drought tolerance. The survey uncovered 120,770 unique transcripts expressed by the contrasting accessions. Of these, 57,610 aligned with known cDNA sequences, allowing the annotation of 32,373 unitags. A total of 1,127 unitags were up-regulated only in the tolerant accession, whereas 1,557 were up-regulated in both as compared to their controls. An expression profile concerning the most representative Gene Ontology (GO) categories for the tolerant accession revealed the expression “protein binding” as the most represented for “Molecular Function”, whereas CDPK and CBL were the most up-regulated protein families in this category. Furthermore, particular genes expressed different isoforms according to the accession, showing the potential to operate in the distinction of physiological behaviors. Besides, heat maps comprising GO categories related to abiotic stress response and the unitags regulation observed in the expression contrasts covering tolerant and sensitive accessions, revealed the unitags potential for plant breeding. Candidate genes related to “hormone response” (LOX, ERF1b, XET), “water response” (PUB, BMY), “salt stress response” (WRKY, MYB) and “oxidative stress response” (PER) figured among the most promising molecular targets. Additionally, nine transcripts (HMGR, XET, WRKY20, RAP2-4, EREBP, NAC3, PER, GPX5 and BMY) validated by RT-qPCR (four different time points) confirmed their differential expression and pointed that already after 25 minutes a transcriptional reorganization started in response to the new condition, with important differences between both accessions. </p> </div

Number of unitags differentially expressed for each accession, and mapped in genomic regions* with predicted coverage by RNA-Seq*. (A) unitags mapped in introns; (B) unitags mapped in exon/intron borders; (C) unitags mapped in genomic regions without any predicted gene.

<div><p>* According to the soybean genome browser (Phytozome database: <a href="http://www.phytozome.net/" target="_blank">http://www.phytozome.net/</a>).</p> <p>UR: up-regulated; DR: down-regulated.</p></div

Number of unitags anchored in different soybean genomic regions*, with or without the coverage of RNA-Seq data*.

<p>* According to the soybean genome browser (Phytozome database: <a href="http://www.phytozome.net/" target="_blank">http://www.phytozome.net/</a>).</p