Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

/pdf/the-tomato-genome-sequence-provides-insights-into-fleshy-7a55qpnrdm.pdf

The tomato genome sequence provides insights into fleshy fruit evolution

We have developed a DNA extraction procedure for milligram amounts of plant tissue. Yields ranged from 0.3-200 nanograms of DNA per milligram of tissue. The factors affecting yield are discussed. Fresh tissue, as well as herbarium specimens (22-118 years old) and mummified seeds and embryos (500 to greater than 44 600 years old) were used. All tissues attempted (57 types from 29 species) yielded measurable amounts of DNA. In no case tested was inhibition observed for restriction enzymes BamHI or EcoRI.

Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues

The number of angiosperm species for which nuclear DNA amount estimates have been made has nearly trebled since the last collected lists of such values were published, and therefore, publication of a more comprehensive list is overdue. This paper lists absolute nuclear DNA amounts for 753 angiosperm species. The data were assembled primarily for reference purposes, and so the species are listed in alphabetical order, as this was felt to be more helpful to cyto- and biochemists whom, it is anticipated, will be among its major users. The paper also reviews aspects of the history, nomenclature, methods, accuracy and problems of nuclear DNA estimation in angiosperms. No attempt is made to reconsider those aspects of nuclear DNA estimation which have been fully revised previously, although the bibliography of such aspects is given. Instead, the paper is intended as a source of basic information regarding the terminology, practice and limitations of nuclear DNA estimation, especially by Feulgen microdensitometry, as currently practiced.

Nuclear DNA Amounts in Angiosperms

Plant cell walls are the starting materials for many commercial products, from lumber, paper and textiles to thickeners, films and explosives. The cell wall is secreted by each cell in the plant body, forming a thin fibreglass-like network with remarkable strength and flexibility. During growth, plant cells secrete a protein called expansin, which unlocks the network of wall polysaccharides, permitting turgor-driven cell enlargement. Germinating grass pollen also secretes an unusual expansin that loosens maternal cell walls to aid penetration of the stigma by the pollen tube. Expansin's action has puzzling implications for plant cell-wall structure. The recent explosion of gene sequences and expression data has given new hints of additional biological functions for expansins.

Loosening of plant cell walls by expansins

Genome sequences reveal that a deluge of DNA from organelles has constantly been bombarding the nucleus since the origin of organelles. Recent experiments have shown that DNA is transferred from organelles to the nucleus at frequencies that were previously unimaginable. Endosymbiotic gene transfer is a ubiquitous, continuing and natural process that pervades nuclear DNA dynamics. This relentless influx of organelle DNA has abolished organelle autonomy and increased nuclear complexity.

/pdf/endosymbiotic-gene-transfer-organelle-genomes-forge-3p99gqxe22.pdf

Endosymbiotic Gene Transfer: Organelle Genomes Forge Eukaryotic Chromosomes

In higher plants, DNA transfer from the plastid (chloroplast) genome to the nucleus is a frequent, ongoing process. However, there has been uncertainty over whether this transfer occurs by a direct DNA mechanism or whether RNA intermediates are involved. Previous experiments utilising transplastomic Nicotiana tabacum (tp7 and tp17) enabled the detection of plastid-to-nucleus transfer in real time. To determine whether RNA intermediates are involved in this transfer, transplastomic lines (tpneoACG) were generated containing, in their plastid genomes, a nuclear promoter-driven kanamycin resistance gene (neo) with a start codon that required plastid RNA editing but otherwise identical to tp7 and tp17. Therefore it was expected that kanamycin resistance would only be acquired following RNA-mediated transfer of neo to the nucleus. Screening of tpneoACG progeny revealed several kanamycin-resistant plants, each of which contained the neo gene located in the nucleus. Surprisingly, neo was unedited in all these plants, indicating that neoACG was active in the absence of an edited start codon and suggesting that RNA intermediates were not involved in the transfers. However, analysis of tpneoACG revealed that only a low proportion of transcripts potentially able to mediate neo transfer were edited, thus precluding unequivocal conclusions regarding the role of RNA in plastid-to-nucleus transfer. The low proportion of edited transcripts was found to be due to predominant antisense neo transcripts, rather than to low editing efficiency of the sense transcripts. This study highlights a number of important considerations in the design of experiments utilising plastid RNA editing. The results also suggest that RNA editing sites reduce but do not eliminate functional plastid-to-nucleus gene transfer. This is relevant both in an evolutionary context and in placing RNA editing-dependent genes in the plastid genome as a means of transgene containment.

Introducing an RNA editing requirement into a plastid-localised transgene reduces but does not eliminate functional gene transfer to the nucleus

The regulation of activity of ribosomal RNA genes has been studied in euploid and aneuploid varieties of hyacinth. The gene/gene product relationship was determined by measuring the specific gene product (stable rRNA) and the total gene product (protein) in varieties with different dosages of rRNA genes. The results show that the cellular rRNA content is positively regulated, that maximum gene utilization is not normally employed, and that the degree of utilization responds to the total genome rather than to the specific rRNA gene dosage. The mechanism of control of this regulation appears to be at the transcriptional level.

Quantitative regulation of gene activity in plants.

The sequences of the Internal Transcribed Spacer regions (ITS1 and ITS2) within the genes coding for cytoplasmic ribosomal (r) RNAs on the A chromosome complement of 34 members of the higher plant genus Brachycome (synonym Brachyscome) have been compared. The ITS1 sequence of species within the B. lineariloba complex contains a 56 bp tract that is absent from at least 12 Brachycome species but is present in other species within Brachycome as well as other Asteraceae. Phylogenetic data support the suggestion that the number of chromosomes reduced in several independent Brachycome lineages during speciation. Comparisons with the B chromosome ITS2 of B. dichromosomatica cytodeme A1 suggests an origin of the B chromosome at a time prior to the divergence of the four cytodemes of B. dichromosomatica.

Jeremy N. Timmis

Papers

Introducing an RNA editing requirement into a plastid-localised transgene reduces but does not eliminate functional gene transfer to the nucleus

Quantitative regulation of gene activity in plants.

Internal transcribed spacer sequence analyses indicate cytoevolutionary patterns within Brachycome Cass. (Asteraceae)

Organelle evolution meets biotechnology.

Endosymbiotic Evolution: RNA Intermediates in Endosymbiotic Gene Transfer