The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video

Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases. At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them. One such popular video currently available is ‘Using the MaizeGDB Genome Browser’, which describes how the maize genome was sequenced and assembled as well as how the sequence can be visualized and interacted with via the MaizeGDB Genome Browser

High-Throughput Sequencing of Three Lemnoideae (Duckweeds) Chloroplast Genomes from Total DNA

BACKGROUND: Chloroplast genomes provide a wealth of information for evolutionary and population genetic studies. Chloroplasts play a particularly important role in the adaption for aquatic plants because they float on water and their major surface is exposed continuously to sunlight. The subfamily of Lemnoideae represents such a collection of aquatic species that because of photosynthesis represents one of the fastest growing plant species on earth. METHODS: We sequenced the chloroplast genomes from three different genera of Lemnoideae, Spirodela polyrhiza, Wolffiella lingulata and Wolffia australiana by high-throughput DNA sequencing of genomic DNA using the SOLiD platform. Unfractionated total DNA contains high copies of plastid DNA so that sequences from the nucleus and mitochondria can easily be filtered computationally. Remaining sequence reads were assembled into contiguous sequences (contigs) using SOLiD software tools. Contigs were mapped to a reference genome of Lemna minor and gaps, selected by PCR, were sequenced on the ABI3730xl platform. CONCLUSIONS: This combinatorial approach yielded whole genomic contiguous sequences in a cost-effective manner. Over 1,000-time coverage of chloroplast from total DNA were reached by the SOLiD platform in a single spot on a quadrant slide without purification. Comparative analysis indicated that the chloroplast genome was conserved in gene number and organization with respect to the reference genome of L. minor. However, higher nucleotide substitution, abundant deletions and insertions occurred in non-coding regions of these genomes, indicating a greater genomic dynamics than expected from the comparison of other related species in the Pooideae. Noticeably, there was no transition bias over transversion in Lemnoideae. The data should have immediate applications in evolutionary biology and plant taxonomy with increased resolution and statistical power

Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize

We compared the genetic architecture of thirteen maize morphological traits in a large population of recombinant inbred lines. Four traits from the male inflorescence (tassel) and three traits from the female inflorescence (ear) were measured and studied using linkage and genome-wide association analyses and compared to three flowering and three leaf traits previously studied in the same population. Inflorescence loci have larger effects than flowering and leaf loci, and ear effects are larger than tassel effects. Ear trait models also have lower predictive ability than tassel, flowering, or leaf trait models. Pleiotropic loci were identified that control elongation of ear and tassel, consistent with their common developmental origin. For these pleiotropic loci, the ear effects are larger than tassel effects even though the same causal polymorphisms are likely involved. This implies that the observed differences in genetic architecture are not due to distinct features of the underlying polymorphisms. Our results support the hypothesis that genetic architecture is a function of trait stability over evolutionary time, since the traits that changed most during the relatively recent domestication of maize have the largest effects

Complete Chloroplast Genome Sequence of a Major Invasive Species, Crofton Weed (Ageratina adenophora)

Crofton weed (Ageratina adenophora) is one of the most hazardous invasive plant species, which causes serious economic losses and environmental damages worldwide. However, the sequence resource and genome information of A. adenophora are rather limited, making phylogenetic identification and evolutionary studies very difficult. Here, we report the complete sequence of the A. adenophora chloroplast (cp) genome based on Illumina sequencing.The A. adenophora cp genome is 150, 689 bp in length including a small single-copy (SSC) region of 18, 358 bp and a large single-copy (LSC) region of 84, 815 bp separated by a pair of inverted repeats (IRs) of 23, 755 bp. The genome contains 130 unique genes and 18 duplicated in the IR regions, with the gene content and organization similar to other Asteraceae cp genomes. Comparative analysis identified five DNA regions (ndhD-ccsA, psbI-trnS, ndhF-ycf1, ndhI-ndhG and atpA-trnR) containing parsimony-informative characters higher than 2%, which may be potential informative markers for barcoding and phylogenetic analysis. Repeat structure, codon usage and contraction of the IR were also investigated to reveal the pattern of evolution. Phylogenetic analysis demonstrated a sister relationship between A. adenophora and Guizotia abyssinica and supported a monophyly of the Asterales.We have assembled and analyzed the chloroplast genome of A. adenophora in this study, which was the first sequenced plastome in the Eupatorieae tribe. The complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies within this invasive species and also within the Asteraceae family

Chromatin-associated regulation of sorbitol synthesis in flower buds of peach

[EN] Key message PpeS6PDH gene is postulated to mediate sorbitol synthesis in flower buds of peach concomitantly with specific chromatin modifications. Abstract Perennial plants have evolved an adaptive mechanism involving protection of meristems within specialized structures named buds in order to survive low temperatures and water deprivation during winter. A seasonal period of dormancy further improves tolerance of buds to environmental stresses through specific mechanisms poorly known at the molecular level. We have shown that peach PpeS6PDH gene is down-regulated in flower buds after dormancy release, concomitantly with changes in the methylation level at specific lysine residues of histone H3 (H3K27 and H3K4) in the chromatin around the translation start site of the gene. PpeS6PDH encodes a NADPH-dependent sorbitol-6-phosphate dehydrogenase, the key enzyme for biosynthesis of sorbitol. Consistently, sorbitol accumulates in dormant buds showing higher PpeS6PDH expression. Moreover, PpeS6PDH gene expression is affected by cold and water deficit stress. Particularly, its expression is up-regulated by low temperature in buds and leaves, whereas desiccation treatment induces PpeS6PDH in buds and represses the gene in leaves. These data reveal the concurrent participation of chromatin modification mechanisms, transcriptional regulation of PpeS6PDH and sorbitol accumulation in flower buds of peach. In addition to its role as a major translocatable photosynthate in Rosaceae species, sorbitol is a widespread compatible solute and cryoprotectant, which suggests its participation in tolerance to environmental stresses in flower buds of peach.This work was funded by the Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA)-FEDER (RF2013-00043-C02-02) and the Ministry of Science and Innovation of Spain (AGL2010-20595). AL was funded by a fellowship co-financed by the European Social Fund and the Instituto Valenciano de Investigaciones Agrarias (IVIA).Lloret, A.; Martinez Fuentes, A.; Agustí Fonfría, M.; Badenes, ML.; Rios, G. (2017). Chromatin-associated regulation of sorbitol synthesis in flower buds of peach. Plant Molecular Biology. 95(4-5):507-517. https://doi.org/10.1007/s11103-017-0669-6S507517954-5Andersen CL, Jensen JL, Ørntoft TF (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64:5245–5250. doi: 10.1158/0008-5472.CAN-04-0496Bai S, Saito T, Ito A et al (2016) Small RNA and PARE sequencing in flower bud reveal the involvement of sRNAs in endodormancy release of Japanese pear (Pyrus pyrifolia ‘Kosui’). BMC Genomics 17:230. doi: 10.1186/s12864-016-2514-8Bielenberg DG, Wang Y, Li Z et al (2008) Sequencing and annotation of the evergrowing locus in peach (Prunus persica [L.] Batsch) reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation. Tree Genet Genomes 4:495–507. doi: 10.1007/s11295-007-0126-9Bieleski RL (1969) Accumulation and translocation of sorbitol in apple phloem. Aust J Biol Sci 22:611–620. doi: 10.1071/BI9690611Bieleski RL (1982) Sugar alcohols. In: Loewus F, Tanner W (eds) Encyclopedia of plant physiology, new series 13A. Springer-Verlag, Berlin, pp 158–192Bortiri E, Oh SH, Gao FY, Potter D (2002) The phylogenetic utility of nucleotide sequences of sorbitol 6-phosphate dehydrogenase in Prunus (Rosaceae). Am J Bot 89:1697–1708. doi: 10.3732/ajb.89.10.1697Chouard P (1960) Vernalization and its relations to dormancy. Annu Rev Plant Physiol 11:191–238. doi: 10.1146/annurev.pp.11.060160.001203Conde D, Le Gac AL, Perales M et al (2017) Chilling-responsive DEMETER-LIKE DNA demethylase mediates in poplar bud break. Plant Cell Environ 40:2236–2249. doi: 10.1111/pce.13019Couvillon GA, Erez A (1985) Influence of prolonged exposure to chilling temperatures on bud break and heat requirement for bloom of several fruit species. J Amer Soc Hort Sci 110:47–50de la Fuente L, Conesa A, Lloret A, Badenes ML, Ríos G (2015) Genome-wide changes in histone H3 lysine 27 trimethylation associated with bud dormancy release in peach. Tree Genet Genomes 11:45. doi: 10.1007/s11295-015-0869-7Deng W, Buzas DM, Ying H et al (2013) Arabidopsis polycomb repressive complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes. BMC Genomics 14:593. doi: 10.1186/1471-2164-14-593Escobar-Gutiérrez AJ, Gaudillère JP (1996) Distribution, metabolism and role of sorbitol in higher plants—A review. Agronomie 16:281–298. doi: 10.1051/agro:19960502Escobar-Gutiérrez AJ, Zipperlin B, Carbonne F, Moing A, Gaudillére JP (1998) Photosynthesis, carbon partitioning and metabolite content during drought stress in peach seedlings. Aust J Plant Physiol 25:197–205. doi: 10.1071/PP97121Eshghi S, Tafazoli E, Dokhani S, Rahemi M, Emam Y (2007) Changes in carbohydrate contents in shoot tips, leaves and roots of strawberry (Fragaria x ananassa Duch) during flower-bud differentiation. Sci Hortic 113:255–260. doi: 10.1016/j.scienta.2007.03.014Everard JD, Cantini C, Grumet R, Plummer J, Loescher WH (1997) Molecular cloning of mannose-6-phosphate reductase and its developmental expression in celery. Plant Physiol 113:1427–1435. doi: 10.1104/pp.113.4.1427Fennell A (2014) Genomics and functional genomics of winter low temperature tolerance in temperate fruit crops. Crit Rev Plant Sci 33:125–140. doi: 10.1080/07352689.2014.870410Figueroa CM, Iglesias AA (2010) Aldose-6-phosphate reductase from apple leaves: importance of the quaternary structure for enzyme activity. Biochimie 92:81–88. doi: 10.1016/j.biochi.2009.09.013Gao M, Tao R, Miura K, Dandekar AM, Sugiura A (2001) Transformation of Japanese persimmon (Diospyros kaki Thunb) with apple cDNA encoding NADP-dependent sorbitol-6-phosphate dehydrogenase. Plant Sci 160:837–845. doi: 10.1016/S0168-9452(00)00458-1Grant CR, ap Rees T (1981) Sorbitol metabolism by apple seedlings. Phytochemistry 20:1505–1511. doi: 10.1016/S0031-9422(00)98521-2Hartman MD, Figueroa CM, Arias DG, Iglesias AA (2017) Inhibition of recombinant aldose-6-phosphate reductase from peach leaves by hexose-phosphates, inorganic phosphate and oxidants. Plant Cell Physiol 58:145–155. doi: 10.1093/pcp/pcw180Horvath DP, Anderson JV, Chao WS, Foley ME (2003) Knowing when to grow: signals regulating bud dormancy. Trends Plant Sci 8:534–540. doi: 10.1016/j.tplants.2003.09.013Horvath DP, Sung S, Kim D, Chao W, Anderson J (2010) Characterization, expression and function of DORMANCY ASSOCIATED MADS-BOX genes from leafy spurge. Plant Mol Biol 73:169–179. doi: 10.1007/s11103-009-9596-5Hussain S, Niu Q, Yang F, Hussain N, Teng Y (2015) The possible role of chilling in floral and vegetative bud dormancy release in Pyrus pyrifolia. Biol Plant 59:726–734. doi: 10.1007/s10535-015-0547-5Hyndman D, Baumanb DR, Herediac VV, Penning TM (2003) The aldo-keto reductase superfamily homepage. Chem Biol Interact 143–144:621–631. doi: 10.1016/S0009-2797(02)00193-XIto A, Sakamoto D, Moriguchi T (2012) Carbohydrate metabolism and its possible roles in endodormancy transition in Japanese pear. Sci Hortic 144:187–194. doi: 10.1016/j.scienta.2012.07.009Ito A, Sugiura T, Sakamoto D, Moriguchi T (2013) Effects of dormancy progression and low-temperature response on changes in the sorbitol concentration in xylem sap of Japanese pear during winter season. Tree Physiol 33:398–408. doi: 10.1093/treephys/tpt021Jung S, Bassett C, Bielenberg DG et al (2015) A standard nomenclature for gene designation in the Rosaceae. Tree Genet Genomes 11:108. doi: 10.1007/s11295-015-0931-5Kanayama Y, Mori H, Imaseki H, Yamaki S (1992) Nucleotide sequence of a cDNA encoding NADP-sorbitol-6-phosphate dehydrogenase from apple. Plant Physiol 100:1607–1608Kanayama Y, Watanabe M, Moriguchi R, Deguchi M, Kanahama K, Yamaki S (2006) Effects of low temperature and abscisic acid on the expression of the sorbitol-6-phosphate dehydrogenase gene in apple leaves. J Japan Soc Hort Sci 75:20–25. doi: 10.2503/jjshs.75.20Kumar G, Rattan UK, Singh AK (2016a) Chilling-mediated DNA methylation changes during dormancy and its release reveal the importance of epigenetic regulation during winter dormancy in apple (Malus x domestica Borkh). PLoS ONE 11:e0149934. doi: 10.1371/journal.pone.0149934Kumar S, Stecher G, Tamura K (2016b) MEGA7: molecular evolutionary genetics analysis version 70 for bigger datasets. Mol Biol Evol 33:1870–1874. doi: 10.1093/molbev/msw054Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685. doi: 10.1038/227680a0Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. doi: 10.1093/bioinformatics/btm404Leida C, Terol J, Martí G et al (2010) Identification of genes associated with bud dormancy release in Prunus persica by suppression subtractive hybridization. Tree Physiol 30:655–666. doi: 10.1093/treephys/tpq008Leida C, Conesa A, Llácer G, Badenes ML, Ríos G (2012) Histone modifications and expression of DAM6 gene in peach are modulated during bud dormancy release in a cultivar-dependent manner. New Phytol 193:67–80. doi: 10.1111/j.1469-8137.2011.03863.xLiang D, Cui M, Wu S, Ma F-W (2012) Genomic structure, sub-cellular localization, and promoter analysis of the gene encoding sorbitol-6-phosphate dehydrogenase from apple. Plant Mol Biol Rep 30:904–914. doi: 10.1007/s11105-011-0409-zLiu D, Ni J, Wu R, Teng Y (2013) High temperature alters sorbitol metabolism in Pyrus pyrifolia leaves and fruit flesh during late stages of fruit enlargement. J Am Soc Hortic Sci 138:443–451Lloret A, Conejero A, Leida C et al (2017) Dual regulation of water retention and cell growth by a stress-associated protein (SAP) gene in Prunus. Sci Rep 7:332. doi: 10.1038/s41598-017-00471-7Lo Bianco R, Rieger M, Sung S-JS (2000) Effect of drought on sorbitol and sucrose metabolism in sinks and sources of peach. Physiol Plant 108:71–78. doi: 10.1034/j.1399-3054.2000.108001071.xLoescher WH (1987) Physiology and metabolism of sugar alcohols in higher-plants. Physiol Plant 70:553–557. doi: 10.1111/j.1399-3054.1987.tb02857.xLoescher WH, Marlow GC, Kennedy RA (1982) Sorbitol metabolism and sink-source interconversions in developing apple leaves. Plant Physiol 70:335–339. doi: 10.1104/pp.70.2.335Marquat C, Vandamme M, Gendraud M, Pétel G (1999) Dormancy in vegetative buds of peach: relation between carbohydrate absorption potentials and carbohydrate concentration in the bud during dormancy and its release. Sci Hortic 79:151–162. doi: 10.1016/S0304-4238(98)00203-9Niu Q, Li J, Cai D et al (2016) Dormancy-associated MADS-box genes and microRNAs jointly control dormancy transition in pear (Pyrus pyrifolia white pear group) flower bud. J Exp Bot 67:239–257. doi: 10.1093/jxb/erv454Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP (2004) Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper—excel-based tool using pair-wise correlations. Biotechnol Lett 26:509–515. doi: 10.1023/B:BILE.0000019559.84305.47Ríos G, Leida C, Conejero A, Badenes ML (2014) Epigenetic regulation of bud dormancy events in perennial plants. Front Plant Sci 5:247. doi: 10.3389/fpls.2014.00247Saito T, Bai S, Imai T, Ito A, Nakajima I, Moriguchi T (2015) Histone modification and signalling cascade of the dormancy-associated MADS-box gene, PpMADS13-1, in Japanese pear (Pyrus pyrifolia) during endodormancy. Plant Cell Environ 38:1157–1166. doi: 10.1111/pce.12469Santamaría ME, Hasbún R, Valera MJ et al (2009) Acetylated H4 histone and genomic DNA methylation patterns during bud set and bud burst in Castanea sativa. J Plant Physiol 166:1360–1369. doi: 10.1016/j.jplph.2009.02.014Shen B, Hohmann S, Jensen RG, Bohnert HJ (1999) Roles of sugar alcohols in osmotic stress adaptation replacement of glycerol by mannitol and sorbitol in yeast. Plant Physiol 121:45–52. doi: 10.1104/pp.121.1.45Sheveleva EV, Marquez S, Chmara W, Zegeer A, Jensen RG, Bohnert HJ (1998) Sorbitol-6-phosphate dehydrogenase expression in transgenic tobacco high amounts of sorbitol lead to necrotic lesions. Plant Physiol 117:831–839. doi: 10.1104/pp.117.3.831Silver N, Best S, Jian J, Thein SL (2006) Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR. BMC Mol Biol 7:33. doi: 10.1186/1471-2199-7-33Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577. doi: 10.1080/10635150701472164Tao R, Uratsu SL, Dandekar AM (1995) Sorbitol synthesis in transgenic tobacco with apple cDNA encoding NADP-dependent sorbitol-6-phosphate dehydrogenase. Plant Cell Physiol 36:525–532. doi: 10.1093/oxfordjournals.pcp.a078789Teo G, Suzuki Y, Uratsu SL et al (2006) Silencing leaf sorbitol synthesis alters long-distance partitioning and apple fruit quality. Proc Natl Acad Sci USA 103:18842–18847. doi: 10.1073/pnas.0605873103Trotel P, Bouchereau A, Niogret MF, Larher F (1996) The fate of osmo-accumulated proline in leaf discs of Rape (Brassica napus L) incubated in a medium of low osmolarity. Plant Sci 118:31–45. doi: 10.1016/0168-9452(96)04422-6Verde I, Abbott AG, Scalabrin S et al (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494. doi: 10.1038/ng.2586Webb KL, Burley JWA (1962) Sorbitol translocation in apple. Science 137:766. doi: 10.1126/science.137.3532.766Wisniewski M, Norelli J, Artlip T (2015) Overexpression of a peach CBF gene in apple: a model for understanding the integration of growth, dormancy, and cold hardiness in woody plants. Front Plant Sci 6:85. doi: 10.3389/fpls.2015.00085Yadav R, Prasad R (2014) Identification and functional characterization of sorbitol-6-phosphate dehydrogenase protein from rice and structural elucidation by in silico approach. Planta 240:223–238. doi: 10.1007/s00425-014-2076-

High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

BACKGROUND: Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies. METHODOLOGY/PRINCIPAL FINDINGS: Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae. CONCLUSIONS/SIGNIFICANCE: The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes

A Set of 100 Chloroplast DNA Primer Pairs to Study Population Genetics and Phylogeny in Monocotyledons

Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding (exon) and non-coding regions (intron and intergenic spacer). They span the different chloroplast regions: 72 are located in the LSC, 13 in the Small Single Copy (SSC) and 15 in the Inverted Repeat region (IR). Amplification and sequencing were tested in 13 species of Monocotyledons: Dioscorea abyssinica, D. praehensilis, D. rotundata, D. dumetorum, D. bulbifera, Trichopus sempervirens (Dioscoreaceae), Phoenix canariensis, P. dactylifera, Astrocaryum scopatum, A. murumuru, Ceroxylon echinulatum (Arecaceae), Digitaria excilis and Pennisetum glaucum (Poaceae). The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR). We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC. Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable