Phylogenomic relationship of feijoa (<Emphasis Type="Italic">Acca sellowiana</Emphasis> (O.Berg) Burret) with other Myrtaceae based on complete chloroplast genome sequences

Given their distribution, importance, and richness, Myrtaceae species comprise a model system for studying the evolution of tropical plant diversity. In addition, chloroplast (cp) genome sequencing is an efficient tool for phylogenetic relationship studies. Feijoa [Acca sellowiana (O. Berg) Burret; CN: pineapple-guava] is a Myrtaceae species that occurs naturally in southern Brazil and northern Uruguay. Feijoa is known for its exquisite perfume and flavorful fruits, pharmacological properties, ornamental value and increasing economic relevance. In the present work, we reported the complete cp genome of feijoa. The feijoa cp genome is a circular molecule of 159,370 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC 88,028 bp) and a Small Single Copy region (SSC 18,598 bp) separated by Inverted Repeat regions (IRs 26,372 bp). The genome structure, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. When compared to other cp genome sequences of Myrtaceae, feijoa showed closest relationship with pitanga (Eugenia uniflora L.). Furthermore, a comparison of pitanga synonymous (Ks) and nonsynonymous (Ka) substitution rates revealed extremely low values. Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of three Myrtoideae clades.     

The Complete Chloroplast Genome of Banana (Musa acuminata,Zingiberales): Insight into Plastid Monocotyledon Evolution

Background

Banana (genus Musa) is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-)specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus.

Methodology/Principal Findings

The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp) and a Small Single Copy region (SSC, 10,768 bp) separated by Inverted Repeat regions (IRs, 35,433 bp). Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1) and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed.

Conclusion

The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas.     

Relationship between cytogenetic aberrations by CGH coupled with tissue microdissection and DNA ploidy by laser scanning cytometry in head and neck squamous cell carcinoma

BACKGROUND: The relationship between DNA sequence copy number aberrations (DSCNAs) and DNA ploidy in head and neck squamous cell carcinomas (HNSCCs) is still controversial. Materials and Methods We analyzed DSCNAs by comparative genomic hybridization (CGH) combined with microdissection and DNA ploidy by laser scanning cytometry (LSC) in 18 surgically removed HNSCCs and compared the data. RESULTS: Copy number increases were most frequently observed on chromosomes 3q (16 cases), 8q (13 cases), and 12p (11 cases). Copy number decreases were observed on chromosome 3p (14 cases). LSC revealed DNA aneuploidy in 10 of the 18 cases. All DNA aneuploid tumors exhibited gain or amplification of DNA copy number at 12p11-12.1, whereas gain of DNA copy number was found in only 1 of 8 diploid tumors. DSCNAs were more frequent in DNA aneuploid tumors than in diploid tumors (P < 0.005). CONCLUSIONS: The present observations indicate a close relationship between DSCNAs and DNA ploidy in HNSCCs.     

Development of nuclear microsatellite markers for the fonio, Digitaria exilis (Poaceae), an understudied West African cereal

? Premise of the study: We developed nuclear microsatellite primers to explore the genetic diversity, population genetic structure, and evolutionary history of the fonio (Digitaria exilis), an understudied cereal cultivated in West Africa. ? Methods and Results: We used a microsatellite-enriched library approach to isolate and characterize 38 nuclear primer pairs (31 di-, five tri-, and two tetranucleotide repeats), of which 21 were polymorphic and exhibited a clear pattern in 36 accessions from West Africa. The number of alleles per locus ranged from two to 22, with a mean of 4.71, and expected heterozygosity ranged from 0.03 to 0.93. ? Conclusions: The developed set of 21 polymorphic SSR markers will provide tools for population and evolutionary genetics studies of the cultivated fonio.     

The Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L. cv. ‘Aseel’)

Date palm (Phoenix dactylifera L.) is an economically important and widely cultivated palm of the family Arecaceae. We sequenced the complete date palm chloroplast genome (cpDNA) from Pakistani cv. ??Aseel??, using a combination of Sanger-based and next-generation sequencing technologies. Being very similar to a sequence from a Saudi Arabian date palm cultivar ??Khalas?? published recently, the size of the genome was 158,458?bp with a pair of inverted repeat (IR) regions of 27,276?bp that were separated by a large single-copy (LSC) region of 86,195?bp and a small single-copy (SSC) region of 17,711?bp. Genome annotation demonstrated a total of 138 genes, of which 89 were protein coding, 39 were tRNA, and eight were rRNA genes. Comparison of cpDNA sequences of cultivars ??Aseel?? and ??Khalas?? showed following intervarietal variations in the LSC region; (a) two SNPs in intergenic spacers and one SNP in the rpoc1 gene, (b) polymorphism in two mono-nucleotide simple sequence repeats (SSR), and (c) a 4-bp indel in the accD-psaI intergenic spacer. The SSC region has a polymorphic site in the mono-nucleotide SSR located at position 120,710. We also compared cv. ??Aseel?? cpDNA sequence with partial P. dactylifera cpDNA sequence entries deposited in Genbank and identified a number of potentially useful polymorphisms in this species. Analysis of date palm cpDNA sequences revealed a close relationship with Typha latifolia. Occurrence of small numbers of forward and inverted repeats in date palm cpDNA indicated conserved genome arrangement.     

Genome walking with consensus primers: application to the large single copy region of chloroplast DNA

Conserved chloroplast (cp) DNA primer pairs are useful in plant molecular genetics, evolution and ecology. We have designed 20 conserved cpDNA primer pairs that, in combination with 18 previously described ones, amplify overlapping fragments (mean size of 2.5 kb) spanning the large single copy (LSC) region from Eudicots. These 38 primer pairs as well as eight primer pairs flanking cpDNA microsatellites were tested on 20 plant species belonging to 13 families. At least 79% and up to 100% of the LSC (> 86 kb) can be amplified. Many primer pairs are robust and work with all species.     

Cross-species microsatellite amplification in Vasconcellea and related genera and their use in germplasm classification.

To generate inexpensive and efficient DNA markers for addressing a number of population genetics problems and identification of wild hybrids in Vasconcellea, we have evaluated the use of simple sequence repeat (SSR) primers previously developed for other species. A set of 103 Vasconcellea accessions and some individuals of the related genera Carica and Jacaratia were analyzed with 10 primer pairs directing amplification of chloroplast microsatellites in Nicotiana tabacum and 9 nuclear SSR primer pairs recently identified in Vasconcellea x heilbornii. Heterologous amplification of chloroplast SSRs was successful for 8 of the 10 loci, of which 6 showed polymorphism. Seven of the 9 nuclear SSR primer pairs were useful in Vasconcellea and often also in Jacaratia and Carica, all revealing polymorphism. Exclusive haplotypes for each described taxon were identified based on chloroplast microsatellite data. Clustering based on separate nuclear and chloroplast data resulted in a clear grouping per taxon, but only low resolution was obtained above species level. The codominancy of nuclear SSRs and the general high polymorphism rate of SSR markers will make them more useful in future population genetics studies and diversity assessment in conservation programs.     

Development and characterization of microsatellite markers in a clonal plant,Dioscorea japonica Thunb.

We developed 10 microsatellite loci from genomic DNA of a dioecious clonal plant, Dioscorea japonica. Out of 384 clones, 148 contained microsatellite repeats. Polymerase chain reaction primer pairs were designed for 95 of these clones from their sequence data, of which, 10 pairs produced successful amplification. Thirty‐eight individuals were genotyped for allelic diversity. We detected three to nine alleles per locus, and the expected heterozygosity ranged from 0.461 to 0.851.     

用扩增片段的长度多态性分子标记探讨盾叶薯蓣的遗传多样性

用扩增片段的长度多态性(amplified fragment length polymorphism,AFLP)标记分析研究了中国5个盾叶薯蓣居群30个个体的遗传多样性。筛选出9对AFLP引物,从中检测到14698条清晰可见的条带,其中多态性带12628条,多态性比率85.92%。Shannon信息指数(I)为0.3656±0.1721,物种水平的Nei基因多样性(H)为0.2322±0.2200。遗传变异分析表明,物种水平的遗传分化系数Gst为0.4827,说明其群体间存在一定的遗传分化,居群间的基因流Nm为0.5358,居群间遗传交换较小。聚类分析结果显示5个居群盾叶薯蓣有较为丰富的遗传变异,且与地理分布有相关性。     

The chloroplast genome sequence from <Emphasis Type="Italic">Eugenia uniflora</Emphasis>, a Myrtaceae from Neotropics

Eugenia uniflora is a plant native to tropical America that holds great ecological and economic importance. The complete chloroplast (cp) genome sequence of Eugenia uniflora, a member of the Neotropical Myrtaceae family, is reported here. The genome is 158,445 bp in length and exhibits a typical quadripartite structure of the large (LSC, 87,459 bp) and small (SSC, 18,318 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 26,334 bp). It contains 111 unique genes, including 77 protein-coding genes, 30 tRNAs and 4 rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Comparison of the entire cp genomes of E. uniflora L. and three other Myrtaceae revealed an expansion of 43 bp in the intergenic spacer located between the IRA/large single-copy (LSC) border and the first gene of LSC region. Simple sequence repeat (SSR) analysis revealed that most SSRs are AT rich, which contribute to the overall AT richness of the cp genome. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the noncoding regions. Phylogenetic analysis among 58 species based on 57 cp genes demonstrated a closer relationship between E. uniflora L. and Syzygium cumini (L). Skeels compared to the Eucalyptus clade in the Myrtaceae family. The complete cp genome sequence of E. uniflora reported here has importance for population genetics, as well as phylogenetic and evolutionary studies in this species and other Myrtaceae species from Neotropical regions.     

长爪栘[木衣]叶绿体基因组特征系统发育及密码子偏好性分析

长爪栘[木衣](Docynia longiunguis Q.Luo & J.L.Liu)是我国特有的栘[木衣]属植物,具有较高的食药用价值.对其叶绿体基因组进行分析,有助于阐明栘[木衣]属内的系统发育关系,为长爪栘[木衣]资源的开发利用及进一步研究奠定基础.结合其近缘种云南移[木衣]叶绿体基因组数据,在进行全序列比对后...     

Isolation,characterization and cross‐species amplification of microsatellite DNA loci in the tropical American yam Dioscorea trifida

We developed microsatellite markers in American yam (Dioscorea trifida). A microsatellite sequence‐enriched genomic library was screened, and after sequencing, primers were designed for 20 microsatellites. Among these, eight primer pairs yielded amplification products that were both interpretable and polymorphic in 24 yam cultivars. The number of alleles per locus ranged from two to 13 and the overall expected heterozygosity was around 0.5. Six of the eight Dioscorea trifida microsatellite loci gave amplification products in other Dioscorea species.     

Physiological markers of stress susceptibility in maize and triticale under different soil compactions and/or soil water contents

Differences between two maize and two triticale genotypes grown in low soil compaction (LSC), moderate soil compaction (MSC) and severe soil compaction (SSC) and with a limited (D) or excess (W) soil water content were observed as a decrease in shoot (S) and root (R) biomass, leaf greening (SPAD) and increase in membrane injury (LI), root and leaf water potential (ψ), photosynthesis (Pn), transpiration (E) and stomata conductance (g_S). Close correlations between ψ_L and ψ_R, and between differences ψ_L and ψ_R (Δψ) were found. Drought or waterlogging with LSC conditions in both maize genotypes resulted in higher WUE than in control plants (LSC C), but under the SSC WUE declined. However, for triticale differences in WUE, between treatments were small and insignificant. In general, changes in markers were greater for genotypes sensitive to the soil compaction (Ankora, CHD-12) than in resistant ones (Tina, CHD-247) and were higher in seedlings grown under SSC conditions.

Abbreviations: ψ_R, ψ_L: root and leaf water potential; C: control; D: drought; E: transpiration rate; FWC: field water capacity; g_S: stomatal conductance; LSC, MSC, SSC: low, moderate and severe soil compaction; P_n: photosynthesis rate; W: waterlogging     

A set of 16 consensus primer pairs amplifying the complete mitochondrial genomes of orange-spotted grouper (Epinephelus coioides) and Hong Kong grouper (Epinephelus akaara)

Groupers are of considerable economic value; however, their classification and evolutionary relationships have long been hindered by the overwhelming number of species and lack of morphological specializations. Mitochondrial genome is a source of original markers that are potentially useful in the study of phylogeny and population genetics of groupers. We describe a set of 16 new primer pairs that allow PCR amplification of the entire mitochondrial genomes of orange-spotted grouper and Hong Kong grouper. This primer set has been defined for consensus over eight other grouper species, facilitating further studies on the molecular evolution and population genetics of groupers.     

New microsatellite loci in the dwarf yams Dioscorea group Epipetrum (Dioscoreaceae)

? Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of two taxa of the Chilean Epipetrum group of Dioscorea to assess their levels of genetic diversity and population differentiation. ? Methods and Results: Eleven microsatellite loci were identified. Six out of nine microsatellites from D. biloba amplified in D. humilis, and the two microsatellites from D. humilis amplified in both taxa. Two different sets of eight loci amplified in each of the two tested taxa, D. biloba and D. humilis. The average number of alleles was 5.75 and 5 for D. biloba and D. humilis, respectively. Higher levels of mean genetic diversity were found in D. biloba (H(E) = 0.639) than in D. humilis (H(E) = 0.414). ? Conclusions: These microsatellite primers will be useful in population genetic studies and to establish conservation strategies in the endangered taxa of the Epipetrum group of Dioscorea.     

应用SRAP标记构建山药种质资源DNA指纹图谱

利用30对多态性良好的SRAP引物对90份山药种质资源进行PCR扩增,构建扩增图谱,共扩增到722个位点,多态性位点581个,多态性比例为80.47%,每对引物组合检测多态性位点3~30个,每对引物能鉴别6~51份山药种质资源;采用DNA数据分析软件对扩增出的多态性位点进行分析,构建山药种质资源方框指纹图谱,该图谱清晰地反映出每对引物能扩增的多态位点数、鉴别资源份数及资源具体编号,资源在该引物组合下所能检测得到的多态位点数及所处的具体位置等信息;从10对SRAP引物组合中挑选出的21个多态性位点,根据谱带的有无转化成的1/0字符串编码,形成山药种质资源DNA数字指纹图谱,该图谱可鉴别区分90份山药种质资源中的82份资源。同时这些指纹图谱可为下一步的山药品种鉴定,种质资源评价、利用,分子标记辅助育种及品种权保护提供技术支撑。     

Complete nucleotide sequence of the cotton (Gossypium barbadense L.) chloroplast genome with a comparative analysis of sequences among 9 dicot plants

Recently, the complete chloroplast genome sequences of many important crop plants were determined, and this can be considered a major step forward toward exploiting the usefulness of chloroplast genetic engineering technology. Economically, cotton is one of the most important crop plants for many countries. To further our understanding of this important crop, we determined the complete nucleotide sequence of the chloroplast genome from cotton (Gossypium barbadense L.). The chloroplast genome of cotton is 160,317 base pairs (bp) in length, and is composed of a large single copy (LSC) of 88,841 bp, a small single copy (SSC) of 20,294 bp, and two identical inverted repeat (IR) regions of 25,591 bp each. The genome contains 114 unique genes, of which 17 genes are duplicated in the IRs. In addition, many open reading frames (ORFs) and hypothetical chloroplast reading frames (ycfs) with unknown functions were deduced. Compared to the chloroplast genomes from 8 other dicot plants, the cotton chloroplast genome showed a high degree of similarity of the overall structure, gene organization, and gene content. Furthermore, the sequences of the genes showed high degrees of identity at the DNA and amino acid levels. The cotton chloroplast genome was somewhat longer than the chloroplast genomes of most of the other dicot plants compared here. However, this elongation of the cotton chloroplast genome was found to be due mainly to expansions of the intergenic regions and introns (non-coding DNA). Moreover, these expansions occurred predominantly in the LSC and SSC regions.     

Orientation of the lateral semicircular canal in Xenarthra and its links with head posture and phylogeny

The orientation of the semicircular canals of the inner ear in the skull of vertebrates is one of the determinants of the capacity of this system to detect a given rotational movement of the head. Past functional studies on the spatial orientation of the semicircular canals essentially focused on the lateral semicircular canal (LSC), which is supposedly held close to horizontal during rest and/or alert behaviors. However, they generally investigated this feature in only a few and distantly related taxa. Based on 3D‐models reconstructed from µCT‐scans of skulls, we examined the diversity of orientations of the LSC within one of the four major clades of placental mammals, that is, the superorder Xenarthra, with a data set that includes almost all extant genera and two extinct taxa. We observed a wide diversity of LSC orientations relative to the basicranium at both intraspecific and interspecific scales. The estimated phylogenetic imprint on the orientation of the LSC was significant but rather low within the superorder, though some phylogenetic conservatism was detected for armadillos that were characterized by a strongly tilted LSC. A convergence between extant suspensory sloths was also detected, both genera showing a weakly tilted LSC. Our preliminary analysis of usual head posture in extant xenarthrans based on photographs of living animals further revealed that the LSC orientation in armadillos is congruent with a strongly nose‐down head posture. It also portrayed a more complex situation for sloths and anteaters. Finally, we also demonstrate that the conformation of the cranial vault and nuchal crests as well as the orientation of the posterior part of the petrosal may covary with the LSC orientation in Xenarthra. Possible inferences for the head postures of extinct xenarthrans such as giant ground sloths are discussed in the light of these results.     

Molecular marker based taxonomy and phylogeny of Guinea yam (Dioscorea rotundata - D. cayenensis).

Four different molecular techniques were used to assess relationships among 21 accessions of Guinea yam (Dioscorea rotundata and Dioscorea cayenensis) and 21 accessions belonging to seven putative progenitor species. Random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) analysis yielded 246 informative characters that were transformed into a matrix of pairwise distances and analyzed by neighbor joining or split decomposition. Both methods gave congruent results. Well-separated groups were formed that corresponded to their species designation. Dioscorea rotundata and D. cayenensis accessions were clearly separated from each other, supporting the concept that both are distinct species. Two morphological intermediates grouped together with D. rotundata. All investigated species fell into two main clusters, one comprising D. rotundata, D. cayenensis, Dioscorea abyssinica, Dioscorea liebrechtsiana, and Dioscorea praehensilis, the other comprising Dioscorea smilacifolia, Dioscorea minutiflora, Dioscorea burkilliana, and Dioscorea togoensis. The same grouping was also obtained by comparative sequence analysis of chloroplast DNA, which supports earlier studies of nuclear rDNA variation and chloroplast restriction fragment length polymorphisms. We also analyzed the same set of Dioscorea samples with the recently developed random amplified microsatellite polymorphism (RAMPO) technique. A series of diagnostic RAMPO bands was identified that clearly distinguished between D. rotundata and D. cayenensis. Some of these bands could also be traced back to the putative progenitors of both species. The evolutionary origin of Guinea yam is discussed in light of the present results.