Utility of the trnH–psbA Intergenic Spacer Region and Its Combinations as Plant DNA Barcodes: A Meta-Analysis

Background

The trnH–psbA intergenic spacer region has been used in many DNA barcoding studies. However, a comprehensive evaluation with rigorous sequence preprocessing and statistical testing on the utility of trnH–psbA and its combinations as DNA barcodes is lacking.

Methodology/Principal Findings

Sequences were searched from GenBank for a meta-analysis on the usefulness of trnH–psbA and its combinations as DNA barcodes. After preprocessing, we constructed full and matching data sets that contained 17 983 trnH–psbA sequences and 2190 sets of trnH–psbA, matK, rbcL, and ITS2 sequences from the same sample, repectively. These datasets were used to analyze the ability of trnH–psbA and its combinations to discriminate species by the BLAST and BLAST+P methods. The Fisher''s exact test was used to evaluate the significance of performance differences. For the full data set, the identification success rates of trnH–psbA exceeded 70% in 18 families and 12 genera, respectively. For the matching data set, the identification rates of trnH–psbA were significantly higher than those of the other loci in two families and four genera. Similarly, the identification rates of trnH–psbA+ITS2 were significantly higher than those of matK+rbcL in 18 families and 21 genera.

Conclusion/Significane

This study provides valuable information on the higher utility of trnH–psbA and its combinations. We found that trnH–psbA+ITS2 combination performs better or equally well compared with other combinations in most taxonomic groups investigated. This information will guide the optimal usage of trnH–psbA and its combinations for species identification.     

Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA

Background

Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns.

Methodology/Principal Findings

In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level.

Conclusions

Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.     

Insecticidal activities of Ginkgo biloba seed coat extracts against Spodoptera exigua (Lepidoptera: Noctuidae)

The present study relates to a methanol extract of the seed coat of Ginkgo biloba, and tested particularly on the third instar larvae of Spodoptera exigua. The extract was found to have an inhibitory effect on the growth of the larvae besides bringing a change in the nutrient reserves in the body of the insect. Topical application of five different doses of the methanol extract resulted in a mortal effect to third instar larvae of S. exigua that is very much dependent on the dose as well as duration of exposure. Lower doses revealed lower mortality after 24 h of application. At doses of 1.00, 2.00, 4.00, 8.00 and 16.00 ng/larva, mortalities were 9.25, 26.07, 50.32, 56.28 and 92.44%, respectively. The dose for 50% mortality (LD₅₀) of methanol extracts by applied by a topical method with 1 µL of acetone solution was 1.92 ng/larva. Nutrient reserves like protein, glycogen and lipid are known to regulate pupation and adult emergence. These reserves have been found to be lower in treated larvae, indicating the insecticidal role of methanol extracts from G. biloba against third instar larvae of S. exigua.     

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

The presence of duplicates introduced by PCR amplification is a major issue in paired short reads from next-generation sequencing platforms. These duplicates might have a serious impact on research applications, such as scaffolding in whole-genome sequencing and discovering large-scale genome variations, and are usually removed. We present FastUniq as a fast de novo tool for removal of duplicates in paired short reads. FastUniq identifies duplicates by comparing sequences between read pairs and does not require complete genome sequences as prerequisites. FastUniq is capable of simultaneously handling reads with different lengths and results in highly efficient running time, which increases linearly at an average speed of 87 million reads per 10 minutes. FastUniq is freely available at http://sourceforge.net/projects/fastuniq/.     

Paternal genetic structure of Hainan aborigines isolated at the entrance to East Asia

Background

At the southern entrance to East Asia, early population migration has affected most of the Y-chromosome variations of East Asians.

Methodology/Principal Findings

To assess the isolated genetic structure of Hainan Island and the original genetic structure at the southern entrance, we studied the Y chromosome diversity of 405 Hainan Island aborigines from all the six populations, who have little influence of the recent mainland population relocations and admixtures. Here we report that haplogroups O1a* and O2a* are dominant among Hainan aborigines. In addition, the frequency of the mainland dominant haplogroup O3 is quite low among these aborigines, indicating that they have lived rather isolated. Clustering analyses suggests that the Hainan aborigines have been segregated since about 20 thousand years ago, after two dominant haplogroups entered East Asia (31 to 36 thousand years ago).

Conclusions/Significance

Our results suggest that Hainan aborigines have been isolated at the entrance to East Asia for about 20 thousand years, whose distinctive genetic characteristics could be used as important controls in many population genetic studies.     

Mitochondrial DNA Evidence for a Diversified Origin of Workers Building Mausoleum for First Emperor of China

Variant studies on ancient DNA have attempted to reveal individual origin. Here, based on cloning sequencing and polymerase chain reaction-restriction fragment length polymorphisms, we analyzed polymorphisms in the first hypervariable region and coding regions of mitochondrial DNA of 19 human bone remains which were excavated from a tomb near the Terra Cotta Warriors and dated some 2,200 years before present. With the aim of shedding light on origins of these samples who were supposed to be workers building the mausoleum for the First Emperor of China, we compared them with 2,164 mtDNA profiles from 32 contemporary Chinese populations at both population and individual levels. Our results showed that mausoleum-building workers may be derived from very diverse sources of origin.     

DNA分子标记在动物个体识别与亲权鉴定方面的应用

自从DNA分子标记技术建立以来,各种DNA分子标记相继被广泛地应用于遗传图谱的构建,评估遗传多样性以及个体识别,亲权鉴定等方面,综述了利用DNA分子标记技术,进行动物个体识别与亲权鉴定的原理,研究进展,现状及其应用前景与存在的问题。     

Riccia fruticulosa O.F.Müll., 1782 and blue Metzgeria (Marchantiophyta) in Europe

Riccia fruticulosa O.F.Müll., 1782 from Norway is a valid name, referring to Riccardia palmata (Hedw.) Carruth. In 1785 Dickson misidentified British plants of a blue Metzgeria as R. fruticulosa . The European blue species of Metzgeria is conspecific with M. violacea (Ach.) Dumort., which replaces M. fruticulosa auct. The true origin of the type of Jungermannia violacea Ach., 1805 is probably Tierra del Fuego (rather than Dusky Bay, New Zealand), where the species is widespread. Reports from Australasia, Asia and Africa are all erroneous. The blue colour of Jungermanniales is found only in living plants and is derived from the oil-bodies. In contrast, that of Metzgeria appears only after death; its biological function is unknown.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 142 , 229−235.     

Low-temperature stratification strategies and growth regulators for rapid induction of Paris polyphylla var. yunnanensis seed germination

The seeds of Paris polyphylla var. yunnanensis are deeply dormant, and they remain dormant for 18 months or longer in their natural environment. Periodic exposure of the seeds to a low-temperature of 4 °C broke the dormancy in about 16 weeks (112 days). The most effective temperature stratification scheme was an interval of 14 days at 4 °C and 14 days at 22 °C. Both GA₃ and ethephon significantly enhanced the germination rate during the stratification treatment. The seed coat, particularly the mesophyll outer layer of the seed coat, strongly inhibited the germination. With removal of the seed coat and exposure of the uncoated seeds to 600 mg/l GA₃ for 48 h before the temperature stratification of 14 days at 4 °C and 14 days at 22 °C for 112 days, a germination percentage as high as 95.3% of the seeds was attained in about 160 days.     

The new species Ettingshausenia sarbaensis (Angiospermae) from the Cenomanian-Turonian of Western Kazakhstan in light of the problem of classification of dispersed cretaceous Platanus-like leaves

Based on morphological and epidermal characters of the leaf, a new species, Ettingshausenia sarbaensis sp. nov., from the Cenomanian-Turonian of western Kazakhstan is described. In fossil Platanus-like leaves, the unique epidermal structure, with the combination of encyclocytic, laterocytic, and paracytic stomata and the presence of trichomes on one or from two to seven epidermal cells, is shown for the first time. Based on variations in morphological and epidermal characters, two morphotypes corresponding to groups of sun and shade leaves are recognized. The expediency of consideration of dispersed Cretaceous Platanus-like leaves within the framework of morphological classification of leaves is discussed.