Phyllosphere eukaryotic microalgal communities in rainforests:Drivers and diversityOA

Phyllosphere algae are common in tropical rainforests,forming visible biofilms or spots on plant leaf surfaces.However,knowledge of phyllosphere algal diversity and the environmental factors that drive that diversity is limited.The aim of this study is to identify the environmental factors that drive phyllosphere algal community composition and diversity in rainforests.For this purpose,we used single molecule real-time sequencing of full-length 18S rDNA to characterize the composition of phyllos...     

High Genetic Diversity in a Rare, Narrowly Endemic Primrose Species： Primula interjacens by ISSR Analysis

Prirnula interjacens Chen (Primulaceae) is a rare and narrow endemic species of centralsouth of Yunnan Province in China. This species consists of two varieties: P.interjacens var. interjacens known with only one population, and P.interjacens var. epilosa with two populations. Intersimple sequence repeat (ISSR) marker was used to detect the genetic diversity of the three extant populations. We expected a low genetic diversity level, but our results revealed a high level of intraspecific genetic diversity (at population level: P=59.75%, HE=0.2368, and Hpop=0.3459; at species level: P=75.47%, HT= 0.320 5, and Hsp = 0.4618), probably resulting from floral heteromorphism and preferring outcrossing. A moderate level of genetic differentiation among populations was detected based on Nei‘s genetic diversity analysis (26.13%) and Shannon‘s diversity index (25.09%). Although P./ntedacens var. intedacens and P. interjacens var. epilosa were morphologically distinct, UPGMA cluster analysis showed that the two varieties had no distinct genetic differentiation and may be treated as a single taxon. Conservation measures are suggested, including in situ and ex situ strategies, based on the observed population genetic information.     

Analysis of genetic relationship in mutant silkworm strains of Bombyx mori using inter simple sequence repeat （ISSR） markers

Amplified inter simple sequence repeats (ISSR) markers were used to determine genetic relationships among mutant silkworm strains of Bombyx mori. Fifteen ISSR primers containing simple sequence repeat (SSR) motifs were used in this study. A total of 113 markers were produced among 20 mutant swains, of which 73.45% were found to be polymorphic. In selected mutant genetic stocks, the average number of observed allele was (1.7080±0.4567), effective alleles (1.5194±0.3950) and genetic diversity (Ht) (0.2901±0.0415). The dendrogram produced using the unweighted pair group method with arithmetic means (UPGMA) and cluster analysis made using Nei's genetic distance resulted in the formation of one major group containing 6 groups separated 20 mutant silkworm strains. Therefore, ISSR amplification is a valuable method for determining the genetic variability among mutant silkworm swains. This efficient molecular marker would be useful for characterizing a considerable number of silkworm swains maintained at the germplasm center.     

Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei （Primulaceae）： implications for its conservation

Omphalogramma souliei Franch. is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. souliei in NW Yunnan, China. The genetic diversity at the species level is low with P=42.5% （percentage of polymorphic bands） and Hsp=0.1762 （total genetic diversity）. However, a high level of genetic differentiation among populations was detected based on different measures （Nei＇s genetic diversity analysis： Gst=0.6038; AMOVA analysis： Fst=0.6797）. Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenogamy predominated and autogamy played an assistant role in O. souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed.     

Geographic patterns of taxonomic and phylogenetic β-diversity of angiosperm genera in regional floras across the worldOA

Beta diversity(β-diversity) is the scalar between local(α) and regional(γ) diversity.Understanding geographic patterns of β-diversity is central to ecology,biogeography,and conservation biology.A full understanding of the origin and maintenance of geographic patterns of β-diversity requires exploring both taxonomic and phylogenetic β-diversity,as well as their respective turnover and nestedness components,and exploring phylogenetic p-diversity at different evolutionary depths.In this study,we ex...     

Genetic diversity in Chinese modern wheat varieties revealed by microsatellite markers

Genetic diversity of 1680 modern varieties in Chinese candidate core collections was analyzed at 78 SSR loci by fluorescence detection system. A total of 1336 alleles were detected, of which 1253 alleles could be annotated into 71 loci. For these 71 loci, the alleles ranged from 4 to 44 with an average of 17.6, and the PIC values changed from 0.19 to 0.89 with an average of 0.69. (1) In the three genomes of wheat, the average genetic richness was B>A>D, and the genetic diversity indexes were B>D>A. (2) Among the seven homoeologous groups, the average genetic richness was 2=7>3>4>6>5>1, and the genetic diversity indexes were 7>3>2>4>6>5>1. As a whole, group 7 possessed the highest genetic diversity, while groups 1 and 5 were the lowest. (3) In the 21 wheat chromosomes, 7A, 3B and 2D possessed much higher genetic diversity, while 2A, 1B, 4D, 5D and 1D were the lowest. (4) The highest average genetic diversity index existed in varieties bred in the 1950s, and then it declined continually. However, the change tendency of genetic diversity among decades was not greatly sharp. This was further illustrated by changes of the average genetic distance between varieties. In the 1950s it was the largest (0.731). Since the 1960s, it has decreased gradually (0.711, 0.706, 0.696, 0.695). The genetic base of modern varieties is becoming narrower and narrower. This should be given enough attention by breeders and policy makers.     

Does the Genetic Code Have A Eukaryotic Origin?

In the RNA world, RNA is assumed to be the dominant macromolecule performing most, if not all, core "house-keeping" functions. The ribo-cell hypothesis suggests that the genetic code and the translation machinery may both be born of the RNA world, and the introduction of DNA to ribo-cells may take over the informational role of RNA gradually, such as a mature set of genetic code and mechanism enabling stable inheritance of sequence and its variation. In this context, we modeled the genetic code in two content variables-GC and purine contents-of protein-coding sequences and measured the purine content sensitivities for each codon when the sensitivity (% usage) is plotted as a function of GC content variation. The analysis leads to a new pattern-the symmetric pattern-where the sensitivity of purine content variation shows diagonally symmetry in the codon table more significantly in the two GC content invariable quarters in addition to the two existing patterns where the table is divided into either four GC content sensitivity quarters or two amino acid diversity halves. The most insensitive codon sets are GUN (valine) and CAN (CAR for asparagine and CAY for aspartic acid) and the most biased amino acid is valine (always over-estimated) followed by alanine (always under-estimated). The unique position of valine and its codons suggests its key roles in the final recruitment of the complete codon set of the canonical table. The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes.     

Glacial Refugia of Ginkgo biloba and Human Impact on Its Genetic Diversity： Evidence from Chloroplast DNA

Variations in the trnK region of chloroplast DNA were investigated in the present study using polymerase chain reactionrestriction fragment length polymorphism to detect the genetic structure and to infer the possible glacial refugia of Ginkgo biloba L. in China. In total, 220 individuals from 12 populations in China and three populations outside China were analyzed, representing the largest number of populations studied by molecular markers to date. Nineteen haplotypes were produced and haplotype A was found in all populations. Populations in south-western China, including WC, JF, PX, and SP, contained 14 of the 19 haplotypes and their genetic diversity ranged from 0.771 4 to 0.867 6. The TM population from China also showed a high genetic diversity （H = 0.848 5）. Most of the genetic variation existed within populations and the differentiation among populations was low （GsT = 0.2）. According to haplotype distribution and the historical record, we suggest that populations of G. biloba have been subjected to extensive human impact, which has compounded our attempt to infer glacial refugia for Ginkgo. Nevertheless, the present results suggest that the center of genetic diversity of Ginkgo is mainly in south-western China and in situ conservation is needed to protect and preserve the genetic resources.     

Effects of Logging on the Genetic Diversity of Quercus tiaoloshanica Chun et Ko in a Tropical Montane Forest of Hainan Island, Southern China

Quercus tiaoloshanica Chun et Ko, which has a narrow range of distribution, is one of the important endemic species of the tropical montane rain forest on Hainan Island, southern China. Long-term logging and habitat destruction have resulted in population decline and distribution retreat of Q. tiaoloshanica. To determine the impact of logging on the genetic diversity of Q. tiaoloshanica, the authors investigated the genetic structures using amplified fragment length polymorphism markers in four regenerated stands after logging and in one unlogged stand. Compared with the unlogged stand, the effective number of alleles per locus dropped by 1.0% in selective logging stands and by 2.0% in clear logging stands, corresponding to reductions of 3.8% and 5.2%, respectively, in mean Nei＇s gene diversity and 2.9% and 3.5%, respectively, in mean Shannon diversity index. No substantial genetic erosion was detected in any of the regenerated stands owing to the high tree density and high heterogeneity of the Q. tiaoloshanica stands investigated. Meanwhile, there was no natural regeneration of the species observed in a Dacrydium pierrei Hickel plantation 700 m away from the regenerated stands, suggesting the limited ability of seed dispersal of Q. tiaoloshanica. Clear logging should be undertaken cautiously because the total number of plant species dropped by 15.2% in the clear-logged stands compared with the unlogged stand. To conserve the genetic diversity of this species, as well as the plant biodiversity of tropical forests, the habitats of Q. tiaoloshanica should be protected against exploitation in terms of agricultural or other forms of land use, and some mature trees should be preserved as seed sources to maintain an adequate regeneration base for this species in the management of logging.     

Evolutionary Genomics of Weedy Rice in the USA

Red rice is an interfertiie, weedy form of cultivated rice (Oryza sativa L.) that competes aggressively with the cropin the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America andthe weed has been proposed to have evolved through multiple mechanisms, including "de-domestication" of UScrop cultivars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedyOryza strains. The phenotype of US red rice ranges from "crop mimics", which share some domestication traitswith the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity haveindicated that many weed strains are closely related to Asian taxa (including indica and aus rice varieties, whichhave never been cultivated in the US, and the Asian crop progenitor O. rufipogon), whereas others show geneticsimilarity to the tropical japonica varieties cultivated in the southern US. Herein, we review what is known aboutthe evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to furthercharacterize the evolutionary genomics of this aggressive weed.     

Genetic structure and phylogeography of a relict tree fern,Sphaeropteris brunoniana (Cyatheaceae) from China and Laos inferred from cpDNA sequence variations:Implications for conservation

In this study, we analyzed the genetic structure and phylogeography of Sphaeropteris brunoniana from China and Laos. Combining cpDNA trnL-trnF and atpB-rbcL sequence variations, five haplotypes were identi- fied from the 10 investigated populations. Moderate haplotype diversity (h = 0.66580) and low nucleotide diver- sity (π = 0.23 × 10 ?3 ) were detected. The S. brunoniana in Yunnan region had much higher genetic diversity (h = 0.60195, π = 0.35 × 10 ?3 ) than that of Hainan–Laos (h = 0.00000, π = 0.00). A...     

Characterization of 12 polymorphic microsatellite markers in the Chinese tree shrew (Tupaia belangeri chinensis)

The Chinese tree shrew (Tupaia belangeri chinensis) is a small experimental animal with a close affinity to primates. This species has long been proposed to be an alternative experimental animal to primates in biomedical research. Despite decades of study, there is no pure breed for this animal, and the overall genetic diversity of wild tree shrews remains largely unknown. In order to obtain a set of genetic markers for evaluating the genetic diversity of tree shrew wild populations and tracing the lineages in inbreeding populations, we developed 12 polymorphic microsatellite markers from the genomic DNA of the tree shrew. An analysis of a wild population of 117 individuals collected from the suburb of Kunming, China, showed that these loci exhibited a highly expected heterozygosity (0.616). These 12 microsatellites were sufficient for individual identification and parentage analysis. The microsatellite markers developed in this study will be of use in evaluating genetic diversity and lineage tracing for the tree shrew.     

Global patterns of taxonomic and phylogenetic diversity of flowering plants:Biodiversity hotspots and coldspotsOA

Species diversity of angiosperms(flowering plants) varies greatly among regions.Geographic patterns of variation in species diversity are shaped by the interplay of ecological and evolutionary processes.Here,using a comprehensive data set for regional angiosperm floras across the world,we show geographic patterns of taxonomic(species) diversity,phylogenetic diversity,phylogenetic dispersion,and phylogenetic deviation(i.e.,phylogenetic diversity after accounting for taxonomic diversity) across th...     

鱼类免疫球蛋白基因结构及抗体多样性的遗传机制

本文对鱼类免疫球蛋白的基因结构以及抗体多样性产生的遗传机制作一综述。免疫球蛋白重链和轻链是由不同染色体上的多基因座编码的,在鱼类的不同分类单元中具有不同的基因组织方式。鱼类抗体可以识别外界为数众多的抗原,其多样性主要是由以下遗传机制产生的：种系V区编码区段的多样性、V (D) J区段组合的多样性、基因重组的不精确性、基因转换、体细胞突变以及H和L链的随机组合等。 Gene Structure and Genetic Diversity of Immunoglobulins in Fish ZHANG Yong-an,NIE Pin,ZHU Zuo-yan State Key Laboratory of Freshwater Ecology and Biotechnology,Institute of Hydrobiology,Chinese Academy of Sciences,Wuhan 430072,China Abstract:The current knowledge concerning the structure of fish immunoglobulin (Ig) genes and the genetic mechanisms in generating fish antibody diversities is reviewed.The heavy (H-) and light (L-) chains of the immunoglobulin are encoded by multigenic loci on separate chromosomes.In different taxa of fish,the Ig genes are organized in different patterns.Fish antibody can recognize various foreign antigens,and the antibody diversity is generated by the following genetic mechanisms:the sequence diversity within the segments encoding the variable domain,the combinatorial diversity of V (D) J segments,the imprecision of rearrangements,gene conversion,somatic hypermutation,and the combination of H- and L-chain. Key words：immunoglobulin; gene; antibody; diversity; fish     

Sequence Analysis of Segment 8 of Five Chinese Isolates of Rice Gall Dwarf Virus and Expression of a Main Outer Capsid Protein in Escherichia coli

The rice gall dwarf disease, caused by the Rice gall dwarf virus (RGDV) is a serious disease occurring in rice in many regions of Guangdong province. As a basis to control the disease we have studied the genomic diversity of a variety of isolates from different locations. Genome segment 8(S8), encoding a main outer capsid protein (Pns8) of RGDV five isolates (BL, CH, DQ, GZ, XY) from Guangdong province was cloned and sequenced. The results revealed that all the S8 segments of the five isolates consisted of 1 578 nucleotides and had a single open reading frame (ORF) extending for 1 301 nucleotides from nucleotide 21 which encoded a polypeptide of 426 amino acids with an estimated molecular weight of 47.4 kDa. The S8 full-length sequence and the ORF sequence shared 97.3%-98.8% and 97.3%-99.1% nucleotide sequence identities within the five Chinese isolates, and shared 94.8%-95.6% and 95.0%-96.0% identities with those of the Thailand isolate respectively. The deduced amino acid sequence of Pns8 in GZ isolate was identical to that in the Thailand isolate, while the amino acid sequence variability of Pns8 within five Chinese isolates ranged from 0.5% to 2.1%. These results indicate that the S8 segment of RGDV is highly conserved in different isolates from different locations. The S8 cDNA from the XY isolate was cloned into the plasmid vector pET-28b( ) and a fused expression protein with an apparent molecular mass of 51kDa was specifically detected in an analysis of Escherichia coli Rossetta(DE3)Ⅱcells. To our knowledge, this is the first report on analysis of the RGDV segment 8 sequence and genetic comparison of different RGDV isolates and their protein expression.     

Examining the genetic diversity of Stipa grandis under various grazing pressures

The Stipa grandis steppe in the Inner Mongolia Autonomous Region occupies an area of 2798081 hm2. On the basis of the genetic variation, it was found that its adaptability to the environmental conditions under grazing pressure was significant. Using the Inter-Simple Sequence Repeat (ISSR) procedure, the changes to the genetic diversity of the Stipa grandis population under different grazing pressures were observed. Plant samples were collected from a series of grazing gradients of the Stipa grandis steppe in Dalinuoer National Nature Reserve in the Inner Mongolia (located at 116°38′–116°41′E and 43°25′–43°27′N.), which has the following vegetation types in abundance: Leymus chinensis is the constructive species; the dominant species include Stipa grandis, Cleistogenes squarrosa, and Artemisia frigida; the companion species is Potentilla acaulis and others. According to the grazing pressure, the following four grazing gradients were identified from the dwellings of the herdsmen to the enclosure site: (1) no grazing (CK enclosure site); (2) light grazing (LG); (3) moderate grazing (MG); (4) heavy grazing (HG). Young leaves of each Stipa grandis were collected during the growing season. The results showed that the Stipa grandis showed abundant genetic diversity despite the fact that certain polymorphic loci were lost; at the same time, new polymorphic loci emerged when grazing pressure increased; a total of 10 primers were used, and 74 bands were produced in total, of which 65 bands were polymorphic; the total percentage of polymorphism was 89%; the percentage of polymorphic loci of the Stipa grandis population decreased with the increase of grazing pressure; the percentage of polymorphic loci was 62.2% in the no-grazing (CK) population, 64.9% in the light-grazing (LG) population, 58.1% in the moderate-grazing (MG) population, and 56.8% in the heavy-grazing (HG) population; the genetic diversity of the population in the descending order using the Shannon's information index is as follows: (1) light grazing (0.3486); (2) no grazing (0.3339); (3) moderate grazing (0.3249); (4) heavy grazing (0.2735) with the same distributional pattern as the Nei's genetic diversity index. The test showed the following: As the grazing pressures increased, the change of genetic diversity decreased; the genetic differentiation coefficient among the population (Gst) was 0.1984, which showed the presence of small partial genetic diversity (19.8%) among populations; gene flow (Nm*) between primers varied from 0.9806 to 3.4463, and the mean gene flow (Nm*) was 2.0202; the UPGMA cluster figure that was constructed on the basis of the genetic distance matrix showed four populations that became genetically closer at each step: (1) The first group was the moderate-grazing (MG) population and the heavy- grazing (HG) population; (2) The second group consisted of the no-grazing (CK) population and the light-grazing (LG) population; (3) The two groups gathered together.     

Genetic Variation and Clonal Diversity of the Two Divergent Types of Clonal Populations of Leymus chinensis Tzvel on the Song Liao Steppe in the West of Northeastern China

The genetic variation and clonal diversity of two divergent types (grey-green and yellow-green) of clonal populations of Leymus chinensis Tzvel at 14 loci were compared. Total gene diversity (HT) and the coefficient of genetic differentiation (GST) were all higher for the yellow-green type (HT = 0.270; GST =0.186) than for the grey-green type (HT = 0.250; GST = 0.157) of L. chinensis. Rare alleles usually occurred as heterozygotes rather than homozygotes and significant deviations from Hardy-Weinberg equilibrium were found only at a few loci. This indicated that these two types of populations were mainly out-crossing. Clonal diversity, evenness of clones, and mean clone size were not significantly different between the two types. We found that differences between the clone size and genetic variation of the yellow-green type of populations occurred with different climate and habitat population groups. However, for the grey-green type of populations, these genetic variations decreased under conditions of different climate and habitat population groups.     

Examining the genetic diversity of Stipa grandis under various grazing pressures

The Stipa grandis steppe in the Inner Mongolia Autonomous Region occupies an area of 2798081 hm2. On the basis of the genetic variation, it was found that its adaptability to the environmental conditions under grazing pressure was significant. Using the Inter-Simple Sequence Repeat (ISSR) procedure, the changes to the genetic diversity of the Stipa grandis population under different grazing pressures were observed. Plant samples were collected from a series of grazing gradients of the Stipa grandis steppe in Dalinuoer National Nature Reserve in the Inner Mongolia (located at 116°38′–116°41′E and 43°25′–43°27′N.), which has the following vegetation types in abundance: Leymus chinensis is the constructive species; the dominant species include Stipa grandis, Cleistogenes squarrosa, and Artemisia frigida; the companion species is Potentilla acaulis and others. According to the grazing pressure, the following four grazing gradients were identified from the dwellings of the herdsmen to the enclosure site: (1) no grazing (CK enclosure site); (2) light grazing (LG); (3) moderate grazing (MG); (4) heavy grazing (HG). Young leaves of each Stipa grandis were collected during the growing season. The results showed that the Stipa grandis showed abundant genetic diversity despite the fact that certain polymorphic loci were lost; at the same time, new polymorphic loci emerged when grazing pressure increased; a total of 10 primers were used, and 74 bands were produced in total, of which 65 bands were polymorphic; the total percentage of polymorphism was 89%; the percentage of polymorphic loci of the Stipa grandis population decreased with the increase of grazing pressure; the percentage of polymorphic loci was 62.2% in the no-grazing (CK) population, 64.9% in the light-grazing (LG) population, 58.1% in the moderate-grazing (MG) population, and 56.8% in the heavy-grazing (HG) population; the genetic diversity of the population in the descending order using the Shannon's information index is as follows: (1) light grazing (0.3486); (2) no grazing (0.3339); (3) moderate grazing (0.3249); (4) heavy grazing (0.2735) with the same distributional pattern as the Nei's genetic diversity index. The test showed the following: As the grazing pressures increased, the change of genetic diversity decreased; the genetic differentiation coefficient among the population (Gst) was 0.1984, which showed the presence of small partial genetic diversity (19.8%) among populations; gene flow (Nm*) between primers varied from 0.9806 to 3.4463, and the mean gene flow (Nm*) was 2.0202; the UPGMA cluster figure that was constructed on the basis of the genetic distance matrix showed four populations that became genetically closer at each step: (1) The first group was the moderate-grazing (MG) population and the heavy- grazing (HG) population; (2) The second group consisted of the no-grazing (CK) population and the light-grazing (LG) population; (3) The two groups gathered together.     

Analysis of genetic diversity in the endangered Hucho taimen from China

Hucho taimen are listed as endangered in China. The population size has declined recently, prompting an increase in the level of listing from grade three in 2002 to grade five in 2006. We analyzed the genetic diversity of wild populations using 17 microsatellite markers to establish a scientific basis for conservation of this species. We collected tissue samples from four populations in the Heilongjiang River basin: Huma River (HM), Hutou (HT), Haiqing (HQ), and Zhuaji (ZJ). A total of 21 loci were amplified, 18 of which were polymorphic. The number of alleles per locus ranged from 2 to 9 (mean: 4.1905). There were 13 highly polymorphic loci and 5 moderately polymorphic loci. Analysis of five genetic diversity parameters (Na, Ne, Ho, He, and PIC) suggested moderate levels of diversity within the populations. The populations were ranked HT > HQ > ZJ > HM, but the differences in diversity were not statistically significant (P > 0.05). A comparison of variation among all four populations suggested Hardy–Weinberg disequilibrium at 20% of the loci. Genetic differentiation (Fst) was 0.0644 and the gene flow among populations was estimated at 3.36 individuals per generation. The majority of diversity (93.88%) occurred among individuals within a population. In contrast, relatively little (6.12%) of the genetic diversity was distributed between the populations. An analysis of genetic differentiation and genetic distance between pairs of populations revealed that both parameters were higher in comparisons of the HM population to the HT, HQ, and ZJ populations than among the three latter populations. This suggests that the HM population has a distinct genetic structure. We hypothesize that habitat degradation and excessive fishing, not low genetic diversity, has caused the decline in H. taimen populations. However, this species should be protected from further declines in genetic diversity.     

A Chromosome-level Genome Assembly of Wild Castor Provides New Insights into its Adaptive Evolution in Tropical Desert

Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry condition.To investigate the potential genetic basis of adaptation to both highland and tropical deserts,we generated a chromosome-level genome sequence assembly of the wild castor accession WT05,with a genome size of 316 Mb,a scaffold N50 of 31.93 Mb,and a contig N50 of 8.96 Mb,respectively.Compared with cultivated castor and other Euphorbiac...