2013 Vol. 31 No. 5
2013, 31(5): 429-438.
DOI: 10.3724/SP.J.1142.2013.50429
Abstract：
The D2 protein of the Photosystem Ⅱ (PSⅡ) reaction center complex is encoded by the chloroplast gene psbD.To gain a better understanding of the adaptive radiation of core leptosporangiate ferns in low-light environments,we sequenced psbD in twelve species and collected eight published sequences to represent extant ferns in order level.We then evaluated the selection pressure of D2 protein based on ω values (nonsynonymous synonymous substitution ratio).The results of statistical tests based on different models indicated that most sites and branches were under strong negative selection,but tree ferns exhibited a slower evolutionary rate and higher ω value compared with other ferns.Co-evolution analysis based on different approaches showed that the D2-R168,D2-H245 and D2-M272 of tree ferns were involved in the same co-evolution network.
The D2 protein of the Photosystem Ⅱ (PSⅡ) reaction center complex is encoded by the chloroplast gene psbD.To gain a better understanding of the adaptive radiation of core leptosporangiate ferns in low-light environments,we sequenced psbD in twelve species and collected eight published sequences to represent extant ferns in order level.We then evaluated the selection pressure of D2 protein based on ω values (nonsynonymous synonymous substitution ratio).The results of statistical tests based on different models indicated that most sites and branches were under strong negative selection,but tree ferns exhibited a slower evolutionary rate and higher ω value compared with other ferns.Co-evolution analysis based on different approaches showed that the D2-R168,D2-H245 and D2-M272 of tree ferns were involved in the same co-evolution network.
2013, 31(5): 439-444.
DOI: 10.3724/SP.J.1142.2013.50439
Abstract：
The morphology and ultrastructure of pollen grains of Melodorum fruticosum Lour. are described based on observations using a scanning electron microscope (SEM) and transmission electron microscope (TEM). Pollen grains of M. fruticosum were globose or oblate shape,with no visible aperture or any indication of a pole,and the ornamentation was rugulate. The pollen wall was composed of an outer exine and an inner intine layer. The exine consisted of three distinct layers：tectum,infratectum and foot layer. The tectum was continuous and uniformly thickened. The infratectum was mixed with granules and columellae,and nearly one half of the total exine in thickness. The foot layer was composed of undulating foliations. The endexine was homogeneous and lamellated. The intine was two-layered,and varied from two to one half times the exine in thickness. Except for the especially thickened infratectum and foot layer foliations without white line in M. fruticosum,the pollen characters were similar to those of Uvarieae. Moreover,data on the relationship of aperture types,variations of sporoderm thickness and evolution of tectum in Annonaceae were determined and discussed.
The morphology and ultrastructure of pollen grains of Melodorum fruticosum Lour. are described based on observations using a scanning electron microscope (SEM) and transmission electron microscope (TEM). Pollen grains of M. fruticosum were globose or oblate shape,with no visible aperture or any indication of a pole,and the ornamentation was rugulate. The pollen wall was composed of an outer exine and an inner intine layer. The exine consisted of three distinct layers：tectum,infratectum and foot layer. The tectum was continuous and uniformly thickened. The infratectum was mixed with granules and columellae,and nearly one half of the total exine in thickness. The foot layer was composed of undulating foliations. The endexine was homogeneous and lamellated. The intine was two-layered,and varied from two to one half times the exine in thickness. Except for the especially thickened infratectum and foot layer foliations without white line in M. fruticosum,the pollen characters were similar to those of Uvarieae. Moreover,data on the relationship of aperture types,variations of sporoderm thickness and evolution of tectum in Annonaceae were determined and discussed.
2013, 31(5): 445-453.
DOI: 10.3724/SP.J.1142.2013.50445
Abstract：
A total of 84 taxa (including 32 genera,75 species and 9 varieties) of diatoms from Gahai Lake were reported in this paper.Of these taxa,4 species were new records in China:Gomphonema laticollum E.Reichardt,Navicula antonii Lange-Bertalot,Navicula seibigiana Lange-Bertalot,and Stauroneis reichardii Lange-Bertalot.The characteristic of species distribution and ecology was discussed.
A total of 84 taxa (including 32 genera,75 species and 9 varieties) of diatoms from Gahai Lake were reported in this paper.Of these taxa,4 species were new records in China:Gomphonema laticollum E.Reichardt,Navicula antonii Lange-Bertalot,Navicula seibigiana Lange-Bertalot,and Stauroneis reichardii Lange-Bertalot.The characteristic of species distribution and ecology was discussed.
2013, 31(5): 454-460.
DOI: 10.3724/SP.J.1142.2013.50454
Abstract：
The phylogenetic structure of a community is composed of all genetic relationships between species across the community.Understanding the phylogenetic structure of a community will help reveal the relative importance of habitat filtering,competitive exclusion and the stochastic processes constructing the community.We studied a rare plant community in a 1 hm2 permanent plot in Houhe Nature Reserve,Hubei Province.We examined the effects of spatial scales (5 m×5 m,10 m×10 m,20 m×20 m,30 m×30 m,40 m×40 m,and 50 m×50 m) and DBH classes (5 cm≤DBH<10 cm,10 cm≤DBH<15cm,15 cm≤DBH<20 cm,and DBH≥20 cm) at spatial scales (10 m×10 m,20 m×20 m,30 m×30 m,40 m×40 m,and 50 m×50 m) on phylogenetic structure of the community in a subtropical evergreen and deciduous broadleaf mixed forest.The results demonstrated that,with increasing spatial scale,the phylogenetic structure tended to cluster.The degree of phylogenetic clustering decreased with increasing DBH classes.However,the degree of phylogenetic clustering was very high at the scale of DBH≥20 cm.The phylogenetic structures of the communities were random at the scale of 25 m2 and clustered at scales of 100 m2 and larger,indicating that neutrality may play a leading role at small scales and niche processes may be more important at large scales for community assembly in subtropical evergreen and deciduous broadleaf mixed forest in this case.
The phylogenetic structure of a community is composed of all genetic relationships between species across the community.Understanding the phylogenetic structure of a community will help reveal the relative importance of habitat filtering,competitive exclusion and the stochastic processes constructing the community.We studied a rare plant community in a 1 hm2 permanent plot in Houhe Nature Reserve,Hubei Province.We examined the effects of spatial scales (5 m×5 m,10 m×10 m,20 m×20 m,30 m×30 m,40 m×40 m,and 50 m×50 m) and DBH classes (5 cm≤DBH<10 cm,10 cm≤DBH<15cm,15 cm≤DBH<20 cm,and DBH≥20 cm) at spatial scales (10 m×10 m,20 m×20 m,30 m×30 m,40 m×40 m,and 50 m×50 m) on phylogenetic structure of the community in a subtropical evergreen and deciduous broadleaf mixed forest.The results demonstrated that,with increasing spatial scale,the phylogenetic structure tended to cluster.The degree of phylogenetic clustering decreased with increasing DBH classes.However,the degree of phylogenetic clustering was very high at the scale of DBH≥20 cm.The phylogenetic structures of the communities were random at the scale of 25 m2 and clustered at scales of 100 m2 and larger,indicating that neutrality may play a leading role at small scales and niche processes may be more important at large scales for community assembly in subtropical evergreen and deciduous broadleaf mixed forest in this case.
2013, 31(5): 461-466.
DOI: 10.3724/SP.J.1142.2013.50461
Abstract：
Results from a study on Sarcosperma laurinum communities from Qi-ao Island in Zhuhai city, Guangdong province,showed that: (1) 61 species of vascular plants belonging to 38 families and 51 genera were found in the Sarcosperma laurinum community, with the floristic components of the community exhibiting a south subtropical property; (2) Analysis for the age structure of the community showed that the dominant species belonged to some stable populations,and the frequency index of the community was A>B>C>DD=13.70,H=4.12,E=0.39,E'=0.82.Results indicated that the diversity and evenness indices were closed to those of a climax community from a typical subtropical evergreen broad-leaved forest.
Results from a study on Sarcosperma laurinum communities from Qi-ao Island in Zhuhai city, Guangdong province,showed that: (1) 61 species of vascular plants belonging to 38 families and 51 genera were found in the Sarcosperma laurinum community, with the floristic components of the community exhibiting a south subtropical property; (2) Analysis for the age structure of the community showed that the dominant species belonged to some stable populations,and the frequency index of the community was A>B>C>DD=13.70,H=4.12,E=0.39,E'=0.82.Results indicated that the diversity and evenness indices were closed to those of a climax community from a typical subtropical evergreen broad-leaved forest.
2013, 31(5): 467-476.
DOI: 10.3724/SP.J.1142.2013.50467
Abstract：
Based on field investigation, sample collection, and comprehensive analysis of the riparian vegetation in mountain rivers, the riparian flora characteristics were investigated. The results showed that 574 vascular plants belonging to 390 genera and 145 families in the mountain rivers of the Jiulongjiang River headstream were identified, among which pteridophyte had 29 families, 54 genera and 80 species; gymnosperm had 6 families, 8 genera and 10 species; and, angiosperm had 110 families, 328 genera and 484 species. Through comprehensive analysis several typical characteristics of the mountain river riparian vegetation (taking reaches of the Jiulongjiang River headstream as an example) were found as follows: (1) a rich floral composition, with the dominant families and genera highly prominent; monotypic, oligotypic and oligotaxic genera, and oligotypic and oligotaxic families formed a large proportion; (2) flora of ancient origin; rare and relict plants were abundant; and, (3) complicated geographical elements and flora connected extensively with most parts of the world fully reflected natural and human disturbance such as regional climate, topography and human activities. Results indicated that the riparian zone had an extremely important function in conserving regional biodiversity.
Based on field investigation, sample collection, and comprehensive analysis of the riparian vegetation in mountain rivers, the riparian flora characteristics were investigated. The results showed that 574 vascular plants belonging to 390 genera and 145 families in the mountain rivers of the Jiulongjiang River headstream were identified, among which pteridophyte had 29 families, 54 genera and 80 species; gymnosperm had 6 families, 8 genera and 10 species; and, angiosperm had 110 families, 328 genera and 484 species. Through comprehensive analysis several typical characteristics of the mountain river riparian vegetation (taking reaches of the Jiulongjiang River headstream as an example) were found as follows: (1) a rich floral composition, with the dominant families and genera highly prominent; monotypic, oligotypic and oligotaxic genera, and oligotypic and oligotaxic families formed a large proportion; (2) flora of ancient origin; rare and relict plants were abundant; and, (3) complicated geographical elements and flora connected extensively with most parts of the world fully reflected natural and human disturbance such as regional climate, topography and human activities. Results indicated that the riparian zone had an extremely important function in conserving regional biodiversity.
2013, 31(5): 477-484.
DOI: 10.3724/SP.J.1142.2013.50477
Abstract：
The diversity of plant species of the Yesanhe Nature Reserve was studied by field investigation and indoor analysis.The results showed there were 1106 species (including infraspecific taxon) of wild spermatophyte belonging to 533 genera and 150 families.The 150 families of wild spermatophyte were divided into 11 areal-types and 10 variety-types.Tropical elements were the dominant components, in which tropical families contributed 56.88% in total (excluding cosmopolitan families).The 533 genera of wild spermatophyte were divided into 14 area-types and 17 variety-types.Temperate elements were dominant components,in which temperate genera contributed 59.06% in total (excluding cosmopolitan genera).Compared with the flora of five neighboring areas,the flora of the Yesanhe Nature Reserve showed high similarity with Mulinzi Nature Reserve.The purpose of this study was to protect biological diversity and provide background information for the construction of Yesanhe Nature Reserve.
The diversity of plant species of the Yesanhe Nature Reserve was studied by field investigation and indoor analysis.The results showed there were 1106 species (including infraspecific taxon) of wild spermatophyte belonging to 533 genera and 150 families.The 150 families of wild spermatophyte were divided into 11 areal-types and 10 variety-types.Tropical elements were the dominant components, in which tropical families contributed 56.88% in total (excluding cosmopolitan families).The 533 genera of wild spermatophyte were divided into 14 area-types and 17 variety-types.Temperate elements were dominant components,in which temperate genera contributed 59.06% in total (excluding cosmopolitan genera).Compared with the flora of five neighboring areas,the flora of the Yesanhe Nature Reserve showed high similarity with Mulinzi Nature Reserve.The purpose of this study was to protect biological diversity and provide background information for the construction of Yesanhe Nature Reserve.
2013, 31(5): 485-492.
DOI: 10.3724/SP.J.1142.2013.50485
Abstract：
Using the program MISA, a total of 12319 EST-SSRs were sought out from 79536 ESTs of aquatic plant Nymphoides peltata. Dinucleotide and trinucleotide SSRs were the two main motif types, accounting for 57.31% and 30.87%, respectively. The most abundant di-and tri- motifs were AG/CT (29.76%) and AAG/CTT (8.66%), respectively. We randomly selected 130 primer pairs to evaluate their application and polymorphism across two populations of N. peltata. Seventy-eight SSR markers were amplified successfully, yielding clear and discernible bands, among which 37 were found to be polymorphic and the polymorphic rate was 47.44%. Using the polymorphic SSR markers, a total of 114 alleles were detected. The number of alleles per locus ranged from 2 to 6 (mean 3.08). Observed heterozygosity (Ho) and expected value (He) per locus varied from 0.229 to 1.000 and from 0.351 to 0.756, respectively. Polymorphism information content (PIC) ranged from 0.286 to 0.698, with an average of 0.495.The results indicated that the development of SSR molecular markers from the EST dataset generated by next generation sequencing in the aquatic plant N.peltata is valuable and effective. These newly generated SSR makers will provide new tools for studying genetic diversity and population genetic structure of N.peltata.
Using the program MISA, a total of 12319 EST-SSRs were sought out from 79536 ESTs of aquatic plant Nymphoides peltata. Dinucleotide and trinucleotide SSRs were the two main motif types, accounting for 57.31% and 30.87%, respectively. The most abundant di-and tri- motifs were AG/CT (29.76%) and AAG/CTT (8.66%), respectively. We randomly selected 130 primer pairs to evaluate their application and polymorphism across two populations of N. peltata. Seventy-eight SSR markers were amplified successfully, yielding clear and discernible bands, among which 37 were found to be polymorphic and the polymorphic rate was 47.44%. Using the polymorphic SSR markers, a total of 114 alleles were detected. The number of alleles per locus ranged from 2 to 6 (mean 3.08). Observed heterozygosity (Ho) and expected value (He) per locus varied from 0.229 to 1.000 and from 0.351 to 0.756, respectively. Polymorphism information content (PIC) ranged from 0.286 to 0.698, with an average of 0.495.The results indicated that the development of SSR molecular markers from the EST dataset generated by next generation sequencing in the aquatic plant N.peltata is valuable and effective. These newly generated SSR makers will provide new tools for studying genetic diversity and population genetic structure of N.peltata.
2013, 31(5): 493-499.
DOI: 10.3724/SP.J.1142.2013.50493
Abstract：
To provide genetic markers for the study of ecological adaptability to responsive drought- and salinity-stress for Medicago ruthenica Trautv.,we selected eight pairs of good polymorphism and high stability primers from 70 pairs of drought-and salinity-responsive EST-SSR markers published for chickpea.DNA sequences were amplified with eight pairs of SSR primers by SSR-PCR technique.One hundred and eleven alleles were detected,on average,13.88 alleles were detected per site.The mean values of observed heterozygosity and expected heterozygosity were 0.497 and 0.687,respectively.Polymorphism information content value ranged from 0.313 to 0.883, and the mean value was 0.649.These results indicate that the eight EST-SSR markers can be used to estimate genetic diversity of M.ruthenica,and genetic diversity was at a high level.Polymorphism EST-SSR markers can be used to investigate ecological adaptive evolution.The results contribute to revealing the genetic variation of drought- and salt-tolerance genotypes and understanding the distribution pattern and ecological adaptation mechanism of M.ruthenica populations.
To provide genetic markers for the study of ecological adaptability to responsive drought- and salinity-stress for Medicago ruthenica Trautv.,we selected eight pairs of good polymorphism and high stability primers from 70 pairs of drought-and salinity-responsive EST-SSR markers published for chickpea.DNA sequences were amplified with eight pairs of SSR primers by SSR-PCR technique.One hundred and eleven alleles were detected,on average,13.88 alleles were detected per site.The mean values of observed heterozygosity and expected heterozygosity were 0.497 and 0.687,respectively.Polymorphism information content value ranged from 0.313 to 0.883, and the mean value was 0.649.These results indicate that the eight EST-SSR markers can be used to estimate genetic diversity of M.ruthenica,and genetic diversity was at a high level.Polymorphism EST-SSR markers can be used to investigate ecological adaptive evolution.The results contribute to revealing the genetic variation of drought- and salt-tolerance genotypes and understanding the distribution pattern and ecological adaptation mechanism of M.ruthenica populations.
2013, 31(5): 500-509.
DOI: 10.3724/SP.J.1142.2013.50500
Abstract：
To date,only 100 SSR markers in Dendrobium have been developed,which are far from sufficient for research applications.To develop molecular markers,we mined SSR of Dendrobium from public nucleotide data through bioinformation methods.Some 1343 Uni-DNA sequences were assembled from the 3599 DNA sequences of Dendrobium from GenBank.By scanning the Uni-DNA sequences,283 SSRs were distributed in 205 Uni-DNA sequences,with an average frequency of 1 SSR per 2815 bp.Sequence alignment indicated that 86 of the 205 SSR-DNA sequences had already been used to design primers.In this study,76 primer pairs were designed from the remaining 119 sequences for transferability analysis among 32 Dendrobium species.Results showed that 47 primer pairs were amplified effectively with transfer rates ranging from 51.1% to 95.7% (average 75.9%).Of which,46 primer pairs were able to detect polymorphism among the Dendrobium species with 2-8 alleles (average 4.0 alleles).Ten pairs of polymorphic primers were selected to detect polymorphism in 60 accessions of D.officinale,and 2-5 alleles (average 3.4 alleles) were found per SSR locus.Based on the SSR amplification pattern,the 60 accessions of D.officinale were clustered into five clusters,and phenotypes were closer within clusters than between clusters.The sequencing of the amplified fragment of DM121 revealed that allele variation within D.officinale was attributed mainly to the variation of SSR repeat numbers,whereas allele variations among Dendrobium species were also caused by a single base indel and substitution in the microsatellite flanking region.
To date,only 100 SSR markers in Dendrobium have been developed,which are far from sufficient for research applications.To develop molecular markers,we mined SSR of Dendrobium from public nucleotide data through bioinformation methods.Some 1343 Uni-DNA sequences were assembled from the 3599 DNA sequences of Dendrobium from GenBank.By scanning the Uni-DNA sequences,283 SSRs were distributed in 205 Uni-DNA sequences,with an average frequency of 1 SSR per 2815 bp.Sequence alignment indicated that 86 of the 205 SSR-DNA sequences had already been used to design primers.In this study,76 primer pairs were designed from the remaining 119 sequences for transferability analysis among 32 Dendrobium species.Results showed that 47 primer pairs were amplified effectively with transfer rates ranging from 51.1% to 95.7% (average 75.9%).Of which,46 primer pairs were able to detect polymorphism among the Dendrobium species with 2-8 alleles (average 4.0 alleles).Ten pairs of polymorphic primers were selected to detect polymorphism in 60 accessions of D.officinale,and 2-5 alleles (average 3.4 alleles) were found per SSR locus.Based on the SSR amplification pattern,the 60 accessions of D.officinale were clustered into five clusters,and phenotypes were closer within clusters than between clusters.The sequencing of the amplified fragment of DM121 revealed that allele variation within D.officinale was attributed mainly to the variation of SSR repeat numbers,whereas allele variations among Dendrobium species were also caused by a single base indel and substitution in the microsatellite flanking region.
2013, 31(5): 510-516.
DOI: 10.3724/SP.J.1142.2013.50510
Abstract：
Orchidaceae is one of the most species-rich families in the world. The biodiversity of Chinese orchids has earned much attention due to the complex geographic environment and climate type in China. Due to uneven distribution of orchid resources,most field surveys and studies have been carried out in the Yangtze River Basin and regions to its south. The biodiversity of orchids in North China has largely been ignored. To protect orchid species,we conducted floristic study and conservation analysis in Songshan National Nature Reserve,Beijing. In total,18 species in 12 genera were recorded. One species (Galearis roborowskyi) was recorded for the first time in Beijing. For life form,terrestrial orchids were dominant with 14 species (77.78%),and the remaining orchids (22.22%) were saprophytic. For floristic types of genera,North Temperate was dominant with six genera (50.00%),followed by Old World Temperate with three genera (25.00%),Cosmopolitan with two genera (16.67%),and Old World Tropics with one genus (8.33%). For floristic types of species,East Asia was dominant with nine species (50.00%),followed by Old World Temperate with five species (27.78%),and North Temperate with four species (22.22%). The orchids usually grew under deciduous broadleaf mixed forest in north ravine and Mini-haituo Mountain. Considering the conservation status,we suggest habitat assessment,inspection for orchid population dynamics,ex situ preservation for orchids in urgent danger and scientific propaganda are the strategies to conserve biodiversity in Songshan National Nature Reserve.
Orchidaceae is one of the most species-rich families in the world. The biodiversity of Chinese orchids has earned much attention due to the complex geographic environment and climate type in China. Due to uneven distribution of orchid resources,most field surveys and studies have been carried out in the Yangtze River Basin and regions to its south. The biodiversity of orchids in North China has largely been ignored. To protect orchid species,we conducted floristic study and conservation analysis in Songshan National Nature Reserve,Beijing. In total,18 species in 12 genera were recorded. One species (Galearis roborowskyi) was recorded for the first time in Beijing. For life form,terrestrial orchids were dominant with 14 species (77.78%),and the remaining orchids (22.22%) were saprophytic. For floristic types of genera,North Temperate was dominant with six genera (50.00%),followed by Old World Temperate with three genera (25.00%),Cosmopolitan with two genera (16.67%),and Old World Tropics with one genus (8.33%). For floristic types of species,East Asia was dominant with nine species (50.00%),followed by Old World Temperate with five species (27.78%),and North Temperate with four species (22.22%). The orchids usually grew under deciduous broadleaf mixed forest in north ravine and Mini-haituo Mountain. Considering the conservation status,we suggest habitat assessment,inspection for orchid population dynamics,ex situ preservation for orchids in urgent danger and scientific propaganda are the strategies to conserve biodiversity in Songshan National Nature Reserve.
2013, 31(5): 517-524.
DOI: 10.3724/SP.J.1142.2013.50517
Abstract：
Lycium ruthenicum (Solanaceae) is an important medicinal plant mainly distributed in Northwestern China.In recent years,however,the distribution range of this species has been reduced greatly due to human overexploitation and deterioration of its habitat.Studying the population genetics of this species is essential for the conservation and sustainable utilization of the plant germplasm resource.In this study,we used seven ISSR markers to measure genetic diversity of 115 individuals from eight natural populations of L.ruthenicum in Xinjiang (six populations) and Gansu (two populations).A total of 64 DNA fragments were scored,and 78.1% of polymorphic loci (PPL) found.High level of genetic diversity was detected in L.ruthenicum (H=0.29;Ⅰ=0.43).AMOVA analysis indicated that most variance (77.0%) resided within populations,with only a small proportion of total variation residing between populations (23%,FST=0.23).Results of the Mantel test (r=0.3602,p=0.910) and UPGMA cluster of the Xinjiang populations indicated that there was no significant relationship between geographical distance and genetic distance.UPGMA cluster of all sampled individuals showed that individuals from each population did not cluster together.The probable causes that have contributed to the current pattern of genetic structure were discussed and suggestions on future protection of the L.ruthenicum from southern Xinjiang were also given.
Lycium ruthenicum (Solanaceae) is an important medicinal plant mainly distributed in Northwestern China.In recent years,however,the distribution range of this species has been reduced greatly due to human overexploitation and deterioration of its habitat.Studying the population genetics of this species is essential for the conservation and sustainable utilization of the plant germplasm resource.In this study,we used seven ISSR markers to measure genetic diversity of 115 individuals from eight natural populations of L.ruthenicum in Xinjiang (six populations) and Gansu (two populations).A total of 64 DNA fragments were scored,and 78.1% of polymorphic loci (PPL) found.High level of genetic diversity was detected in L.ruthenicum (H=0.29;Ⅰ=0.43).AMOVA analysis indicated that most variance (77.0%) resided within populations,with only a small proportion of total variation residing between populations (23%,FST=0.23).Results of the Mantel test (r=0.3602,p=0.910) and UPGMA cluster of the Xinjiang populations indicated that there was no significant relationship between geographical distance and genetic distance.UPGMA cluster of all sampled individuals showed that individuals from each population did not cluster together.The probable causes that have contributed to the current pattern of genetic structure were discussed and suggestions on future protection of the L.ruthenicum from southern Xinjiang were also given.
