scholarly journals De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese Endemic Acer miaotaiense (Aceraceae)

Genes ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 378 ◽  
Author(s):  
Xiang Li ◽  
Meng Li ◽  
Lu Hou ◽  
Zhiyong Zhang ◽  
Xiaoming Pang ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Population Genetic ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Principal Component ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Endangered Plant ◽  
Population Genetic Analysis

Acer miaotaiense (P. C. Tsoong) is a rare and highly endangered plant in China. Because of the lack of genomic information and the limited number of available molecular markers, there are insufficient tools to determine the genetic diversity of this species. Here, 93,305 unigenes were obtained by multiple assembled contigs with a transcriptome sequencing program. Furthermore, 12,819 expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were generated, 300 were randomly selected and synthesized, 19 primer pairs were identified as highly polymorphic (average number of alleles (Na) = 8, expected heterozygosity (He) = 0.635, polymorphism information content (PIC) = 0.604) and were further used for population genetic analysis. All 261 samples were grouped into two genetic clusters by UPGMA, a principal component analyses and a STRUCTURE analyses. A moderate level of genetic differentiation (genetic differentiation index (Fst) = 0.059–0.116, gene flow = 1.904–3.993) among the populations and the major genetic variance (81.01%) within populations were revealed by the AMOVA. Based on the results, scientific conservation strategies should be established using in situ and ex situ conservation strategies. The study provides useful genetic information for the protection of precious wild resources and for further research on the origin and evolution of this endangered plant and its related species.

scholarly journals Distinct Genetic Structure Reflects Ploidy Level Differentiation in Newly Discovered, Extremely Small Populations of Xanthocyparis vietnamensis from Southwestern China

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuliang Jiang ◽  
Tsam Ju ◽  
Linda E. Neaves ◽  
Jialiang Li ◽  
Weining Tan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
Genetic Differentiation ◽  
Ploidy Level ◽  
Population Genetic ◽  
Ex Situ ◽  
Southwestern China ◽  
Small Populations ◽  
Population Groups ◽  
Quaternary Climate

Population genetic assessment is crucial for the conservation and management of threatened species. Xanthocyparis vietnamensis is an endangered species that is currently restricted to karst mountains in southwestern China and Vietnam. This rare conifer was first recorded in 2002 from northern Vietnam and then in 2013 from Guangxi, China, yet nothing is known about its genetic diversity nor ploidy level variation, although previous cytological study suggest that Vietnamese populations are tetraploids. There have been about 45 individuals found to date in Guangxi, China. Here, we genotyped 33 X. vietnamensis individuals using 20 newly developed, polymorphic microsatellite loci, to assess the genetic variability of its extremely small populations. The genetic diversity of X. vietnamensis (HE = 0.511) was lower than that of two other heliophile species, Calocedrus macrolepis and Fokienia hodginsii, which have similar distribution ranges. This is consistent with the signature of a genetic bottleneck detected in X. vietnamensis. Although the population genetic differentiation coefficient across loci is moderate (FST = 0.125), STRUCTURE analysis revealed two distinct genetic clusters, namely the northern and southern population groups; DAPC analysis grouped the southern populations together in one cluster separate from the northern populations; AMOVA analysis detected a significant genetic differentiation between the two population groups (FRT = 0.089, p < 0.05), and BARRIER analysis detected a genetic barrier between them. Moreover, we detected differentiation in ploidy level between northern and southern populations, sampled individuals from the former and the later are all diploid and tetraploid cytotypes with mean genome sizes of 26.08 and 48.02 pg/2C, respectively. We deduced that heterogeneous geomorphology and historical events (e.g., human deforestation, Quaternary climate oscillations) may have contributed to population fragmentation and small population size in X. vietnamensis. Considering both genetic and ploidy level differentiation, we propose that two different management units (northern and southern) should be considered and a combination of in situ and ex situ conservation measures should be employed to preserve populations of this endangered species in southwestern China in the light of our findings.

scholarly journals Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5606 ◽  
Author(s):  
Jun Zeng ◽  
Jie Chen ◽  
Yixuan Kou ◽  
Yujin Wang
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Population Genetic Analysis ◽  
Protein Databases ◽  
Genetic Groups ◽  
Conifer Tree ◽  
Torreya Grandis ◽  
Expressed Sequence ◽  
Distribution Frequency

Torreya grandis (Taxaceae) is an ancient conifer species endemic to southeast China. Because of its nutrient-rich and delicious seeds, this species has been utilized for centuries by the Chinese. However, transcriptome data and transcriptome-derived microsatellite markers for population genetics studies are still insufficient for understanding of this species’ genetic basis. In this study, a transcriptome from T. grandis leaves was generated using Illumina sequencing. A total of 69,920 unigenes were generated after de novo assembly, and annotated by searching against seven protein databases. In addition, 2,065 expressed sequence tag–simple sequence repeats (EST-SSRs) were detected, with the distribution frequency of 2.75% of total unigenes and average number of 0.03 SSRs per unigene. Among these EST-SSRs, 1,339 primer pairs were successfully designed, and 106 primer pairs were randomly selected for the development of potential molecular markers. Among them, 11 EST-SSR markers revealed a moderate level of genetic diversity, and were used to investigate the population structure of T. grandis. Two different genetic groups within this species were revealed using these EST-SSR markers, indicating that these markers developed in this study can be effectively applied to the population genetic analysis of T. grandis.

scholarly journals REDISCOVERY OF ALDROVANDA VESICULOSA L. (DROSERACEAE), AN ENDANGERED PLANT, AFTER SIX DECADES IN INDIA FROM MANIPUR WITH STUDIES ON MICROMORPHOLOGY AND PHYSICO-CHEMISTRY OF WATER

REINWARDTIA ◽  
2019 ◽  
Vol 18 (2) ◽  
Author(s):  
Romita Devi Ngangbam ◽  
Naorem Premita Devi ◽  
Maibam Haripriya Devi ◽  
Potsangbam Kumar Singh
Keyword(s):  
Iucn Red List ◽  
Small Population ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Endangered Plant ◽  
General Description ◽  
Physico Chemical ◽  
Chemical Studies ◽  
Insectivorous Plant ◽  
Taxonomic Studies

NGANGBAM, R. D., DEVI, N. P., DEVI, M. H. & SINGH, P. K. 2019. Rediscovery of Aldrovanda vesiculosa L. (Droseraceae), an endangered plant, from Manipur in India after six decades, with studies on micromorphology and physico-chemistry of water. Reinwardtia 18(2): 71‒80. — A small population of the aquatic insectivorous plant Aldrovanda vesiculosa L. of Droseraceae family was found growing in Yena pat, a small lake having an area of about 0.939 km2 in Bishnupur district, Manipur state, India. This marks its rediscovery in India after a long gap of 64 years. The present status of the species in the updated IUCN Red List of Threatened Species version 2018.2 is endangered and considered extinct from India. A general description and micromorpho-taxonomic studies are included. As the species is a bioindicator, physico-chemical studies of the water were also investigated so as to provide aid in both in-situ and ex-situ conservation strategies. Immediate conservation initiatives are warranted to maintain the species after its rediscovery.

scholarly journals Transcriptome Sequencing of the Endangered Species Elongate Loach (Leptobotia elongata) From the Yangtze River: De novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

2021 ◽  
Vol 8 ◽  
Author(s):  
Yunbang Zhang ◽  
Jian Gao ◽  
Yunhai Zhang ◽  
Yuanchao Zou ◽  
Xiaojuan Cao
Keyword(s):  
Endangered Species ◽  
Genetic Information ◽  
Transcriptome Sequencing ◽  
Yangtze River ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Habitat Destruction ◽  
The Yangtze River ◽  
Simple Sequence

Elongate loach (Leptobotia elongata) is endemic to middle and upper reaches of the Yangtze River in China. Due to overfishing and habitat destruction, this loach has become an endangered species. So far, lack of reliable genetic information and molecular markers has hindered the conservation and utilization of elongate loach resources. Therefore, we here performed an Illumina sequencing and de novo transcriptome assembly in elongate loach, and then developed polymorphic simple sequence repeat markers (SSRs). After assembly, 51,185 unigenes were obtained, with an average length of 1,496 bp. A total of 23,901 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified, distributing in 14,422 unigenes, with a distribution frequency of 28.18%. Out of 16,885 designed EST-SSR primers, 150 primers (3 or 4 base repetition-dominated) were synthesized for polymorphic EST-SSR development. Then, 52 polymorphic EST-SSRs were identified, with polymorphism information contents (PIC) ranging from 0.03 to 0.88 (average 0.54). In conclusion, this was the first report of transcriptome sequencing of elongate loach. Meanwhile, we developed a set of polymorphic EST-SSRs for the loach. This study will provide an important basis, namely genetic information and polymorphic SSRs, for further population genetics and breeding studies of this endangered and economic loach in China.

scholarly journals Population Genetic Analysis of Pinus Koraiensis in China Inferred Using EST-SSR Markers

2020 ◽  
Author(s):  
Xiang Li ◽  
Minghui Zhao ◽  
Yujin Xu ◽  
Yan Li ◽  
Mulualem Tigabu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Association Studies ◽  
Genetic Erosion ◽  
Conservation Strategies ◽  
Distribution Area ◽  
Pinus Koraiensis ◽  
Genome Wide Association Studies ◽  
Conifer Species

Abstract Background Pinus koraiensis (commonly known as Korean pine), is a well-known conifer species in China with high economic, ornamental and ecological values. More than 50% of the P. koraiensis forests in the world are distributed in Northeast China, a region with abundant germplasm resources. However, these natural P. koraiensis populations are in danger of genetic erosion caused by continuous climate changes and frequent human activity. Little work has been conducted on the population genetic structure and genetic differentiation of P. koraiensis in China. Here, representative individuals from 16 natural P. koraiensis populations were sampled and genotyped, and polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers were used to comprehensively evaluate genetic diversity, population structure and differentiation of P. koraiensis populations in China.ResultsA total of 480 samples from 16 populations were collected in the natural distribution area of P. koraiensis. Analysis of molecular variance (AMOVA) of the EST-SSR marker data showed that 33% of the total genetic variation was among populations and 67% was within populations. A high level of genetic diversity was found across P. koraiensis populations (average Na=10.33, Ne=2.514, He=0.521), and the highest levels of genetic diversity were found in Heihe (He=0.449), Zhanhe (He=0.413), Liangshui (He=0.370) and Tieli (He=0.414) populations. Moreover, pairwise Fst values reveled significant genetic differentiation among populations (mean Fst=0.177). Structure and Neighbor-joining (NJ) tree analyses and principal component analysis (PCA) revealed two genetic clusters: cluster 1 from Xiaoxinganling Mountains and cluster 2 from Changbaishan Mountains, which were consistent with the geographical distributions of the natural populations. ConclusionsThe findings provide new genetic information for future genome-wide association studies (GWAS), marker-assisted selection (MAS) and genomic selection (GS) in natural P. koraiensis breeding programs and can aid the development of conservation strategies for this valuable conifer species.

scholarly journals Castanea spp. Agrobiodiversity Conservation: Genotype Influence on Chemical and Sensorial Traits of Cultivars Grown on the Same Clonal Rootstock

Foods ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1062 ◽  
Author(s):  
Gabriele L. Beccaro ◽  
Dario Donno ◽  
Guglielmo Gianni Lione ◽  
Marta De Biaggi ◽  
Giovanni Gamba ◽  
...  
Keyword(s):  
Management Strategies ◽  
Principal Component ◽  
Global Strategy ◽  
Conditional Inference ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Significant Variable ◽  
Large Species ◽  
Multivariate Approach ◽  
Large Variability

A large species diversity characterises the wide distribution of chestnuts in Asia, North America, and Europe, hence reflecting not only the adaptation of the genus Castanea to diverse environmental conditions, but also to different management strategies encompassing orchards. The characterisation and description of chestnut populations and cultivars are crucial to develop effective conservation strategies of one of the most important Italian and European fruit and wood species. Chestnut cultivars grown in the same pedoclimatic conditions and on the same clonal rootstock were characterised with sensory, spectrophotometric, and chromatographic analysis to determine the phytochemical composition and nutraceutical properties. A multivariate approach, including principal component analysis and conditional inference tree models, was also performed. The ease of peeling, seed colour, and intensity of sweetness were the sensory descriptors that allowed us to differentiate C. sativa cultivars. Antioxidant capacity ranged from 9.30 ± 0.39 mmol Fe+2 kg−1 DW (‘Bouche de Bètizac’) to 19.96 ± 1.89 mmol Fe+2 kg−1 DW (‘Garrone Rosso’). Monoterpenes represented the main component, reaching 88% for hybrids, followed by polyphenols (10–25% for hybrids and chestnuts, respectively). A multivariate approach showed that phenolic acids and tannins were the bioactive classes with the highest discriminating power among different genotypes, and that genotype is a significant variable (p < 0.05). In addition, most of the analysed chestnut cultivars showed a content of bioactive compounds similar to or higher than the main hazelnut, walnut, and almond varieties. Chestnut agrobiodiversity could be intended as strictly associated to the genotype effect and underlines the large variability within the genus Castanea, and therefore, the importance of in farm and ex situ conservation of local germplasm is part of a global strategy aimed at increasing the levels of agrobiodiversity.

Sign in / Sign up

Export Citation Format

Share Document