Phylogenetic analysis, genetic diversity and relationships between the recently segregated species of Corynandra and Cleoserrata from the genus Cleome using DNA barcoding and molecular markers

Tamboli, Asif S.; Patil, Swapnil M.; Gholave, Avinash R.; Kadam, Suhas K.; Kotibhaskar, Shreya Vijaykumar; Yadav, S. R.; Govindwar, Sanjay P.

doi:10.1016/j.crvi.2016.02.005

Cited by 12 publications

(5 citation statements)

References 35 publications

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“…Genetic diversity is one of the important indices for the evaluation of genetic diversity among crop species (Narzary et al, 2009;Tamboli et al, 2016). The genetic diversity in this study ranged from 0.41 to 0.93, suggesting a significant amount of variation among the 16 accessions evaluated (Table 2).…”

Section: Rapd Polymorphismmentioning

confidence: 75%

Biodiversity assessment of African locust bean (Parkia biglobosa) accessions from Savanna and Forest zones of Nigeria as revealed by seed storage proteins and RAPD markers

Akin-Idowu¹,

Aduloju²,

Akinyoola³

et al. 2021

GenResJ

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Understanding the level and distribution of genetic diversity in African locust bean (Parkia biglobosa) would strengthen breeding and conservation programmes towards domestication and sustainable use of this species. Sixteen accessions of P. globosa were assessed for variability based on seed morphology, seed protein and DNA profiling. Significant variation in seed characteristics were observed across locations. Seed protein profiling by SDS-PAGE revealed homogeneity as most bands were found common in all accessions, indicating that the protein profiles are highly conserved. Protein profiling separated the 16 accessions into four major clusters at 0.93 similarity coefficient. Most accessions grouping into Cluster 1 had a similarity coefficient of close to 100% and were from the Derived Savanna suggesting the presence of duplicates. Accessions NH/2016/P14, NH/2016/P03 and NH/2016/P04 grouped into clusters II, III and IV; respectively. Sixteen RAPD markers generated a total of 256 bands of which 63.67% were polymorphic. Gene diversity ranged from 0.41 to 0.93 and Polymorphic Information Content (PIC) from 0.39 to 0.93. The RAPD-based dendrogram separated accessions into six groups at 0.68 similarity coefficient. Based on a polymorphic seed storage protein marker a genetically distinct accession NH/2016/P04 could be exploited for breeding purposes. The homogeneity of alleles and narrow genetic base as revealed by RAPD and SDS-PAGE analyses suggests possible loss of intraspecific genetic diversity. Thus, intensification of germplasm collections across the different agroecological zones and characterization using specific markers will give a better understanding of diversity of P. biglobosa in order to enhance selection towards conservation, breeding and sustainable utilization.

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Section: Rapd Polymorphismmentioning

confidence: 75%

Biodiversity assessment of African locust bean (Parkia biglobosa) accessions from Savanna and Forest zones of Nigeria as revealed by seed storage proteins and RAPD markers

Akin-Idowu¹,

Aduloju²,

Akinyoola³

et al. 2021

GenResJ

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“…It is worth noting that the identified pollen species in the eDNA sequence are native flowering plants found in the Peninsular Malaysia region where the sample was collected. These species have been previously reported in various studies, such as C. viscosa [ 6 ], S. cumini [ 7 ], and S. taccada [ 8 ].…”

Section: Data Descriptionmentioning

confidence: 99%

The first ITS2 sequence data set of eDNA from honey of Malaysian giant honeybees (Apis dorsata) and stingless bees (Heterotrigona itama) reveals plant species diversity

Huda,

ullah,

Wahab

et al. 2023

BMC Res Notes

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Objectives Pollen is a useful tool for identifying the provenance and complex ecosystems surrounding honey production in Malaysian forests. As native key pollinators in Malaysia, Apis dorsata and Heterotrigona itama forage on various plant/pollen species to collect honey. This study aims to generate a dataset that uncovers the presence of these plant/pollen species and their relative abundance in the honey of A. dorsata and H. itama. The information gathered from this study can be used to determine the geographical and botanical origin and authenticity of the honey produced by these two species. Results Sequence data were obtained for both A. dorsata and H. itama. The raw sequence data for A. dorsata was 5 Mb, which was assembled into 5 contigs with a size of 6,098,728 bp, an N50 of 15,534, and a GC average of 57.42. Similarly, the raw sequence data for H. itama was 6.3 Mb, which was assembled into 11 contigs with a size of 7,642,048 bp, an N50 of 17,180, and a GC average of 55.38. In the honey sample of A. dorsata, we identified five different plant/pollen species, with only one of the five species exhibiting a relative abundance of less than 1%. For H. itama, we identified seven different plant/pollen species, with only three of the species exhibiting a relative abundance of less than 1%. All of the identified plant species were native to Peninsular Malaysia, especially the East Coast area of Terengganu. Data description Our data offers valuable insights into honey’s geographical and botanical origin and authenticity. Metagenomic studies could help identify the plant species that honeybees forage and provide preliminary data for researchers studying the biological development of A. dorsata and H. itama. The identification of various flowers from the eDNA of honey that are known for their medicinal properties could aid in regional honey with accurate product origin labeling, which is crucial for guaranteeing product authenticity to consumers.

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“…Among them, Inter-Simple Sequence Repeat (ISSR) is fast and e cient, with the characteristics of high polymorphism, high reliability, low cost, and does not require pre-determination of target sequence information [4,5]. Another marker, DNA barcodes, proposed in 2003 can not only be used in biological identi cation, but also in genetic diversity analysis [6,7].…”

Section: Introductionmentioning

confidence: 99%

DNA Barcode Reference Library Construction and Genetic Diversity and Structure Analysis of Amomum Villosum Lour. Populations in Guangdong Province

Gong

Zhang

Ding

et al. 2021

Preprint

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Background Amomum villosum Lour. is the plant of a famous traditional Chinese medicine Amomi Fructus and its habitat has been frequently destroyed that seriously threatened its germplasm resources. The genetic diversity has great significance to the optimization of germplasm resources and protection of populations, but that of A. villosum is unclear. In this study, we analyzed the genetic diversity and genetic structures of A. villosum populations in Guangdong and constructed a local reference DNA barcode library for the purpose of more appropriate protecting measures. Methods DNA barcoding and ISSR markers were used to investigate the population genetics of A. villosum. Five universal DNA barcodes were amplified and constructed a DNA barcode reference library. Parameters including percentage of polymorphic sites (PPB), number of alleles (Na), effective number of alleles (Ne), Nei's gene diversity index (H) and Shannon's polymorphism information index (I) were calculated for the assessment of genetic diversity. Genetic structure was revealed by Nei’s gene differentiation coefficient (Gst), total population genetic diversity (Ht), intra-group genetic diversity (Hs) and gene flow (Nm). AMOVA analysis, Mantel tests, UPGMA dendrogram and PCoA analysis were used to elucidate the genetic differentiation and the relationship among populations. Results 531 sequences of five DNA barcodes were gained and all the sequences of the each barcode had no variation sites. A total of 66 ISSR bands were generated from A. villosum populations by the selected 6 ISSR primers. And 56 bands were amplified polymorphic with the percentage was 84.85% for all the seven A. villosum populations. The A. villosum populations showed high genetic diversity (H = 0.3281, I = 0.4895) whereas the gene flow was weak (Nm = 0.6143). Gst (0.4487) and AMOVA analysis indicated that there’s obvious genetic differentiation among A. villosum populations and more genetic variations existed in within population. The genetic relationship of each population was relatively close as the genetic distances were between 0.0844 and 0.3347. Conclusions Overall, this study confirmed a high genetic diversity but weak gene flow of A. villosum in Guangdong province, especially in Amomi Fructus’s Daodi producing area, Yangchun city. And a local DNA barcode reference library containing 531 sequences were subsequently constructed; facilitating the identification, conservation, breeding and cultivation of A. villosum.

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Phylogenetic analysis, genetic diversity and relationships between the recently segregated species of Corynandra and Cleoserrata from the genus Cleome using DNA barcoding and molecular markers

Cited by 12 publications

References 35 publications

Biodiversity assessment of African locust bean (Parkia biglobosa) accessions from Savanna and Forest zones of Nigeria as revealed by seed storage proteins and RAPD markers

Biodiversity assessment of African locust bean (Parkia biglobosa) accessions from Savanna and Forest zones of Nigeria as revealed by seed storage proteins and RAPD markers

The first ITS2 sequence data set of eDNA from honey of Malaysian giant honeybees (Apis dorsata) and stingless bees (Heterotrigona itama) reveals plant species diversity

DNA Barcode Reference Library Construction and Genetic Diversity and Structure Analysis of Amomum Villosum Lour. Populations in Guangdong Province

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