Moses Wambulwa | University of Chinese Academy of Sciences (original) (raw)

Papers by Moses Wambulwa

Research paper thumbnail of Tea data-wambulwa.xls

Research paper thumbnail of SSR alleles at 23 loci for 280 tea accessions from 8 countries in Africa. Missing data points are denoted by a zero ("0")

Research paper thumbnail of Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences

Research paper thumbnail of From the Wild to the Cup: Tracking Footprints of the Tea Species in Time and Space

Frontiers in Nutrition, 2021

Tea is one of the world's most popular beverages, known for its cultural significance and num... more Tea is one of the world's most popular beverages, known for its cultural significance and numerous health benefits. A clear understanding of the origin and history of domestication of the tea species is a fundamental pre-requisite for effective germplasm conservation and improvement. Though there is a general consensus about the center of origin of the tea plant, the evolutionary origin and expansion history of the species remain shrouded in controversy, with studies often reporting conflicting findings. This mini review provides a concise summary of the current state of knowledge regarding the origin, domestication, and dissemination of the species around the world. We note that tea was domesticated around 3000 B.C. either from non-tea wild relatives (probably Camellia grandibracteata and/or C. leptophylla) or intra-specifically from the wild Camellia sinensis var. assamica trees, and that the genetic origins of the various tea varieties may need further inquiry. Moreover, we f...

Research paper thumbnail of Nuclear microsatellites reveal the genetic architecture and breeding history of tea germplasm of East Africa

Tree Genetics & Genomes, 2016

Tea is the most popular non-alcoholic beverage worldwide and is one of the most important tree ca... more Tea is the most popular non-alcoholic beverage worldwide and is one of the most important tree cash crops in East Africa. However, no comprehensive study has been carried out on the genetic structure and diversity of tea germplasm for this region to date. In the present study, 193 tea accessions held at the ex situ Germplasm Bank of the Tea Research Institute (TRI), Kenya, were analysed using genetic data from 23 polymorphic simple sequence repeat (SSR) loci. A total of 266 alleles were detected with the number of alleles per locus ranging from 4 to 19 with an average of 7.88. Genetic clustering by STRUCTURE was used to correct misidentified accessions based on morphological characters. After reassignment of the tea accessions, Camellia assamica exhibited the lowest genetic diversity (Hs = 0.648) despite being the most widely cultivated tea type in the East African region. C. assamica subsp. lasiocalyx showed the highest genetic diversity (Hs = 0.76), which supported its origin by hybridization among tea types. Tea cultivars cultivated across the region exhibited lower genetic diversity (Hs = 0.661) compared to material held at the ex situ Germplasm Bank of TRI. Tea accessions clustered in the neighbour-joining tree on the basis of geographical origin, pedigree and leaf pigmentation, indicating their common origin. Our results indicated further that East African tea germplasm has a complex breeding history with a majority of the hybrids being F2 generation and backcross plants. C. assamica contributed significantly more genetic materials in the tea breeding programmes in East Africa. This study highlights the importance of ex situ germplasm banks to conserve the highest genetic diversity, which is an important resource for future tea crop improvements in East Africa.

Research paper thumbnail of The influence of host and pathogen genotypes on symptom severity in banana streak disease

AFRICAN JOURNAL OF BIOTECHNOLOGY

Banana is the fourth most important food crop worldwide. However, its production has been threate... more Banana is the fourth most important food crop worldwide. However, its production has been threatened by banana streak disease, caused by banana streak virus (BSV). Despite this situation, little is known about the inter-relationships between symptom severity and cultivar/virus genotypes. Symptom severity assessment for sixty five symptomatic samples was carefully done. The rolling circle amplification technique was used to identify the virus species (isolate) infecting each sample. The Mysore virus isolates (BSMysV) and the banana cultivars containing the balbisiana (B) component were associated with the most severe banana streak disease symptoms.

Research paper thumbnail of Indications for Three Independent Domestication Events for the Tea Plant (Camellia sinensis (L.) O. Kuntze) and New Insights into the Origin of Tea Germplasm in China and India Revealed by Nuclear Microsatellites

Research paper thumbnail of Rolling Circle Amplification Is More Sensitive than PCR and Serology-Based Methods in Detection of Banana streak

Banana (Musa sp.) is a popular and important crop among many communities in East Africa. Banana p... more Banana (Musa sp.) is a popular and important crop among many communities in East Africa. Banana production is however threatened by the wide-spread banana streak disease (BSD), caused by Banana streak virus (BSV). The suc-cess of BSV management is inherently coupled to the availability of a sensitive indexing method. In this study, the sen-sitivity of three BSV detection techniques: rolling circle amplification (RCA), immunocapture PCR (with degenerate and Gold finger primers) and standard PCR was compared. A set of 32 BSD-asymptomatic samples were used to com-pare the techniques. Analysis of variance (ANOVA) for comparison of the four techniques showed that there were sig-nificant differences (P < 0.05) among all the means, with RCA and direct PCR having the highest detection mean values. Owing to its fidelity and capacity to circumvent the amplification of the integrated nuclear viral sequences, the RCA technique is recommended for routine indexing of Musa tissues for BSV. This...

Research paper thumbnail of Paracoccus burnerae (HOMOPTERA; PLANOCOCCIDAE) AS A VECTOR OF Banana streak virus

The Banana streak virus (BSV) is a causative agent of the banana streak disease (BSD) which cause... more The Banana streak virus (BSV) is a causative agent of the banana streak disease (BSD) which causes considerable damage to banana production in tropical countries. The virus is vectored by several mealy bug species. However, the competence of the oleander mealy bug (Paracoccus burnerae), in the transmission of BSV is unknown. Rolling Circle Amplification (RCA) technique was used to select both diseased and healthy plantlets for transmission experiments. RCA was conducted on viruliferous instars of P. burnerae and virus-inoculated plantlet DNA samples. The results revealed that P. burnerae is a vector of BSV. However, during hot conditions (24-30oC), the insect was unable to acquire and transmit BSV. Under cool conditions (9-20oC), a minimum of 6 h of feeding time was necessary for P. burnerae instars to become viruliferous. These results indicate that P. burnerae is a vector of BSV and transmission efficiency depends on the ambient temperature and the feeding time.

Research paper thumbnail of Molecular detection of banana viruses in germplasm from selected areas in Kenya

Research paper thumbnail of Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm (Camellia sinensis (L.) O. Kuntze) Based on nSSR Markers and cpDNA Sequences

Africa is one of the key centers of global tea production. Understanding the genetic diversity an... more Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection Wambulwa et al. Genetic Architecture of African Tea during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa.

Research paper thumbnail of The complete chloroplast genome sequences of an endemic species of Urticaceae (Debregeasia hekouensis)

Mitochondrial DNA Part B

Debregeasia hekouensis, which belongs to the nettle family (Urticaceae), is a local endemic speci... more Debregeasia hekouensis, which belongs to the nettle family (Urticaceae), is a local endemic species in Hekou County, Yunnan Province, China. To provide a basis for the development of effective molecular markers for its conservation, we sequenced the chloroplast (cp) genome of D. hekouensis in the present study. The total length of the chloroplast(cp) genome was 155,941 bp, and exhibited a typical quadripartite structure, with a pair of IRs (inverted repeats; 25,664 bp in length) being separated by a small single copy (SSC) region of 19,085 bp and a large single copy (LSC) region of 85,528 bp. The cp genome contained a total of 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The GC content of the entire cp genome, LSC region, SSC region, and IR region was 36.3%, 34.0%, 29.4%, and 42.7%, respectively. Phylogenetic analysis indicated that D. hekouensis is evolutionarily closer to Debregeasia orientalis and Debregeasia squamata.

Research paper thumbnail of Genetic analysis of walnut cultivars from southwest China: Implications for germplasm improvement

Research paper thumbnail of Spatiotemporal maintenance of flora in the Himalaya biodiversity hotspot: Current knowledge and future perspectives

Research paper thumbnail of Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification

Molecular ecology resources, Jan 22, 2018

Rapid and accurate identification of endangered species is a critical component of bio-surveillan... more Rapid and accurate identification of endangered species is a critical component of bio-surveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or pre-processed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa. Here we construct a comprehensive DNA barcode reference library, and generate distribution maps using species distribution modeling (SDM), for all 15 Taxus species worldwide. We find that trnL-trnF is the ideal barcode for Taxus: it can distinguish all Taxus species, and in combination with ITS identify hybrids. Among five analysis methods tested, NJ was the most effective. Among 4151 individuals screened for trnL-trnF, 7...

Research paper thumbnail of {"__content__"=>"Domestication Origin and Breeding History of the Tea Plant () in China and India Based on Nuclear Microsatellites and cpDNA Sequence Data.", "i"=>{"__content__"=>"Camellia sinensis"}}

Frontiers in plant science, 2017

Although China and India are the two largest tea-producing countries, the domestication origin an... more Although China and India are the two largest tea-producing countries, the domestication origin and breeding history of the tea plant in these two countries remain unclear. Our previous study suggested that the tea plant includes three distinct lineages (China type tea, Chinese Assam type tea and Indian Assam type tea), which were independently domesticated in China and India, respectively. To determine the origin and historical timeline of tea domestication in these two countries we used a combination of 23 nSSRs (402 samples) and three cpDNA regions (101 samples) to genotype domesticated tea plants and its wild relative. Based on a combination of demographic modeling, NewHybrids and Neighbour joining tree analyses, three independent domestication centers were found. In addition, two origins of Chinese Assam type tea were detected: Southern and Western Yunnan of China. Results from demographic modeling suggested that China type tea and Assam type tea first diverged 22,000 year ago d...

Research paper thumbnail of Ten (10) M Ammonium acetate is an efficient molecular concentration for the extraction of genomic DNA from small insects used for rolling circle amplification

AFRICAN JOURNAL OF BIOTECHNOLOGY

Most of the published methods for DNA isolation from vectors (insects) are not always effective i... more Most of the published methods for DNA isolation from vectors (insects) are not always effective in mealy-bugs, aphids and leafhoppers because they have high amount of polyphenols in their body systems. A simple, rapid, reliable labor-effective and carcinogenic compound-free salting out method for isolation of high molecular DNA from these insects is described. The ratio of OD260/OD280 ranged between 1.8 to 2.0. The method was successfully applied to Rolling Circle Amplification and in restriction analysis, indicating the removal of the common inhibitors.

Research paper thumbnail of Paracoccus burnerae (HOMOPTERA; PLANOCOCCIDAE) AS A VECTOR OF Banana streak virus

The Banana streak virus (BSV) is a causative agent of the banana streak disease (BSD) which cause... more The Banana streak virus (BSV) is a causative agent of the banana streak disease (BSD) which causes considerable damage to banana production in tropical countries. The virus is vectored by several mealy bug species. However, the competence of the oleander mealy bug (Paracoccus burnerae), in the transmission of BSV is unknown. Rolling Circle Amplification (RCA) technique was used to select both diseased and healthy plantlets for transmission experiments. RCA was conducted on viruliferous instars of P. burnerae and virus-inoculated plantlet DNA samples. The results revealed that P. burnerae is a vector of BSV. However, during hot conditions (24-30ºC), the insect was unable to acquire and transmit BSV. Under cool conditions (9-20ºC), a minimum of 6 h of feeding time was necessary for P. burnerae instars to become viruliferous. These results indicate that P. burnerae is a vector of BSV and transmission efficiency depends on the ambient temperature and the feeding time.

Research paper thumbnail of Multiple origins and a narrow genepool characterise the African tea germplasm: concordant patterns revealed by nuclear and plastid DNA markers

Scientific reports, Jun 22, 2017

Despite the highly economic value of tea in Africa, its genetic and geographic origins remain lar... more Despite the highly economic value of tea in Africa, its genetic and geographic origins remain largely unexplored. Here we address this by collecting 439 samples across 11 countries in Africa and Asia to investigate the origin and genepool composition of African tea based on 23 nuclear microsatellites loci (nSSRs) and three cpDNA intergenic spacer regions. Our results indicated that the African tea represents a potpourri originating from multiple introductions over time. The nSSR analysis revealed that the majority (79%) of tea accessions collected in Africa belong to Indian Assam tea which have likely originated from India and/or Sri Lanka. The patterns of nSSR variation also showed that Chinese Assam tea is genetically distinct from Indian Assam tea, and has rarely been used in African tea breeding efforts since only 4% of the African tea accessions possessed this genotype. We found a total of 22 cpDNA haplotypes, which grouped into three main geographic clades that were concordant...

Research paper thumbnail of From the Wild to the Cup: Tracking Footprints of the Tea Species in Time and Space

Frontiers in Nutrition, 2021

Tea is one of the world's most popular beverages, known for its cultural significance and numerou... more Tea is one of the world's most popular beverages, known for its cultural significance and numerous health benefits. A clear understanding of the origin and history of domestication of the tea species is a fundamental prerequisite for effective germplasm conservation and improvement. Though there is a general consensus about the center of origin of the tea plant, the evolutionary origin and expansion history of the species remain shrouded in controversy, with studies often reporting conflicting findings. This mini review provides a concise summary of the current state of knowledge regarding the origin, domestication, and dissemination of the species around the world. We note that tea was domesticated around 3000 B.C. either from non-tea wild relatives (probably Camellia grandibracteata and/or C. leptophylla) or intra-specifically from the wild Camellia sinensis var. assamica trees, and that the genetic origins of the various tea varieties may need further inquiry. Moreover, we found that lineage divergence within the tea family was apparently largely driven by a combination of orogenic, climatic, and human-related forces, a fact that could have important implications for conservation of the contemporary tea germplasm. Finally, we demonstrate the robustness of an integrative approach involving linguistics, historical records, and genetics to identify the center of origin of the tea species, and to infer its history of expansion. Throughout the review, we identify areas of debate, and highlight potential research gaps, which lay a foundation for future explorations of the topic.

Research paper thumbnail of Tea data-wambulwa.xls

Research paper thumbnail of SSR alleles at 23 loci for 280 tea accessions from 8 countries in Africa. Missing data points are denoted by a zero ("0")

Research paper thumbnail of Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences

Research paper thumbnail of From the Wild to the Cup: Tracking Footprints of the Tea Species in Time and Space

Frontiers in Nutrition, 2021

Tea is one of the world's most popular beverages, known for its cultural significance and num... more Tea is one of the world's most popular beverages, known for its cultural significance and numerous health benefits. A clear understanding of the origin and history of domestication of the tea species is a fundamental pre-requisite for effective germplasm conservation and improvement. Though there is a general consensus about the center of origin of the tea plant, the evolutionary origin and expansion history of the species remain shrouded in controversy, with studies often reporting conflicting findings. This mini review provides a concise summary of the current state of knowledge regarding the origin, domestication, and dissemination of the species around the world. We note that tea was domesticated around 3000 B.C. either from non-tea wild relatives (probably Camellia grandibracteata and/or C. leptophylla) or intra-specifically from the wild Camellia sinensis var. assamica trees, and that the genetic origins of the various tea varieties may need further inquiry. Moreover, we f...

Research paper thumbnail of Nuclear microsatellites reveal the genetic architecture and breeding history of tea germplasm of East Africa

Tree Genetics & Genomes, 2016

Tea is the most popular non-alcoholic beverage worldwide and is one of the most important tree ca... more Tea is the most popular non-alcoholic beverage worldwide and is one of the most important tree cash crops in East Africa. However, no comprehensive study has been carried out on the genetic structure and diversity of tea germplasm for this region to date. In the present study, 193 tea accessions held at the ex situ Germplasm Bank of the Tea Research Institute (TRI), Kenya, were analysed using genetic data from 23 polymorphic simple sequence repeat (SSR) loci. A total of 266 alleles were detected with the number of alleles per locus ranging from 4 to 19 with an average of 7.88. Genetic clustering by STRUCTURE was used to correct misidentified accessions based on morphological characters. After reassignment of the tea accessions, Camellia assamica exhibited the lowest genetic diversity (Hs = 0.648) despite being the most widely cultivated tea type in the East African region. C. assamica subsp. lasiocalyx showed the highest genetic diversity (Hs = 0.76), which supported its origin by hybridization among tea types. Tea cultivars cultivated across the region exhibited lower genetic diversity (Hs = 0.661) compared to material held at the ex situ Germplasm Bank of TRI. Tea accessions clustered in the neighbour-joining tree on the basis of geographical origin, pedigree and leaf pigmentation, indicating their common origin. Our results indicated further that East African tea germplasm has a complex breeding history with a majority of the hybrids being F2 generation and backcross plants. C. assamica contributed significantly more genetic materials in the tea breeding programmes in East Africa. This study highlights the importance of ex situ germplasm banks to conserve the highest genetic diversity, which is an important resource for future tea crop improvements in East Africa.

Research paper thumbnail of The influence of host and pathogen genotypes on symptom severity in banana streak disease

AFRICAN JOURNAL OF BIOTECHNOLOGY

Banana is the fourth most important food crop worldwide. However, its production has been threate... more Banana is the fourth most important food crop worldwide. However, its production has been threatened by banana streak disease, caused by banana streak virus (BSV). Despite this situation, little is known about the inter-relationships between symptom severity and cultivar/virus genotypes. Symptom severity assessment for sixty five symptomatic samples was carefully done. The rolling circle amplification technique was used to identify the virus species (isolate) infecting each sample. The Mysore virus isolates (BSMysV) and the banana cultivars containing the balbisiana (B) component were associated with the most severe banana streak disease symptoms.

Research paper thumbnail of Indications for Three Independent Domestication Events for the Tea Plant (Camellia sinensis (L.) O. Kuntze) and New Insights into the Origin of Tea Germplasm in China and India Revealed by Nuclear Microsatellites

Research paper thumbnail of Rolling Circle Amplification Is More Sensitive than PCR and Serology-Based Methods in Detection of Banana streak

Banana (Musa sp.) is a popular and important crop among many communities in East Africa. Banana p... more Banana (Musa sp.) is a popular and important crop among many communities in East Africa. Banana production is however threatened by the wide-spread banana streak disease (BSD), caused by Banana streak virus (BSV). The suc-cess of BSV management is inherently coupled to the availability of a sensitive indexing method. In this study, the sen-sitivity of three BSV detection techniques: rolling circle amplification (RCA), immunocapture PCR (with degenerate and Gold finger primers) and standard PCR was compared. A set of 32 BSD-asymptomatic samples were used to com-pare the techniques. Analysis of variance (ANOVA) for comparison of the four techniques showed that there were sig-nificant differences (P < 0.05) among all the means, with RCA and direct PCR having the highest detection mean values. Owing to its fidelity and capacity to circumvent the amplification of the integrated nuclear viral sequences, the RCA technique is recommended for routine indexing of Musa tissues for BSV. This...

Research paper thumbnail of Paracoccus burnerae (HOMOPTERA; PLANOCOCCIDAE) AS A VECTOR OF Banana streak virus

The Banana streak virus (BSV) is a causative agent of the banana streak disease (BSD) which cause... more The Banana streak virus (BSV) is a causative agent of the banana streak disease (BSD) which causes considerable damage to banana production in tropical countries. The virus is vectored by several mealy bug species. However, the competence of the oleander mealy bug (Paracoccus burnerae), in the transmission of BSV is unknown. Rolling Circle Amplification (RCA) technique was used to select both diseased and healthy plantlets for transmission experiments. RCA was conducted on viruliferous instars of P. burnerae and virus-inoculated plantlet DNA samples. The results revealed that P. burnerae is a vector of BSV. However, during hot conditions (24-30oC), the insect was unable to acquire and transmit BSV. Under cool conditions (9-20oC), a minimum of 6 h of feeding time was necessary for P. burnerae instars to become viruliferous. These results indicate that P. burnerae is a vector of BSV and transmission efficiency depends on the ambient temperature and the feeding time.

Research paper thumbnail of Molecular detection of banana viruses in germplasm from selected areas in Kenya

Research paper thumbnail of Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm (Camellia sinensis (L.) O. Kuntze) Based on nSSR Markers and cpDNA Sequences

Africa is one of the key centers of global tea production. Understanding the genetic diversity an... more Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection Wambulwa et al. Genetic Architecture of African Tea during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa.

Research paper thumbnail of The complete chloroplast genome sequences of an endemic species of Urticaceae (Debregeasia hekouensis)

Mitochondrial DNA Part B

Debregeasia hekouensis, which belongs to the nettle family (Urticaceae), is a local endemic speci... more Debregeasia hekouensis, which belongs to the nettle family (Urticaceae), is a local endemic species in Hekou County, Yunnan Province, China. To provide a basis for the development of effective molecular markers for its conservation, we sequenced the chloroplast (cp) genome of D. hekouensis in the present study. The total length of the chloroplast(cp) genome was 155,941 bp, and exhibited a typical quadripartite structure, with a pair of IRs (inverted repeats; 25,664 bp in length) being separated by a small single copy (SSC) region of 19,085 bp and a large single copy (LSC) region of 85,528 bp. The cp genome contained a total of 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The GC content of the entire cp genome, LSC region, SSC region, and IR region was 36.3%, 34.0%, 29.4%, and 42.7%, respectively. Phylogenetic analysis indicated that D. hekouensis is evolutionarily closer to Debregeasia orientalis and Debregeasia squamata.

Research paper thumbnail of Genetic analysis of walnut cultivars from southwest China: Implications for germplasm improvement

Research paper thumbnail of Spatiotemporal maintenance of flora in the Himalaya biodiversity hotspot: Current knowledge and future perspectives

Research paper thumbnail of Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification

Molecular ecology resources, Jan 22, 2018

Rapid and accurate identification of endangered species is a critical component of bio-surveillan... more Rapid and accurate identification of endangered species is a critical component of bio-surveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or pre-processed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa. Here we construct a comprehensive DNA barcode reference library, and generate distribution maps using species distribution modeling (SDM), for all 15 Taxus species worldwide. We find that trnL-trnF is the ideal barcode for Taxus: it can distinguish all Taxus species, and in combination with ITS identify hybrids. Among five analysis methods tested, NJ was the most effective. Among 4151 individuals screened for trnL-trnF, 7...

Research paper thumbnail of {"__content__"=>"Domestication Origin and Breeding History of the Tea Plant () in China and India Based on Nuclear Microsatellites and cpDNA Sequence Data.", "i"=>{"__content__"=>"Camellia sinensis"}}

Frontiers in plant science, 2017

Although China and India are the two largest tea-producing countries, the domestication origin an... more Although China and India are the two largest tea-producing countries, the domestication origin and breeding history of the tea plant in these two countries remain unclear. Our previous study suggested that the tea plant includes three distinct lineages (China type tea, Chinese Assam type tea and Indian Assam type tea), which were independently domesticated in China and India, respectively. To determine the origin and historical timeline of tea domestication in these two countries we used a combination of 23 nSSRs (402 samples) and three cpDNA regions (101 samples) to genotype domesticated tea plants and its wild relative. Based on a combination of demographic modeling, NewHybrids and Neighbour joining tree analyses, three independent domestication centers were found. In addition, two origins of Chinese Assam type tea were detected: Southern and Western Yunnan of China. Results from demographic modeling suggested that China type tea and Assam type tea first diverged 22,000 year ago d...

Research paper thumbnail of Ten (10) M Ammonium acetate is an efficient molecular concentration for the extraction of genomic DNA from small insects used for rolling circle amplification

AFRICAN JOURNAL OF BIOTECHNOLOGY

Most of the published methods for DNA isolation from vectors (insects) are not always effective i... more Most of the published methods for DNA isolation from vectors (insects) are not always effective in mealy-bugs, aphids and leafhoppers because they have high amount of polyphenols in their body systems. A simple, rapid, reliable labor-effective and carcinogenic compound-free salting out method for isolation of high molecular DNA from these insects is described. The ratio of OD260/OD280 ranged between 1.8 to 2.0. The method was successfully applied to Rolling Circle Amplification and in restriction analysis, indicating the removal of the common inhibitors.

Research paper thumbnail of Paracoccus burnerae (HOMOPTERA; PLANOCOCCIDAE) AS A VECTOR OF Banana streak virus

The Banana streak virus (BSV) is a causative agent of the banana streak disease (BSD) which cause... more The Banana streak virus (BSV) is a causative agent of the banana streak disease (BSD) which causes considerable damage to banana production in tropical countries. The virus is vectored by several mealy bug species. However, the competence of the oleander mealy bug (Paracoccus burnerae), in the transmission of BSV is unknown. Rolling Circle Amplification (RCA) technique was used to select both diseased and healthy plantlets for transmission experiments. RCA was conducted on viruliferous instars of P. burnerae and virus-inoculated plantlet DNA samples. The results revealed that P. burnerae is a vector of BSV. However, during hot conditions (24-30ºC), the insect was unable to acquire and transmit BSV. Under cool conditions (9-20ºC), a minimum of 6 h of feeding time was necessary for P. burnerae instars to become viruliferous. These results indicate that P. burnerae is a vector of BSV and transmission efficiency depends on the ambient temperature and the feeding time.

Research paper thumbnail of Multiple origins and a narrow genepool characterise the African tea germplasm: concordant patterns revealed by nuclear and plastid DNA markers

Scientific reports, Jun 22, 2017

Despite the highly economic value of tea in Africa, its genetic and geographic origins remain lar... more Despite the highly economic value of tea in Africa, its genetic and geographic origins remain largely unexplored. Here we address this by collecting 439 samples across 11 countries in Africa and Asia to investigate the origin and genepool composition of African tea based on 23 nuclear microsatellites loci (nSSRs) and three cpDNA intergenic spacer regions. Our results indicated that the African tea represents a potpourri originating from multiple introductions over time. The nSSR analysis revealed that the majority (79%) of tea accessions collected in Africa belong to Indian Assam tea which have likely originated from India and/or Sri Lanka. The patterns of nSSR variation also showed that Chinese Assam tea is genetically distinct from Indian Assam tea, and has rarely been used in African tea breeding efforts since only 4% of the African tea accessions possessed this genotype. We found a total of 22 cpDNA haplotypes, which grouped into three main geographic clades that were concordant...

Research paper thumbnail of From the Wild to the Cup: Tracking Footprints of the Tea Species in Time and Space

Frontiers in Nutrition, 2021

Tea is one of the world's most popular beverages, known for its cultural significance and numerou... more Tea is one of the world's most popular beverages, known for its cultural significance and numerous health benefits. A clear understanding of the origin and history of domestication of the tea species is a fundamental prerequisite for effective germplasm conservation and improvement. Though there is a general consensus about the center of origin of the tea plant, the evolutionary origin and expansion history of the species remain shrouded in controversy, with studies often reporting conflicting findings. This mini review provides a concise summary of the current state of knowledge regarding the origin, domestication, and dissemination of the species around the world. We note that tea was domesticated around 3000 B.C. either from non-tea wild relatives (probably Camellia grandibracteata and/or C. leptophylla) or intra-specifically from the wild Camellia sinensis var. assamica trees, and that the genetic origins of the various tea varieties may need further inquiry. Moreover, we found that lineage divergence within the tea family was apparently largely driven by a combination of orogenic, climatic, and human-related forces, a fact that could have important implications for conservation of the contemporary tea germplasm. Finally, we demonstrate the robustness of an integrative approach involving linguistics, historical records, and genetics to identify the center of origin of the tea species, and to infer its history of expansion. Throughout the review, we identify areas of debate, and highlight potential research gaps, which lay a foundation for future explorations of the topic.