scholarly journals Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7750 ◽  
Author(s):  
Fenglin Zhu ◽  
Han Sun ◽  
Ying Diao ◽  
Xingwen Zheng ◽  
Keqiang Xie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Starch Synthesis ◽  
Development Stage ◽  
Activity Analysis ◽  
Nelumbo Nucifera ◽  
Nucleotide Polymorphisms ◽  
Reverse Transcription Pcr ◽  
Late Developmental Stage ◽  
Nj Tree

Background Starch branching enzyme (SBE) is one of the key enzymes in starch biosynthetic metabolism, determining amylopectin structure. Methods Full length coding sequences (CDS) of SBE genes were cloned using reverse transcription PCR (RT-PCR) technology, and neighbor-joining (NJ) tree was used for phylogenetic analysis. Single nucleotide polymorphisms (SNPs) were determined to assess the genetic polymorphisms and variation indexes between individuals and clusters. Quantitative real time PCR (qRT-PCR) was performed to analyze the spatial and temporal expression of NnSBE genes. The effect of NnSBE genes on amylopectin’s fine structures was explored using affinity and the enzyme activity analysis of two isoforms in amylopectin and amylose. Results In this study, two SBE family genes, NnSBEI and NnSBEIII, were identified in lotus (Nelumbo nucifera Gaertn.). Phylogenetic analysis sorted NnSBEI into SBE family B and NnSBEIII into SBE family A. UPGMA phylogenetic tree divided 45 individuals of lotus into three classes. The homozygous haplotype (A G G A G) of NnSBEIII was observed in seed lotus. During the seed embryo development stage, NnSBEIII reached the peak in the middle of the development stage, while NnSBEI increased in the mid-late developmental stage. The different affinity activity of the two isozymes binding amylopectin and amylose assay indicated NnSBEI has higher activity and wider affinity. Discussion Genetic diversity showed that NnSBE genes received artificial selection during the process of cultivation and domestication in lotus seeds. Furthermore, the expression pattern and affinity activity analysis indicated that NnSBE genes were related to the chain length of amylopectin.

scholarly journals Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.)

2019 ◽  
Author(s):  
Fenglin Zhu ◽  
Han Sun ◽  
Ying Diao ◽  
Xingwen Zheng ◽  
Keqiang Xie ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Starch Synthesis ◽  
Development Stage ◽  
Activity Analysis ◽  
Nelumbo Nucifera ◽  
Nucleotide Polymorphisms ◽  
Reverse Transcription Pcr ◽  
Late Developmental Stage ◽  
Nj Tree ◽  
Pcr Technology

Background. Starch branching enzyme (SBE) is one of the key enzymes in starch biosynthetic metabolism and determines the structure of amylopectin. Methods. Full length of SBE genes were cloned by reverse transcription PCR (RT-PCR) technology, and used neighbor-joining (NJ) tree for phylogenetic analysis. The single nucleotide polymorphisms (SNPs) were determined to assess the genetic polymorphisms and variation indexes between individuals and clusters. Quantitative real time PCR (qRT-PCR) was performed to analyse spatial and temporal expression of SBE genes. Effect of NnSBE genes on fine structure of amylopectin was explore by affinity and enzyme activity analysis of two isoforms in amylopectin and amylose. Results. In this study, two SBE family genes, NnSBEI and NnSBEIII were identified from lotus (Nelumbo nucifera Gaertn.). Phylogenetic analysis divided the NnSBEI into SBE family B and NnSBEIII was belong to SBE family A. The homozygous haplotype (AA GG GG AA GG) of NnSBEIII was observed in seed lotus. During the seed embryo development stage, NnSBEIII reached the peak in middle of development stage and while NnSBEI increased in mid-late developmental stage. The different affinity activity of two isozymes bind amylopectin and amylose assay indicated NnSBEI has higher activity and wider affinity. Discussion. This study showed that NnSBE genes received artificial selection during the process of cultivation and domestication in seed lotus especially. Furthermore, the expression pattern and affinity activity analysis indicated that NnSBE genes was related to chain length of amylopectin.

scholarly journals Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.)

2019 ◽  
Author(s):  
Fenglin Zhu ◽  
Han Sun ◽  
Ying Diao ◽  
Xingwen Zheng ◽  
Keqiang Xie ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Starch Synthesis ◽  
Development Stage ◽  
Activity Analysis ◽  
Nelumbo Nucifera ◽  
Nucleotide Polymorphisms ◽  
Reverse Transcription Pcr ◽  
Late Developmental Stage ◽  
Nj Tree ◽  
Pcr Technology

Background. Starch branching enzyme (SBE) is one of the key enzymes in starch biosynthetic metabolism and determines the structure of amylopectin. Methods. Full length of SBE genes were cloned by reverse transcription PCR (RT-PCR) technology, and used neighbor-joining (NJ) tree for phylogenetic analysis. The single nucleotide polymorphisms (SNPs) were determined to assess the genetic polymorphisms and variation indexes between individuals and clusters. Quantitative real time PCR (qRT-PCR) was performed to analyse spatial and temporal expression of SBE genes. Effect of NnSBE genes on fine structure of amylopectin was explore by affinity and enzyme activity analysis of two isoforms in amylopectin and amylose. Results. In this study, two SBE family genes, NnSBEI and NnSBEIII were identified from lotus (Nelumbo nucifera Gaertn.). Phylogenetic analysis divided the NnSBEI into SBE family B and NnSBEIII was belong to SBE family A. The homozygous haplotype (AA GG GG AA GG) of NnSBEIII was observed in seed lotus. During the seed embryo development stage, NnSBEIII reached the peak in middle of development stage and while NnSBEI increased in mid-late developmental stage. The different affinity activity of two isozymes bind amylopectin and amylose assay indicated NnSBEI has higher activity and wider affinity. Discussion. This study showed that NnSBE genes received artificial selection during the process of cultivation and domestication in seed lotus especially. Furthermore, the expression pattern and affinity activity analysis indicated that NnSBE genes was related to chain length of amylopectin.

scholarly journals Detection, Quantitation, and Phylogenetic Analysis of Noroviruses in Japanese Oysters

2003 ◽  
Vol 69 (10) ◽  
pp. 5782-5786 ◽  
Author(s):  
Tomoko Nishida ◽  
Hirokazu Kimura ◽  
Mika Saitoh ◽  
Michiyo Shinohara ◽  
Masahiko Kato ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Virus Type ◽  
Reverse Transcription ◽  
Real Time Pcr ◽  
The Other ◽  
Capsid Gene ◽  
Neighbor Joining ◽  
Norwalk Virus ◽  
Reverse Transcription Pcr

ABSTRACT Noroviruses (NVs) cause many cases of oyster- or clam-associated gastroenteritis in various countries. We collected 191 samples from Japanese oysters intended for raw consumption that had been harvested from the sea in two different areas between December 2001 and February 2002. To detect, quantitate, and phylogenetically analyze the NV genome in purified concentrates from the stomachs and digestive diverticula of these oysters, we amplified the NV capsid gene by reverse transcription-PCR. Phylogenetic analysis was performed by using the neighbor-joining method. We detected the NV genome in 17 of 191 oysters (9%). Phylogenetic analysis indicated genogroup I (Norwalk virus type) in 3 of the 17 oysters and genogroup II (Snow Mountain virus type) in the other 14. Both genogroups showed wide genetic diversity. To quantify the NV capsid gene in these oysters, we performed real-time PCR using genogroup-specific probes. More than 102 copies of the NV genome were detected in 11 of 17 oysters. The results suggested that about 10% of Japanese oysters intended for raw consumption harbored NVs, and more than 50% of those oysters in which NVs were detected had a large amount.

scholarly journals Genetic diversity and genetic origin of Lanping black-boned sheep investigated by genome-wide single-nucleotide polymorphisms (SNPs)

2020 ◽  
Vol 63 (1) ◽  
pp. 193-201
Author(s):  
Heli Xiong ◽  
Xiaoming He ◽  
Jing Li ◽  
Xingneng Liu ◽  
Chaochao Peng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Structure Analysis ◽  
Genetic Background ◽  
Nucleotide Polymorphisms ◽  
Genetic Origin ◽  
Single Nucleotide ◽  
Sheep Breeds ◽  
Genome Wide ◽  
Nj Tree

Abstract. Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. Here, we genotyped genome-wide SNPs (single nucleotide polymorphisms) of Lanping black-boned sheep and Lanping normal sheep using Illumina OvineSNP50 BeadChip to investigate the genetic diversity and genetic origin of Lanping black-boned sheep. We also downloaded a subset SNP dataset of two Tibet-lineage sheep breeds and four other sheep breeds from the International Sheep Genomics Consortium (ISGC) as a reference for interpreting. Lanping black-boned sheep had a lower genetic diversity level when compared to seven other sheep breeds. Principal component analysis (PCA) showed that Lanping black-boned sheep and Lanping normal sheep were clustered into the Asian group, but there was no clear separation between the two breeds. Structure analysis demonstrated a high ancestry coefficient in Lanping black-boned sheep and Lanping normal sheep. However, the two populations were separated into two distinct branches in a neighbor-joining (NJ) tree. We further evaluated the genetic divergence using population FST, which showed that the genetic differentiation that existed between Lanping black-boned sheep and Lanping normal sheep was higher than that between Tibet sheep and Changthangi sheep, which revealed that Lanping black-boned sheep is a different breed from Lanping normal sheep on the genetic level. In addition, structure analysis and NJ tree showed that Lanping black-boned sheep had a relatively close relation with Tibet sheep. The results reported herein are a first step toward understanding the genetic background of Lanping black-boned sheep, and it will provide informative knowledge on the unique genetic resource conservation and mechanism of novel breed formation.

scholarly journals Molecular epidemiology of paramyxoviruses in Zambian wild rodents and shrews

2014 ◽  
Vol 95 (2) ◽  
pp. 325-330 ◽  
Author(s):  
Michihito Sasaki ◽  
Walter Muleya ◽  
Akihiro Ishii ◽  
Yasuko Orba ◽  
Bernard M. Hang’ombe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Molecular Epidemiology ◽  
South African ◽  
Reverse Transcription ◽  
Wild Rodents ◽  
Reverse Transcription Pcr ◽  
New Information ◽  
High Prevalence ◽  
Pcr Assays

Rodents and shrews are known to harbour various viruses. Paramyxoviruses have been isolated from Asian and Australian rodents, but little is known about them in African rodents. Recently, previously unknown paramyxovirus sequences were found in South African rodents. To date, there have been no reports related to the presence and prevalence of paramyxoviruses in shrews. We found a high prevalence of paramyxoviruses in wild rodents and shrews from Zambia. Semi-nested reverse transcription-PCR assays were used to detect paramyxovirus RNA in 21 % (96/462) of specimens analysed. Phylogenetic analysis revealed that these viruses were novel paramyxoviruses and could be classified as morbillivirus- and henipavirus-related viruses, and previously identified rodent paramyxovirus-related viruses. Our findings suggest the circulation of previously unknown paramyxoviruses in African rodents and shrews, and provide new information regarding the geographical distribution and genetic diversity of paramyxoviruses.

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