Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,ar...Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,are still largely unknown,especially at the genome level,despite their importance in understanding the formation and outbreak of massive green tides.In the present study,the restriction site-associated DNA genotyping approach(2b-RAD)was adopted to identify the genome-wide single-nucleotide polymorphisms(SNPs)of 54 individual thalli including samples collected from Subei Shoal in 2019 and Qingdao coast from 2019 to 2021.SNPs genotype results revealed that most of the thalli in 2019 and 2020 were haploid gametophytes,while only half of the thalli were gametophytes in 2021,indicating flexibility in the reproductive strategies for the formation of the green tides among different years and the dominance of asexual and vegetative reproductive mode for the floating period.Besides,population analysis was conducted,and it revealed a very low genetic diversity among samples from Subei Shoal and the Qingdao coast in the same year and a higher divergence among samples in different years.The results showed the efficiency of 2b-RAD in the exploration of SNPs in U.prolifera and provided the first genome-wide scale evidence for the origin of the large-scale green tides on the Qingdao coast.This study improved our understanding of the reproductive strategy and genetic diversity of the green tide causative species and will help further reveal the biological causes of the green tide in China.展开更多
The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy...The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.展开更多
The genus Chenopodium comprises about 150 species, of which Chenopodium quinoa and C. album are important for their nutritional value. Evaluation of variation in qualitative morphological traits of plants and SNPs in ...The genus Chenopodium comprises about 150 species, of which Chenopodium quinoa and C. album are important for their nutritional value. Evaluation of variation in qualitative morphological traits of plants and SNPs in chloroplast rbc L and mat K gene sequences in 19 accessions representing C. quinoa and C. album indicated that the accessions IC-411824 and IC-411825,which have white seeds, belong to C. quinoa rather than C. album. This observation was also supported by a time tree that indicated IC-411824 and IC-411825 to be a sister clade to accessions of C. quinoa with an estimated age of 1.2 Mya. Whereas multiple alignments of rbc L gene sequences from the 19 accessions revealed 1.26% parsimony-informative sites with 0.68%interspecific sequence diversity, alignment of nucleotide sequences of amplicons representing the mat K gene revealed 4.97% parsimony-informative sites and 2.81% interspecific sequence diversity. Validation of SNPs in the cp rbc L and mat K regions of 36 accessions belonging to C. quinoa and C. album was performed by allele-specific PCR with primers carrying a single base change at the 3′ end. We report the first C. quinoa-specific SNP-based primer, R1RQ-AFR,designed from rbc L sequences, that could differentiate quinoa from 64 genera including13 species of the genus Chenopodium. With an estimated age of 10.5–4.1 million years(Myr), the Himalayan chenopods are evolutionarily younger than the Andean chenopods. The results establish the paraphyletic origin of the genus Chenopodium.展开更多
在涉及多群体样本的医学研究中,群体遗传结构差异是不容忽视的影响因素之一。利用族源信息单核苷酸多态性遗传标记(ancestry-informative single nucleotide polymorphism,AI-SNP),通过分析群体遗传成分、推断个体遗传背景并对群体样本...在涉及多群体样本的医学研究中,群体遗传结构差异是不容忽视的影响因素之一。利用族源信息单核苷酸多态性遗传标记(ancestry-informative single nucleotide polymorphism,AI-SNP),通过分析群体遗传成分、推断个体遗传背景并对群体样本进行预筛选,可以有效降低群体遗传结构差异对医学研究影响。鉴于已发表的研究多为解析大陆间、大陆次级区域间的群体遗传结构差异,本研究拟基于千人基因组计划(GRCh37.p13)中东亚五群体:日本东京群体(Japanese in Tokyo,JPT)、北京汉族(Han Chinese in Beijing,CHB)、南方汉族(Southern Han Chinese,CHS)、西双版纳傣族(Chinese Dai in Xishuangbanna,CDX)、越南京族(Kinh in Ho Chi Minh City,KHV)的数据,以FST值为标准筛选AI-SNP并分析大陆次级区域内群体遗传结构差异。结果表明,研究涉及的东亚群体可分为三簇:JPT、CHB和CHS、CDX和KHV。利用AI-SNP可成功解析个体的遗传背景,而群体代表性遗传成分占比超过80%的个体具有良好的群体代表性。本研究表明,基于FST值筛选一组AI-SNP用于核验样本遗传背景、筛选群体代表性样本的方法在降低大陆次级区域内群体遗传结构差异对群体相关医学研究的影响中具有实际应用价值。展开更多
基金Supported by the Laoshan Laboratory (No.LSKJ202204005)the Mount Tai Scholar Climbing Plan to Song SUNthe Open Fund of CAS Key Laboratory of Marine Ecology and Environmental Sciences,Institute of Oceanology,Chinese Academy of Sciences (No.KLMEES201801)
文摘Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,are still largely unknown,especially at the genome level,despite their importance in understanding the formation and outbreak of massive green tides.In the present study,the restriction site-associated DNA genotyping approach(2b-RAD)was adopted to identify the genome-wide single-nucleotide polymorphisms(SNPs)of 54 individual thalli including samples collected from Subei Shoal in 2019 and Qingdao coast from 2019 to 2021.SNPs genotype results revealed that most of the thalli in 2019 and 2020 were haploid gametophytes,while only half of the thalli were gametophytes in 2021,indicating flexibility in the reproductive strategies for the formation of the green tides among different years and the dominance of asexual and vegetative reproductive mode for the floating period.Besides,population analysis was conducted,and it revealed a very low genetic diversity among samples from Subei Shoal and the Qingdao coast in the same year and a higher divergence among samples in different years.The results showed the efficiency of 2b-RAD in the exploration of SNPs in U.prolifera and provided the first genome-wide scale evidence for the origin of the large-scale green tides on the Qingdao coast.This study improved our understanding of the reproductive strategy and genetic diversity of the green tide causative species and will help further reveal the biological causes of the green tide in China.
基金Supported by the National Key R&D Program of China(Nos.2018YFD0900106,2018YFC1406700)the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2018SDKJ0302-4)the MOA Modern Agricultural Talents Support Project。
文摘The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.
基金Financial support received from Department of Biotechnology,Government of India vide grant No.BT/PR-8953/BCE/08/533/2007project sanctioned against grant No.BT/04/NE/2009financial support from Department of Science&Technology,Government of India in the form of a research fellowship under the INSPIRE program
文摘The genus Chenopodium comprises about 150 species, of which Chenopodium quinoa and C. album are important for their nutritional value. Evaluation of variation in qualitative morphological traits of plants and SNPs in chloroplast rbc L and mat K gene sequences in 19 accessions representing C. quinoa and C. album indicated that the accessions IC-411824 and IC-411825,which have white seeds, belong to C. quinoa rather than C. album. This observation was also supported by a time tree that indicated IC-411824 and IC-411825 to be a sister clade to accessions of C. quinoa with an estimated age of 1.2 Mya. Whereas multiple alignments of rbc L gene sequences from the 19 accessions revealed 1.26% parsimony-informative sites with 0.68%interspecific sequence diversity, alignment of nucleotide sequences of amplicons representing the mat K gene revealed 4.97% parsimony-informative sites and 2.81% interspecific sequence diversity. Validation of SNPs in the cp rbc L and mat K regions of 36 accessions belonging to C. quinoa and C. album was performed by allele-specific PCR with primers carrying a single base change at the 3′ end. We report the first C. quinoa-specific SNP-based primer, R1RQ-AFR,designed from rbc L sequences, that could differentiate quinoa from 64 genera including13 species of the genus Chenopodium. With an estimated age of 10.5–4.1 million years(Myr), the Himalayan chenopods are evolutionarily younger than the Andean chenopods. The results establish the paraphyletic origin of the genus Chenopodium.
文摘在涉及多群体样本的医学研究中,群体遗传结构差异是不容忽视的影响因素之一。利用族源信息单核苷酸多态性遗传标记(ancestry-informative single nucleotide polymorphism,AI-SNP),通过分析群体遗传成分、推断个体遗传背景并对群体样本进行预筛选,可以有效降低群体遗传结构差异对医学研究影响。鉴于已发表的研究多为解析大陆间、大陆次级区域间的群体遗传结构差异,本研究拟基于千人基因组计划(GRCh37.p13)中东亚五群体:日本东京群体(Japanese in Tokyo,JPT)、北京汉族(Han Chinese in Beijing,CHB)、南方汉族(Southern Han Chinese,CHS)、西双版纳傣族(Chinese Dai in Xishuangbanna,CDX)、越南京族(Kinh in Ho Chi Minh City,KHV)的数据,以FST值为标准筛选AI-SNP并分析大陆次级区域内群体遗传结构差异。结果表明,研究涉及的东亚群体可分为三簇:JPT、CHB和CHS、CDX和KHV。利用AI-SNP可成功解析个体的遗传背景,而群体代表性遗传成分占比超过80%的个体具有良好的群体代表性。本研究表明,基于FST值筛选一组AI-SNP用于核验样本遗传背景、筛选群体代表性样本的方法在降低大陆次级区域内群体遗传结构差异对群体相关医学研究的影响中具有实际应用价值。
基金supported by the National High Technology Research and Development Program of China (Grant No. 2011AA10A101 and 2012AA101102)the Ministry of Finance, China (Grant No. 2012RG002-4)
