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Kan J, Zhang S, Wu Z, Bi D. Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics. Genes (Basel) 2024; 15:441. [PMID: 38674377 DOI: 10.3390/genes15040441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, and conservation. As an important group of horticultural ornamentals in the Crassulaceae family, Sempervivum plants are known for their unique rosette-like structures and reproduction through offsets. Despite their popularity, the classification status of Sempervivum remains uncertain, with only a single plastome sequence currently available. Furthermore, codon usage bias (CUB) is a widespread phenomenon of the unbalanced usage of synonymous codons in the coding sequence (CDS). However, due to the limited available plastid data, there has been no research that focused on the CUB analysis among Sempervivum until now. To address these gaps, we sequenced and released the plastomes of seven species and one subspecies from Sempervivum, revealing several consistent patterns. These included a shared 110 bp extension of the rps19 gene, 14 hypervariable regions (HVRs) with distinct nucleotide diversity (π: 0.01173 to 0.02702), and evidence of selective pressures shaping codon usage. Notably, phylogenetic analysis robustly divided the monophyletic clade into two sections: Jovibarba and Sempervivum. In conclusion, this comprehensive plastomic resource provides valuable insights into Sempervivum evolution and offers potential molecular markers for DNA barcoding.
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Affiliation(s)
- Junhu Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - De Bi
- College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
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Xu KL, Zhang ZM, Fang WL, Wang YD, Jin HY, Wei F, Ma SC. Comparative analyses of complete chloroplast genomes reveal interspecific difference and intraspecific variation of Tripterygium genus. Front Plant Sci 2024; 14:1288943. [PMID: 38264022 PMCID: PMC10803662 DOI: 10.3389/fpls.2023.1288943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024]
Abstract
The genus Tripterygium was of great medicinal value and attracted much attention on the taxonomic study using morphological and molecular methods. In this study, we assembled 12 chloroplast genomes of Tripterygium to reveal interspecific difference and intraspecific variation. The sequence length (156,692-157,061 bp) and structure of Tripterygium were conserved. Comparative analyses presented abundant variable regions for further study. Meanwhile, we determined the ndhB gene under positive selection through adaptive evolution analysis. And the phylogenetic analyses based on 15 chloroplast genomes supported the monophyly of Tripterygium hypoglaucum and the potential sister relationship between Tripterygium wilfordii and Tripterygium regelii. Molecular dating analysis indicated that the divergence time within Tripterygium was approximately 5.99 Ma (95% HPD = 3.11-8.68 Ma). The results in our study provided new insights into the taxonomy, evolution process, and phylogenetic construction of Tripterygium using complete plastid genomes.
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Affiliation(s)
- Kai-Ling Xu
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Zhong-Mou Zhang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Wen-Liang Fang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Ya-Dan Wang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Hong-Yu Jin
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Feng Wei
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Shuang-Cheng Ma
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
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Zhang H, Miao Y, Zhang X, Zhang G, Sun X, Zhang M, Feng Z, Huang L. The Complete Chloroplast Genome Sequence of Laportea bulbifera (Sieb. et Zucc.) Wedd. and Comparative Analysis with Its Congeneric Species. Genes (Basel) 2022; 13. [PMID: 36553498 DOI: 10.3390/genes13122230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Laportea bulbifera (L. bulbifera) is an important medicinal plant of Chinese ethnic minorities, with high economic and medicinal value. However, the medicinal materials of the genus Laportea are prone to be misidentified due to the similar morphological characteristics of the original plants. Thus, it is crucial to discover their molecular marker points and to precisely identify these species for their exploitation and conservation. Here, this study reports detailed information on the complete chloroplast (cp) of L. bulbifera. The result indicates that the cp genome of L. bulbifera of 150,005 bp contains 126 genes, among them, 37 tRNA genes and 81 protein-coding genes. The analysis of repetition demonstrated that palindromic repeats are more frequent. In the meantime, 39 SSRs were also identified, the majority of which were mononucleotides Adenine-Thymine (A-T). Furthermore, we compared L. bulbifera with eight published Laportea plastomes, to explore highly polymorphic molecular markers. The analysis identified four hypervariable regions, including rps16, ycf1, trnC-GCA and trnG-GCC. According to the phylogenetic analysis, L. bulbifera was most closely related to Laportea canadensis (L. canadensis), and the molecular clock analysis speculated that the species originated from 1.8216 Mya. Overall, this study provides a more comprehensive analysis of the evolution of L. bulbifera from the perspective of phylogenetic and intrageneric molecular variation in the genus Laportea, which is useful for providing a scientific basis for further identification, taxonomic, and evolutionary studies of the genus.
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Chen Z, Yu X, Yang Y, Wei P, Zhang W, Li X, Liu C, Zhao S, Li X, Liu X. Comparative Analysis of Chloroplast Genomes within Saxifraga (Saxifragaceae) Takes Insights into Their Genomic Evolution and Adaption to the High-Elevation Environment. Genes (Basel) 2022; 13:1673. [PMID: 36140840 DOI: 10.3390/genes13091673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Saxifraga species are widely distributed in alpine and arctic regions in the Northern hemisphere. Highly morphological diversity within this genus brings great difficulties for species identification, and their typical highland living properties make it interesting how they adapt to the extreme environment. Here, we newly generated the chloroplast (cp) genomes of two Saxifraga species and compared them with another five Saxifraga cp genomes to understand the characteristics of cp genomes and their potential roles in highland adaptation. The genome size, structure, gene content, GC content, and codon usage pattern were found to be highly similar. Cp genomes ranged from 146,549 bp to 151,066 bp in length, most of which comprised 130 predicted genes. Yet, due to the expansion of IR regions, the second copy of rps19 in Saxifraga stolonifera was uniquely kept. Through sequence divergence analysis, we identified seven hypervariable regions and detected some signatures of regularity associated with genetic distance. We also identified 52 to 89 SSRs and some long repeats among seven Saxifraga species. Both ML and BI phylogenetic analyses confirmed that seven Saxifraga species formed a monophyletic clade in the Saxifragaceae family, and their intragenus relationship was also well supported. Additionally, the ndhI and ycf1 genes were considered under positive selection in species inhabiting relatively high altitudes. Given the conditions of intense light and low CO2 concentration in the highland, the products of these two genes might participate in the adaptation to the extreme environment.
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Xia X, Peng J, Yang L, Zhao X, Duan A, Wang D. Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus. Life (Basel) 2022; 12:life12060848. [PMID: 35743879 PMCID: PMC9224849 DOI: 10.3390/life12060848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/30/2022] Open
Abstract
The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of the eight Ficus species contained 89−104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). Phylogenetic analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus.
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Affiliation(s)
- Xi Xia
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Jingyu Peng
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100089, China;
| | - Lin Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Xueli Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Anan Duan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Dawei Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
- Correspondence: ; Tel.: +86-138-8891-5161
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Skuza L, Filip E, Szućko I, Bocianowski J. SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species. Int J Mol Sci 2020; 21:ijms21249421. [PMID: 33321948 PMCID: PMC7762986 DOI: 10.3390/ijms21249421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 01/09/2023] Open
Abstract
Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.
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Affiliation(s)
- Lidia Skuza
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland; (E.F.); (I.S.)
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
- Correspondence:
| | - Ewa Filip
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland; (E.F.); (I.S.)
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
| | - Izabela Szućko
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland; (E.F.); (I.S.)
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, 28 Wojska Polskiego, 60-637 Poznań, Poland;
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Hong Z, Wu Z, Zhao K, Yang Z, Zhang N, Guo J, Tembrock LR, Xu D. Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae). Int J Mol Sci 2020; 21:E3758. [PMID: 32466556 PMCID: PMC7312355 DOI: 10.3390/ijms21113758] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/20/2020] [Accepted: 05/24/2020] [Indexed: 12/14/2022] Open
Abstract
Pterocarpus is a genus of trees mainly distributed in tropical Asia, Africa, and South America. Some species of Pterocarpus are rosewood tree species, having important economic value for timber, and for some species, medicinal value as well. Up to now, information about this genus with regard to the genomic characteristics of the chloroplasts has been limited. Based on a combination of next-generation sequencing (Illumina Hiseq) and long-read sequencing (PacBio), the whole chloroplast genomes (cp genomes) of five species (rosewoods) in Pterocarpus (Pterocarpus macrocarpus, P. santalinus, P. indicus, P. pedatus, P. marsupium) have been assembled. The cp genomes of five species in Pterocarpus have similar structural characteristics, gene content, and sequence to other flowering plants. The cp genomes have a typical four-part structure, containing 110 unique genes (77 protein coding genes, 4 rRNAs, 29 tRNAs). Through comparative genomic analysis, abundant simple sequence repeat (SSR)loci (333-349) were detected in Pterocarpus, among which A /T single nucleotide repeats accounted for the highest proportion (72.8-76.4%). In the five cp genomes of Pterocarpus, eight hypervariable regions, including trnH-GUG_psbA, trnS-UGA_psbC, accD-psaI, ndhI-exon2_ndhI-exon1, ndhG_ndhi-exon2, rpoC2-exon2, ccsA, and trnfM-CAU, are proposed for use as DNA barcode regions. In the comparison of gene selection pressures (P. santalinus as the reference genome), purifying selection was inferred as the primary mode of selection in maintaining important biological functions. Phylogenetic analysis shows that Pterocarpus is a monophyletic group. The species P. tinctorius is resolved as early diverging in the genus. Pterocarpus was resolved as sister to the genus Tipuana.
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Affiliation(s)
- Zhou Hong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
| | - Zhiqiang Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
| | - Kunkun Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
| | - Zengjiang Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
| | - Ningnan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
| | - Junyu Guo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA;
| | - Daping Xu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; (Z.H.); (K.Z.); (Z.Y.); (N.Z.); (J.G.)
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Agnihotry S, Sarangi AN, Aggarwal R. Construction & assessment of a unified curated reference database for improving the taxonomic classification of bacteria using 16S rRNA sequence data. Indian J Med Res 2020; 151:93-103. [PMID: 32134020 PMCID: PMC7055167 DOI: 10.4103/ijmr.ijmr_220_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background & objectives: For bacterial community analysis, 16S rRNA sequences are subjected to taxonomic classification through comparison with one of the three commonly used databases [Greengenes, SILVA and Ribosomal Database Project (RDP)]. It was hypothesized that a unified database containing fully annotated, non-redundant sequences from all the three databases, might provide better taxonomic classification during analysis of 16S rRNA sequence data. Hence, a unified 16S rRNA database was constructed and its performance was assessed by using it with four different taxonomic assignment methods, and for data from various hypervariable regions (HVRs) of 16S rRNA gene. Methods: We constructed a unified 16S rRNA database (16S-UDb) by merging non-ambiguous, fully annotated, full-length 16S rRNA sequences from the three databases and compared its performance in taxonomy assignment with that of three original databases. This was done using four different taxonomy assignment methods [mothur Naïve Bayesian Classifier (mothur-nbc), RDP Naïve Bayesian Classifier (rdp-nbc), UCLUST, SortMeRNA] and data from 13 regions of 16S rRNA [seven hypervariable regions (HVR) (V2-V8) and six pairs of adjacent HVRs]. Results: Our unified 16S rRNA database contained 13,078 full-length, fully annotated 16S rRNA sequences. It could assign genus and species to larger proportions (90.05 and 46.82%, respectively, when used with mothur-nbc classifier and the V2+V3 region) of sequences in the test database than the three original 16S rRNA databases (70.88-87.20% and 10.23-24.28%, respectively, with the same classifier and region). Interpretation & conclusions: Our results indicate that for analysis of bacterial mixtures, sequencing of V2-V3 region of 16S rRNA followed by analysis of the data using the mothur-nbc classifier and our 16S-UDb database may be preferred.
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Affiliation(s)
- Shikha Agnihotry
- Biomedical Informatics Centre, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Aditya N Sarangi
- Biomedical Informatics Centre, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Rakesh Aggarwal
- Biomedical Informatics Centre; Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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Yan X, Liu T, Yuan X, Xu Y, Yan H, Hao G. Chloroplast Genomes and Comparative Analyses among Thirteen Taxa within Myrsinaceae s.str. Clade (Myrsinoideae, Primulaceae). Int J Mol Sci 2019; 20:E4534. [PMID: 31540236 DOI: 10.3390/ijms20184534] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/02/2019] [Accepted: 09/10/2019] [Indexed: 01/01/2023] Open
Abstract
The Myrsinaceae s.str. clade is a tropical woody representative in Myrsinoideae of Primulaceae and has ca. 1300 species. The generic limits and alignments of this clade are unclear due to the limited number of genetic markers and/or taxon samplings in previous studies. Here, the chloroplast (cp) genomes of 13 taxa within the Myrsinaceae s.str. clade are sequenced and characterized. These cp genomes are typical quadripartite circle molecules and are highly conserved in size and gene content. Three pseudogenes are identified, of which ycf15 is totally absent from five taxa. Noncoding and large single copy region (LSC) exhibit higher levels of nucleotide diversity (Pi) than other regions. A total of ten hotspot fragments and 796 chloroplast simple sequence repeats (SSR) loci are found across all cp genomes. The results of phylogenetic analysis support the notion that the monophyletic Myrsinaceae s.str. clade has two subclades. Non-synonymous substitution rates (dN) are higher in housekeeping (HK) genes than photosynthetic (PS) genes, but both groups have a nearly identical synonymous substitution rate (dS). The results indicate that the PS genes are under stronger functional constraints compared with the HK genes. Overall, the study provides hypervariable molecular markers for phylogenetic reconstruction and contributes to a better understanding of plastid gene evolution in Myrsinaceae s.str. clade.
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Cho MS, Kim Y, Kim SC, Park J. The complete chloroplast genome of Korean Pyrus ussuriensis Maxim. ( Rosaceae): providing genetic background of two types of P. ussuriensis. Mitochondrial DNA B Resour 2019; 4:2424-2425. [PMID: 33365570 PMCID: PMC7687443 DOI: 10.1080/23802359.2019.1598802] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Pyrus ussuriensis Maxim. is one of the most important pear species cultivated in Asia, grown in northern China, far-east Russia, Korea, and Japan. Here we completed the chloroplast genome of wild P. ussuriensis collected in Bonghwa-gun, Korea, which was 159,986 bp in length consisting of four subregions: 87,947 bp of large single copy (LSC) and 19,255 bp of small single copy (SSC) regions are separated by 26,392 bp of inverted repeat (IR) regions. The genome contained a total of 130 genes including 85 protein-coding genes, eight rRNAs, and 37 tRNAs. The overall GC content was 36.5% and those in the LSC, SSC, and IR regions were 34.2%, 30.4%, and 42.6%, respectively. Phylogenetic analysis of 14 Pyrus chloroplast genomes provided the diverse genetic background for wild P. ussuriensis populations in Korea by confirming that wild P. ussuriensis sequenced in this study contained Pyrus pyrifolia type plastome. It revealed substantial sequence variations up to 121 single nucleotide polymorphisms and 781 insertions and deletions against another wild accession of P. ussuriensis (P. ussuriensis type) collected in Mt. Hambaek, Korea.
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Affiliation(s)
- Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Yongsung Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea.,InfoBoss Co., Ltd., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
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Bricault CA, Yusim K, Seaman MS, Yoon H, Theiler J, Giorgi EE, Wagh K, Theiler M, Hraber P, Macke JP, Kreider EF, Learn GH, Hahn BH, Scheid JF, Kovacs JM, Shields JL, Lavine CL, Ghantous F, Rist M, Bayne MG, Neubauer GH, McMahan K, Peng H, Chéneau C, Jones JJ, Zeng J, Ochsenbauer C, Nkolola JP, Stephenson KE, Chen B, Gnanakaran S, Bonsignori M, Williams LD, Haynes BF, Doria-Rose N, Mascola JR, Montefiori DC, Barouch DH, Korber B. HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design. Cell Host Microbe 2019; 25:59-72.e8. [PMID: 30629920 PMCID: PMC6331341 DOI: 10.1016/j.chom.2018.12.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/06/2018] [Accepted: 11/14/2018] [Indexed: 12/26/2022]
Abstract
Eliciting HIV-1-specific broadly neutralizing antibodies (bNAbs) remains a challenge for vaccine development, and the potential of passively delivered bNAbs for prophylaxis and therapeutics is being explored. We used neutralization data from four large virus panels to comprehensively map viral signatures associated with bNAb sensitivity, including amino acids, hypervariable region characteristics, and clade effects across four different classes of bNAbs. The bNAb signatures defined for the variable loop 2 (V2) epitope region of HIV-1 Env were then employed to inform immunogen design in a proof-of-concept exploration of signature-based epitope targeted (SET) vaccines. V2 bNAb signature-guided mutations were introduced into Env 459C to create a trivalent vaccine, and immunization of guinea pigs with V2-SET vaccines resulted in increased breadth of NAb responses compared with Env 459C alone. These data demonstrate that bNAb signatures can be utilized to engineer HIV-1 Env vaccine immunogens capable of eliciting antibody responses with greater neutralization breadth. HIV-1 bNAb sensitivity signatures from 4 large virus panels mapped across 4 Ab classes Non-contact hypervariable region characteristics are critical for bNAb sensitivity HIV-1 Env 459C used alone as a vaccine can elicit modest tier 2 NAbs in guinea pigs V2 bNAb signature-guided modifications in 459C enhanced neutralization breadth
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Affiliation(s)
- Christine A Bricault
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Karina Yusim
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | | | - Peter Hraber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Edward F Kreider
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Johannes F Scheid
- Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02114, USA
| | - James M Kovacs
- Division of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Departments of Chemistry and Biochemistry, University of Colorado, Colorado Springs, CO 80918, USA
| | - Jennifer L Shields
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Christy L Lavine
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Fadi Ghantous
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Michael Rist
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Madeleine G Bayne
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - George H Neubauer
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Coraline Chéneau
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Jennifer J Jones
- Department of Medicine and CFAR, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jie Zeng
- Department of Medicine and CFAR, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christina Ochsenbauer
- Department of Medicine and CFAR, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Kathryn E Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA
| | - Bing Chen
- Division of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - S Gnanakaran
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - LaTonya D Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicole Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA.
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
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Pan Z, Usui H, Sato A, Shozu M. Complete hydatidiform moles are composed of paternal chromosomes and maternal mitochondria. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:943-950. [PMID: 29037102 DOI: 10.1080/24701394.2017.1389916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Mitochondrial DNA (mtDNA) and genomic DNA are produced in separate subcellular compartments. Human mtDNA is transmitted via maternal transmission in general. Complete hydatidiform moles (CHMs) represent major trophoblastic diseases that are cytogenetically exceptional because the chromosomal genomic DNA is derived only from sperm cells, making them strikingly different from normal concepti. However, few reports have described the mtDNA-transmission pattern in hydatidiform moles. To evaluate mtDNA transmission in androgenetic CHMs, we compared the sequences of hypervariable regions in 16 trios sets of mtDNAs from maternal, paternal, and villous samples of androgenetic CHMs diagnosed by short tandem repeat-polymorphism analysis. All mtDNAs in androgenetic CHMs were maternally derived, in line with the general human inheritance pattern. Three maternal mtDNAs were heteroplasmic. The heterozygous status of maternal mtDNA was reflected in villous tissue, in which variants status was also heterozygous. CHMs are composed of paternal chromosomes and maternal mitochondria.
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Affiliation(s)
- Zijun Pan
- a Department of Reproductive Medicine , Graduate School of Medicine, Chiba University , Chiba , Japan
| | - Hirokazu Usui
- a Department of Reproductive Medicine , Graduate School of Medicine, Chiba University , Chiba , Japan
| | - Asuka Sato
- a Department of Reproductive Medicine , Graduate School of Medicine, Chiba University , Chiba , Japan
| | - Makio Shozu
- a Department of Reproductive Medicine , Graduate School of Medicine, Chiba University , Chiba , Japan
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Dos Santos Rocha A, de Amorim ISS, Simão TDA, da Fonseca ADS, Garrido RG, Mencalha AL. High-Resolution Melting (HRM) of Hypervariable Mitochondrial DNA Regions for Forensic Science. J Forensic Sci 2017; 63:536-540. [PMID: 28834547 DOI: 10.1111/1556-4029.13552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 11/26/2022]
Abstract
Forensic strategies commonly are proceeding by analysis of short tandem repeats (STRs); however, new additional strategies have been proposed for forensic science. Thus, this article standardized the high-resolution melting (HRM) of DNA for forensic analyzes. For HRM, mitochondrial DNA (mtDNA) from eight individuals were extracted from mucosa swabs by DNAzol reagent, samples were amplified by PCR and submitted to HRM analysis to identify differences in hypervariable (HV) regions I and II. To confirm HRM, all PCR products were DNA sequencing. The data suggest that is possible discriminate DNA from different samples by HRM curves. Also, uncommon dual-dissociation was identified in a single PCR product, increasing HRM analyzes by evaluation of melting peaks. Thus, HRM is accurate and useful to screening small differences in HVI and HVII regions from mtDNA and increase the efficiency of laboratory routines based on forensic genetics.
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Affiliation(s)
- Alípio Dos Santos Rocha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil.,Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Isis Salviano Soares de Amorim
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
| | - Tatiana de Almeida Simão
- Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
| | - Adenilson de Souza da Fonseca
- Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Rodrigo Grazinoli Garrido
- Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
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14
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Higashi A, Nagai S, Seoane S, Ueki S. A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo. Biol Lett 2017; 13:rsbl.2016.0976. [PMID: 28404821 DOI: 10.1098/rsbl.2016.0976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/21/2017] [Indexed: 11/12/2022] Open
Abstract
Geographical distributions of phytoplankton species can be defined by events on both evolutionary time and shorter scales, e.g. recent climate changes. Additionally, modern industrial activity, including the transport of live fish and spat for aquaculture and aquatic microorganisms in ship ballast water, may aid the spread of phytoplankton. Obtaining a reliable marker is key to gaining insight into the phylogeographic history of a species. Here, we report a hypervariable mitochondrial gene in the cosmopolitan bloom-forming alga, Heterosigma akashiwo We compared the entire mitochondrial genome sequences of seven H. akashiwo strains from Japanese and North American coastal waters and identified a hypervariable segment. The region codes for a hypothetical protein with no defined function, and its variations between Japanese and North American isolates were prominent, while the sequences were more conserved among Japanese strains and North American isolates. Comparison of the sequence in isolates obtained from different geographical points in the Northern Hemisphere revealed that the sequence variations largely correlated with latitude and longitude (i.e. Pacific/Atlantic oceans). Our results demonstrate the usefulness of the sequence in determining the phylogeographic history of H. akashiwo.
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Affiliation(s)
- Aiko Higashi
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Sergio Seoane
- Department of Plant Biology and Ecology, University of the Basque Country, 48940 Leioa, Spain
| | - Shoko Ueki
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
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15
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Poljak RJ, Amzel LM, Chen BL, Phizackerley RP, Saul F. The three-dimensional structure of the fab' fragment of a human myeloma immunoglobulin at 2.0-angstrom resolution. Proc Natl Acad Sci U S A 1974; 71:3440-4. [PMID: 4215080 PMCID: PMC433789 DOI: 10.1073/pnas.71.9.3440] [Citation(s) in RCA: 162] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The structural analysis of the Fab' fragment of human myeloma immunoglobulin IgGl(lambda) New has been extended to a nominal resolution of 2.0 A. Each of the structural subunits corresponding to the variable and to the constant homology regions of the light and heavy chains contains two irregular beta-sheets which are roughly parallel to each other and surround a tightly packed interior of hydrophobic side chains. About 50-60% of the amino-acid residues are included in beta-pleated sheets. Sequence alignments between the homology regions of Fab' New obtained by comparison of their three-dimensional structures are given. Some of the sequence variations observed in light and heavy chains and the role of the regions of hypervariable sequence in defining the size and shape of the active site of different immunoglobulin molecules are discussed on the basis of the three-dimensional model of Fab' New.
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Poljak RJ, Amzel LM, Avey HP, Chen BL, Phizackerley RP, Saul F. Three-dimensional structure of the Fab' fragment of a human immunoglobulin at 2,8-A resolution. Proc Natl Acad Sci U S A 1973; 70:3305-10. [PMID: 4519624 PMCID: PMC427225 DOI: 10.1073/pnas.70.12.3305] [Citation(s) in RCA: 293] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The structure of the Fab' fragment of a human myeloma immunoglobulin was determined by x-ray crystallographic analysis at 2.8-A resolution. The Fourier map of the electron density was correlated with the aminoacid sequence to obtain a three-dimensional model. Four globular subunits, which correspond to the homology regions of the light and heavy chains, are arranged in a tetrahedral configuration. These subunits closely resemble each other, sharing a basic pattern of polypeptide chain folding. In each subunit, long sequences of tightly packed, hydrogen bonded polypeptide chain run parallel to the major axis of the subunit. No helical conformation can be seen. Different patterns of interchain disulfide linkage and unusual intrachain disulfide bonds that have been observed in other immunoglobulins can be explained with this model. The regions of hypervariable sequences in the light and heavy chains occur at one end of the molecule, in close spatial proximity.
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