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Hongmei Miao

Bio: Hongmei Miao is an academic researcher from Agricultural & Applied Economics Association. The author has contributed to research in topics: Genome & Genome evolution. The author has an hindex of 1, co-authored 7 publications receiving 96 citations.

Papers
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Journal ArticleDOI
TL;DR: The Sesame Genome Working Group (SGWG) has been formed to sequence and assemble the sesame (Sesamum indicum L.) genome and the status and planned analyses are described.
Abstract: The Sesame Genome Working Group (SGWG) has been formed to sequence and assemble the sesame (Sesamum indicum L.) genome. The status of this project and our planned analyses are described.

108 citations

Book ChapterDOI
01 Jan 2021
TL;DR: The complicated sequencing and assembly strategies for the wild species and the first interspecific single nucleotide polymorphism (SNP) genetic map for Sesamum are described and deliberated in this chapter.
Abstract: The Sesame Genome Working Group sequenced the genomes of the six wild Sesamum species, i.e., S. alatum (2n = 26, var. 3651), S. latifollum (2n = 32, var. KEN1), S. angolense (2n = 32, var. K16), S. calycinum (2n = 32, var. KEN8), S. angustifolium (2n = 32, var. G01), and S. radiatum (2n = 64, var. G02), which cover all three types of the basic chromosome number of the genus Sesamum. We describe the complicated sequencing and assembly strategies for the wild species and the first interspecific single nucleotide polymorphism (SNP) genetic map for Sesamum. The chromosome-scaled genome assemblies of the six wild Sesamum species are deliberated in this chapter.

1 citations

Book ChapterDOI
01 Jan 2021
TL;DR: In this article, the main technologies including Sanger sequencing, Roche-454 massive parallel pyrosequencing, Solexa/Illumina sequencing, ABI SOLiD platform, PacBio SMRT platform, HiC sequencing, Oxford nanopore sequencing, and Bionano sequencing platform are briefly discussed.
Abstract: The invention of Sanger sequencing initiated the genome era. The development and application of next-generation sequencing (NGS) technologies facilitated genome sequencing in organisms. Here we introduce the main technologies including Sanger sequencing, Roche-454 massive parallel pyrosequencing, Solexa/Illumina sequencing, ABI SOLiD platform, PacBio SMRT platform, HiC sequencing, Oxford nanopore sequencing, and Bionano sequencing platform, as mostly are applied in the Sesame Genome Project (SGP). The characteristics of each technology are briefly discussed. For the SGP, the hybrid sequencing strategies involving the first generation, NGS, and the third generation sequencing technologies are applied to assemble the fine genome map with high accuracy and completeness. Combined with the genome size estimation and genome characters of sesame, the efficient sequencing strategies are elucidated in this section.

1 citations

Book ChapterDOI
01 Jan 2021
TL;DR: Yuzhi et al. as mentioned in this paper presented a comprehensive genome assembly strategy for sesame comprised the next generation sequencing (NGS), the third assembly platforms, and Hi-C assembly strategy with supplementation of high-dense single nucleotide polymorphism (SNP) genetic map and bacterial artificial chromosome (BAC-FISH) cytogenetic map.
Abstract: Genome assembly strategy is a crucial step for reconstructing high-quality genomes in any genome project. With the continuous innovation of new sequencing platforms, various methods of genome assembly have been developed and applied in genome assembly. In order to construct a fine genome map for sesame, the Sesame Genome Working Group (SGWG) group analyzed and optimized the assembly strategy for sesame according to the various sequencing data and genome characteristics. The comprehensive genome assembly strategy for sesame comprised the next generation sequencing (NGS), the third assembly platforms, and Hi-C assembly strategy with supplementation of high-dense single nucleotide polymorphism (SNP) genetic map and bacterial artificial chromosome—fluorescent in situ hybridization (BAC-FISH) cytogenetic map. Comparison results of the specific and high-efficient assembly techniques in sesame were discussed in this chapter. The final assembled genome of sesame (cv. Yuzhi 11) comprises of 335 megabase (Mb) sequences with high completeness. About 313 Mb sequences are assembled into the 13 chromosome molecules. High accuracy and integrity of the assembled genome indicates the suitable genome assembly for sesame. The results provide an extraordinary example of the application of high-quality genome assembly techniques in higher plants with large genomes.
Book ChapterDOI
01 Jan 2021
TL;DR: The organizational background of SGWG and the targets of the SGP are introduced in this chapter and they include deciphering a great amount of genes or molecular markers and elucidating the sesame genome characters.
Abstract: With the development of sesame industry in the world, the requirement for increasing the breeding efficiency and realizing various breeding objectives with the aid of modern molecular breeding techniques has become more and more urgent. In order to realize molecular breeding and concisely aggregate the elite genes into new varieties in sesame, deciphering a great amount of genes or molecular markers and elucidating the sesame genome characters are the key issues. Based on the above requisites, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, China organized the Sesame Genome Working Group (SGWG) in 2009 and initiated the Sesame Genome Project (SGP) in 2010. The organizational background of SGWG and the targets of the SGP are also introduced in this chapter.

Cited by
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Journal ArticleDOI
TL;DR: It is shown that the super-helical RNA-binding surface of RNA-editing factors is potentially longer than previously recognised, and used the redefined motifs to develop accurate and consistent annotations of PPR sequences from 109 genomes.
Abstract: The pentatricopeptide repeat (PPR) proteins form one of the largest protein families in land plants. They are characterised by tandem 30-40 amino acid motifs that form an extended binding surface capable of sequence-specific recognition of RNA strands. Almost all of them are post-translationally targeted to plastids and mitochondria, where they play important roles in post-transcriptional processes including splicing, RNA editing and the initiation of translation. A code describing how PPR proteins recognise their RNA targets promises to accelerate research on these proteins, but making use of this code requires accurate definition and annotation of all of the various nucleotide-binding motifs in each protein. We have used a structural modelling approach to define 10 different variants of the PPR motif found in plant proteins, in addition to the putative deaminase motif that is found at the C-terminus of many RNA-editing factors. We show that the super-helical RNA-binding surface of RNA-editing factors is potentially longer than previously recognised. We used the redefined motifs to develop accurate and consistent annotations of PPR sequences from 109 genomes. We report a high error rate in PPR gene models in many public plant proteomes, due to gene fusions and insertions of spurious introns. These consistently annotated datasets across a wide range of species are valuable resources for future comparative genomics studies, and an essential pre-requisite for accurate large-scale computational predictions of PPR targets. We have created a web portal (http://www.plantppr.com) that provides open access to these resources for the community.

246 citations

Journal ArticleDOI
TL;DR: The sesame genome will facilitate future research on the evolution of eudicots, as well as the study of lipid biosynthesis and potential genetic improvement of sesame, an important species from the order Lamiales and a high oil crop.
Abstract: Background: Sesame, Sesamum indicum L., is considered the queen of oilseeds for its high oil content and quality, and is grown widely in tropical and subtropical areas as an important source of oil and protein. However, the molecular biology of sesame is largely unexplored. Results: Here, we report a high-quality genome sequence of sesame assembled de novo with a contig N50 of 52.2 kb and a scaffold N50 of 2.1 Mb, containing an estimated 27,148 genes. The results reveal novel, independent whole genome duplication and the absence of the Toll/interleukin-1 receptor domain in resistance genes. Candidate genes and oil biosynthetic pathways contributing to high oil content were discovered by comparative genomic and transcriptomic analyses. These revealed the expansion of type 1 lipid transfer genes by tandem duplication, the contraction of lipid degradation genes, and the differential expression of essential genes in the triacylglycerol biosynthesis pathway, particularly in the early stage of seed development. Resequencing data in 29 sesame accessions from 12 countries suggested that the high genetic diversity of lipid-related genes might be associated with the wide variation in oil content. Additionally, the results shed light on the pivotal stage of seed development, oil accumulation and potential key genes for sesamin production, an important pharmacological constituent of sesame. Conclusions: As an important species from the order Lamiales and a high oil crop, the sesame genome will facilitate future research on the evolution of eudicots, as well as the study of lipid biosynthesis and potential genetic improvement of sesame.

225 citations

Journal ArticleDOI
TL;DR: The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits.
Abstract: The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.

155 citations

Journal ArticleDOI
TL;DR: Two major genes associated with lignification and black pigmentation in the seed coat are associated with large variation in oil content, and these findings may inform breeding and improvement strategies for a broad range of oilseed crops.
Abstract: Oilseed crops are used to produce vegetable oil. Sesame (Sesamum indicum), an oilseed crop grown worldwide, has high oil content and a small diploid genome, but the genetic basis of oil production and quality is unclear. Here we sequence 705 diverse sesame varieties to construct a haplotype map of the sesame genome and de novo assemble two representative varieties to identify sequence variations. We investigate 56 agronomic traits in four environments and identify 549 associated loci. Examination of the major loci identifies 46 candidate causative genes, including genes related to oil content, fatty acid biosynthesis and yield. Several of the candidate genes for oil content encode enzymes involved in oil metabolism. Two major genes associated with lignification and black pigmentation in the seed coat are also associated with large variation in oil content. These findings may inform breeding and improvement strategies for a broad range of oilseed crops.

150 citations

Journal ArticleDOI
TL;DR: The present review discusses the ethnopharmacological values, pharmacological and toxicological evidence of 117 plant species grown in South Africa, which are used traditionally for skin care purposes and almost 35 out of the 117 species are totally unexplored in the area of skin care.

119 citations