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.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.13121

Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants.

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.

/pdf/genome-sequencing-of-the-high-oil-crop-sesame-provides-4lj12byji0.pdf

Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis

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.

/pdf/genome-sequence-of-the-olive-tree-olea-europaea-54lvn3o8fd.pdf

Genome sequence of the olive tree, Olea europaea

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.

/pdf/genetic-discovery-for-oil-production-and-quality-in-sesame-4np7t66iua.pdf

Genetic discovery for oil production and quality in sesame

https://repository.up.ac.za/bitstream/handle/2263/39752/Lall_Are_2014.pdf?sequence=1

Are plants used for skin care in South Africa fully explored

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.

/pdf/genome-sequencing-of-the-important-oilseed-crop-sesamum-79zujggtpq.pdf

Genome sequencing of the important oilseed crop Sesamum indicum L

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.

Genome Sequencing of the Wild Sesamum Speices

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.

Strategies and Tools for Sequencing of the Sesame Genome

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.

Sesame Genome Assembly

Repetitive DNA sequences are the homologous DNA fragments with multiple copies and are the main components in higher plant genomes. Reliable chromosome-scaled genome assembly provided abundant genome information regarding genome structure research in sesame. In this chapter, we present the genome structure character and distribution of interspersed repeat sequences and the tandem repeats in the assembled genome of sesame var. Yuzhi 11 (version 3.0). For S. indicum, the content of interspersed repeat sequences is 46.11%. Of the five groups of interspersed repetitive sequences, i.e., SINEs, LINEs, long terminal repeat (LTR) element, DNA element, and unknown dispersed repeat elements, LTR group is the biggest known repeat type and occupies 11.41% of the assembled genome (335 Mb). Ty1-Copia is the major superfamily in LTR-RTs. In sesame genome, distribution of the tandem repeats, such as rDNA, telomere, and centromere repeats, reflects the character of species. Cytogenetic analyses and genome structure showed that the individual 26 chromosomes in S. indicum have telomeric repeats at the terminal position. The telomeres of sesame are conserved, and the repeat sequences are same with the common repeat unit of TTTAGGG. A total of 1235 telomeric repeat of (TTTAGGG)3 were found in the assembled genome. Meanwhile, about three thousand 45S and 5S rDNA repeats are detected in the assemble genome, which accord with the rDNA content range in other plants. Distribution characters and copy number of telomeres and rDNAs reflect the relative completeness of the assembled sesame genome. In addition, distribution of simple sequence repeats (SSRs) in sesame genome also has been precisely analyzed. A 153 bp centromeric repeat sequence is identified in sesame genome for the first time, which supplies more information for exploring the genome evolution of Sesamum.

Hongmei Miao

Papers

Genome sequencing of the important oilseed crop Sesamum indicum L

Genome Sequencing of the Wild Sesamum Speices

Strategies and Tools for Sequencing of the Sesame Genome

Sesame Genome Assembly

Repetitive Sequences in Sesame Genome