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July 7, 2019

An update on bioinformatics resources for plant genomics research

Next-generation sequencing and traditional Sanger sequencing methods are of great significance in unraveling the complexity of plant genomes. These are constantly generating heaps of sequence data to be analyzed, annotated and stored. This has created a revolutionary demand for bioinformatics tools and software that can perform these functions. A large number of potentially useful bioinformatics tools and plant genome databases are created that have greatly simplified the analysis and storage of vast amounts of sequence data. The information garnered using the available bioinformatics methods have greatly helped in understanding the plant genome structure. Despite the availability of a good number of such tools, the information pouring from single gene-sequencing, and various whole-genome sequencing projects is overwhelming; thus, further innovations and improved methods are needed to sift through this sequence data, and assemble genomes. The current review focuses on diverse bioinformatics approaches and methods developed to systematically analyze and store plant sequence data. Finally, it outlines the bottlenecks in plant genome analysis, and some possible solutions that could be utilized to overcome the problems associated with plant genome analysis.

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July 7, 2019

Genomic clues to the parental origin of the wild flowering cherry Prunus yedoensis var. nudiflora (Rosaceae)

Prunus yedoensis Matsumura is one of the popular ornamental flowering cherry trees native to northeastern Asia, and its wild populations have only been found on Jeju Island, Korea. Previous studies suggested that wild P. yedoensis (P. yedoensis var. nudiflora) is a hybrid species; however, there is no solid evidence on its exact parental origin and genomic organization. In this study, we developed a total of 38 nuclear gene-based DNA markers that can be universally amplifiable in the Prunus species using 586 Prunus Conserved Orthologous Gene Set (Prunus COS). Using the Prunus COS markers, we investigated the genetic structure of wild P. yedoensis populations and evaluated the putative parental species of wild P. yedoensis. Population structure and phylogenetic analysis of 73 wild P. yedoensis accessions and 54 accessions of other Prunus species revealed that the wild P. yedoensis on Jeju Island is a natural homoploid hybrid. Sequence-level comparison of Prunus COS markers between species suggested that wild P. yedoensis might originate from a cross between maternal P. pendula f. ascendens and paternal P. jamasakura. Moreover, approximately 81% of the wild P. yedoensis accessions examined were likely F1 hybrids, whereas the remaining 19% were backcross hybrids resulting from additional asymmetric introgression of parental genotypes. These findings suggest that complex hybridization of the Prunus species on Jeju Island can produce a range of variable hybrid offspring. Overall, this study makes a significant contribution to address issues of the origin, nomenclature, and genetic relationship of ornamental P. yedoensis.

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July 7, 2019

Genome sequence-based marker development and genotyping in potato

Potato (Solanum tuberosum L.) is one of the world’s most economically important food crops and holds major significance for future food security. Despite its importance, the study of potato genetics and breeding has lagged behind mainly due to its polyploid genome and high levels of heterozygosity. Conventional marker and genotyping approaches have been helpful in progressing potato genetic research but have also had limitations in exploiting the outcome from these studies for gene discovery and applied research applications. The sequencing of the potato genome, followed by advancements in marker and genotyping technologies, has brought a step change in the way potato genetic studies are conducted. Potato is now amenable to modern sequence-based marker and genotyping methods with their increased ability to put thousands of markers on any population of interest without a priori knowledge. This has increased the precision and resolution of genetic studies previously not feasible in potato. A diverse range of fixed and flexible genotyping platforms, for a wide variety of research and breeding applications, are now available. Concerted research efforts are now needed to screen the available genetic diversity for this important crop to identify novel and beneficial trait alleles in order to enable efficient and precise introgression breeding permitting breeding of climate smart, and resilient, potato cultivars. This chapter provides an overview of sequence-based marker development and genotyping methods along with their implications for potato research and breeding in the post-genomics era.

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July 7, 2019

Effects of genome structure variation, homeologous genes and repetitive DNA on polyploid crop research in the age of genomics.

Compared to diploid species, allopolyploid crop species possess more complex genomes, higher productivity, and greater adaptability to changing environments. Next generation sequencing techniques have produced high-density genetic maps, whole genome sequences, transcriptomes and epigenomes for important polyploid crops. However, several problems interfere with the full application of next generation sequencing techniques to these crops. Firstly, different types of genomic variation affect sequence assembly and QTL mapping. Secondly, duplicated or homoeologous genes can diverge in function and then lead to emergence of many minor QTL, which increases difficulties in fine mapping, cloning and marker assisted selection. Thirdly, repetitive DNA sequences arising in polyploid crop genomes also impact sequence assembly, and are increasingly being shown to produce small RNAs to regulate gene expression and hence phenotypic traits. We propose that these three key features should be considered together when analyzing polyploid crop genomes. It is apparent that dissection of genomic structural variation, elucidation of the function and mechanism of interaction of homoeologous genes, and investigation of the de novo roles of repeat sequences in agronomic traits are necessary for genomics-based crop breeding in polyploids. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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July 7, 2019

The kiwifruit genome

The whole-genome sequence of Actinidia chinensis var. chinensis ‘Hongyang’ was published in 2013 and was represented as the first publicly available Ericales genome sequence. Publication in 2015 of an improved linkage map for A. chinensis and interspecific comparison analyses coupled with the availability of a second whole-genome sequence of a genotype closely related to ‘Hongyang’ have enabled the kiwifruit research community to improve the existing whole-genome sequence. This chapter describes the original genome sequence and steps towards its improvement.

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July 7, 2019

Chloroplast genomes: diversity, evolution, and applications in genetic engineering.

Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.

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July 7, 2019

Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties.

Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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July 7, 2019

Finished genome sequences of Xanthomonas fragariae, the cause of bacterial angular leaf spot of strawberry.

Xanthomonas fragariae is a foliar pathogen of strawberry that is of significant concern to nursery production of strawberry transplants and field production of strawberry fruit. Long-read sequencing was employed to generate finished genomes for two isolates (each with one chromosome and two plasmids) from symptomatic plants in northern California. Copyright © 2016 Henry and Leveau.

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July 7, 2019

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes.

Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits.© The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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July 7, 2019

The sequenced angiosperm genomes and genome databases.

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

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July 7, 2019

The challenge of analyzing the sugarcane genome.

Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.

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July 7, 2019

Identification of woodland strawberry gene coexpression networks

What we think of as a strawberry is botanically not a berry or even a fruit, but rather multiple fruits (achenes that contain the seeds) on the outside of a swollen receptacle. This technicality aside, strawberries are both economically important and a useful system in which to study seed-fruit communication. While cultivated strawberries have a complex octoploid genome, one of their likely progenitors, the woodland strawberry (Fragaria vesca; Fig. 1), is a rapidly growing model system for the Rosaceae family due to its short generation time and capacity to be transformed. A draft of the woodland strawberry diploid genome sequence was released in 2011 (Shulaev et al., 2011), and the recent publication of a high-quality genome based on PacBio sequencing has added almost 1,500 genes to the annotation (Edger et al., 2018). Genetic and epigenetic resources have also been developed for this species (Xu et al., 2016; Hilmarsson et al., 2017).

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July 7, 2019

The Draft Genome of the MD-2 Pineapple

The main challenge in assembling plant genome is its ploidy level, repeats content, and polymorphism. The second-generation sequencing delivered the throughput and the accuracy that is crucial to whole-genome sequencing but insufficient and remained challenging for some plant species. It is known that genomes produced by next-gen- eration sequencing produced small contigs that would inflate the number of annotated genes (Varshney et al. 2011) and missed on the transposable elements that are abun- dant in plant genome due to their repetitive nature (Michael and Jackson 2013).

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