Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.Background Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases. Results In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses. Conclusions This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.Abstract Background The honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey bee, Apis mellifera, has served as a model species, and its genome sequence has been published. In contrast, the genome of the Asian honey bee, Apis cerana, has not yet been sequenced. A. cerana has been raised in Asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. A cerana has divergent biological traits compared to A. mellifera and it has played a key role in maintaining biodiversity in eastern and southern Asia. Here we report the first whole genome sequence of A. cerana. Results Using de novo assembly methods, we produced a 238 Mbp draft of the A. cerana genome and generated 10,651 genes. A.cerana-specific genes were analyzed to better understand the novel characteristics of this honey bee species. Seventy-two percent of the A. cerana-specific genes had more than one GO term, and 1,696 enzymes were categorized into 125 pathways. Genes involved in chemoreception and immunity were carefully identified and compared to those from other sequenced insect models. These included 10 gustatory receptors, 119 odorant receptors, 10 ionotropic receptors, and 160 immune-related genes. Conclusions This first report of the whole genome sequence of A. cerana provides resources for comparative sociogenomics, especially in the field of social insect communication. These important tools will contribute to a better understanding of the complex behaviors and natural biology of the Asian honey bee and to anticipate its future evolutionary trajectory

Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage

BACKGROUND: Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. RESULTS: Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F₂:₃ progenies and identified one major QTL and three minor QTLs. CONCLUSION: We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]

The barley pan-genome reveals the hidden legacy of mutation breeding

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding

The giant diploid faba genome unlocks variation in a global protein crop

Publisher Copyright: © 2023, The Author(s).Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.Peer reviewe

Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62

The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance

Transcriptome Profiling and Comparative Analysis of Panax ginseng Adventitious Roots

학위논문 (석사)-- 서울대학교 대학원 : 식물생산과학부(작물생명과학전공), 2014. 2. Tae-Jin Yang.Panax ginseng (C. A. Meyer) is a traditional medicinal plant famous for its strong therapeutic effects. However, genomic resources for P. ginseng are still very limited. In this study, we performed de novo assembly of transcriptomes from adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS). The assemblies were generated from ~85 and ~77 million high-quality Illumina HiSeq reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in TAIR databases. We identified candidate genes involved in ginsenoside biosynthesis: 10 transcripts for farnesyl diphosphate synthase to protopanaxatriol synthase and 21 transcripts for UDP-glycosyltransferase. A large number of transcripts (17%) with different GO designations were uniquely detected in adventitious roots compared to normal ginseng roots. In addition, 10,213 and 7,928 cDNA SSRs were identified as potential molecular markers in CP and CS, respectively. Our assembly of ginseng transcriptomes demonstrates the successful application of genomics approaches to large complex genomes. In addition, we have predicted the long noncoding(lncRNA) based on our CP RNA-Seq data. A total of 11,270 lncRNA were identified. Among them, some were precursors of small RNAs such as microRNAs and siRNAs. The assembly and comparative analysis data have been deposited to our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use. Further, To better understand our ginseng genome (P. ginseng), we used Chunpoong (CP) adventitious root RNA-Seq data to identify lncRNAs of P. gisneng. we found 11,270 long noncoding RNAs which had multiexonic structures. A total of 433 lncRNAs showed significant similarity against publicly available lncRNA database of Arabidopsis, Maize, lncRNA database and Rfam. My study provides a preliminary source for future studies of lncRNA content and function in ginseng.ABSTRACT 1 INTRODUCTION 3 MATERIALS AND METHODES 5 1 Plant material and RNA isolation 5 2 Illumina sequencing and quality control 6 3 De novo assembly 6 4 Functional annotation and analysis 7 5 Expression profiling 8 6 Identification of candidate transcripts involved in ginsenoside biosynthesis 8 7 SSR identification 8 8 Adventitious root transcriptome (ART) database creation 9 RESULTS 9 1 Adventitious root growth and morphology of two ginseng cultivars 9 2 De novo assembly and validation of Illumina paired-end sequences 9 3 Functional annotation and classification 13 4 Gene expression profiling 15 5 Transcripts showing biased expression between CP and CS adventitious roots 18 6 Identification of candidate genes involved in ginsenoside biosynthesis 22 7 Comparative analysis of the transcriptomes of adventitious and normal roots 26 8 Identification of cDNA-derived SSR markers 27 9 Adventitious root transcriptome database 30 DISCUSSION 31 1 Assembly of Illumina transcriptome sequences 31 2 Comparative analysis of transcriptomes in adventitious roots 33 3 Genes related to ginsenoside biosynthesis 36 4 Comparative analysis of transcriptomes between roots and adventitious roots 36 CONCLUSION 37 REFERENCES 38 CHAPTER 2 Computational prediction of long noncoding RNAs (lncRNAs) in P ginseng ABSTRACT 49 INTRODUCTION 50 MATERIALS AND METHODES 52 1 Data sources 52 2 The Coding Potential Calculator 53 3 Small RNA database creation 53 RESULTS AND DISCUSSION 53 1 Computational prediction 53 2 Homology based functional search 55 3 Classification of ginseng lncRNAs as small RNA precursors 57 4 Repetitive element content of lncRNAs 59 CONCLUSION 60 REFERENCES 61Maste