The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for Bluetongue virus

Background The new genomic technologies have provided novel insights into the genetics of interactions between vectors, viruses and hosts, which are leading to advances in the control of arboviruses of medical importance. However, the development of tools and resources available for vectors of non-zoonotic arboviruses remains neglected. Biting midges of the genus Culicoides transmit some of the most important arboviruses of wildlife and livestock worldwide, with a global impact on economic productivity, health and welfare. The absence of a suitable reference genome has hindered genomic analyses to date in this important genus of vectors. In the present study, the genome of Culicoides sonorensis, a vector of bluetongue virus (BTV) in the USA, has been sequenced to provide the first reference genome for these vectors. In this study, we also report the use of the reference genome to perform initial transcriptomic analyses of vector competence for BTV. Results Our analyses reveal that the genome is 189 Mb, assembled in 7974 scaffolds. Its annotation using the transcriptomic data generated in this study and in a previous study has identified 15,612 genes. Gene expression analyses of C. sonorensis females infected with BTV performed in this study revealed 165 genes that were differentially expressed between vector competent and refractory females. Two candidate genes, glutathione S-transferase (gst) and the antiviral helicase ski2, previously recognized as involved in vector competence for BTV in C. sonorensis (gst) and repressing dsRNA virus propagation (ski2), were confirmed in this study. Conclusions The reference genome of C. sonorensis has enabled preliminary analyses of the gene expression profiles of vector competent and refractory individuals. The genome and transcriptomes generated in this study provide suitable tools for future research on arbovirus transmission. These provide a valuable resource for these vector lineage, which diverged from other major Dipteran vector families over 200 million years ago. The genome will be a valuable source of comparative data for other important Dipteran vector families including mosquitoes (Culicidae) and sandflies (Psychodidae), and together with the transcriptomic data can yield potential targets for transgenic modification in vector control and functional studies

The complete sequence of the Acacia ligulata chloroplast genome reveals a highly divergent clpP1 gene

Legumes are a highly diverse angiosperm family that include many agriculturally important species. To date, 21 complete chloroplast genomes have been sequenced from legume crops confined to the Papilionoideae subfamily. Here we report the first chloroplast genome from the Mimosoideae, Acacia ligulata, and compare it to the previously sequenced legume genomes. The A. ligulata chloroplast genome is 158,724 bp in size, comprising inverted repeats of 25,925 bp and single-copy regions of 88,576 bp and 18,298 bp. Acacia ligulata lacks the inversion present in many of the Papilionoideae, but is not otherwise significantly different in terms of gene and repeat content. The key feature is its highly divergent clpP1 gene, normally considered essential in chloroplast genomes. In A. ligulata, although transcribed and spliced, it probably encodes a catalytically inactive protein. This study provides a significant resource for further genetic research into Acacia and the Mimosoideae. The divergent clpP1 gene suggests that Acacia will provide an interesting source of information on the evolution and functional diversity of the chloroplast Clp protease comple

Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding

Oncidium is an important ornamental plant but the study of its functional genomics is difficult. Erycina pusilla is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period, and its ability to complete its life cycle in vitro make E. pusilla a good model candidate and parent for hybridization for orchids. Although genetic information remains limited, systematic molecular analysis of its chloroplast genome might provide useful genetic information. By combining bacterial artificial chromosome (BAC) clones and next-generation sequencing (NGS), the chloroplast (cp) genome of E. pusilla was sequenced accurately, efficiently and economically. The cp genome of E. pusilla shares 89 and 84% similarity with Oncidium Gower Ramsey and Phalanopsis aphrodite, respectively. Comparing these 3 cp genomes, 5 regions have been identified as showing diversity. Using PCR analysis of 19 species belonging to the Epidendroideae subfamily, a conserved deletion was found in the rps15-trnN region of the Cymbidieae tribe. Because commercial Oncidium varieties in Taiwan are limited, identification of potential parents using molecular breeding method has become very important. To demonstrate the relationship between taxonomic position and hybrid compatibility of E. pusilla, 4 DNA regions of 36 tropically adapted Oncidiinae varieties have been analyzed. The results indicated that trnF-ndhJ and trnH-psbA were suitable for phylogenetic analysis. E. pusilla proved to be phylogenetically closer to Rodriguezia and Tolumnia than Oncidium, despite its similar floral appearance to Oncidium. These results indicate the hybrid compatibility of E. pusilla, its cp genome providing important information for Oncidium breeding

Genotyping-by-sequencing (GBS) for SNP-based linkage map construction for two Prunus rootstocks from a peach rootstock breeding program

8 Pags.- 2 Figs.- 1 Tabl. The definitive version is available at: https://www.actahort.org/index.htmTrees for commercial production comprise the fruit-bearing scions grafted to a rootstock, thus the choice of an appropriate rootstock is fundamental to orchard success. Even though several SNP-based linkage maps for cultivated Prunus species such as peach, cherries and almond are available, there are no SNP-based linkage maps for Prunus rootstocks. Here, we report on using a Genotyping-by-sequencing (GBS) approach to simultaneously discover and genotype SNPs from two peach rootstocks (‘Adafuel’ × ‘Flordaguard’) and their progeny. The plant material was developed at the EEAD-CSIC Prunus rootstocks breeding program with the goal to establish segregating progeny for a range of characters of importance to rootstock breeding (resistance to iron-chlorosis, root-asphyxia and replant diseases, as well as vigor and other effects on scions such as fruit quality and yield efficiency). High-density parental linkage maps were constructed by genotyping 118 siblings. Sequence reads obtained from GBS were aligned to the P. persica (L.) Batsch reference genome (Peach v2.0). A total of 18,912 high quality SNPs (MAF>0.05; missing data <5%), evenly distributed over the eight chromosomes, were identified. The number of identified SNPs ranged from 1,595 for the chromosome 7 to 4,042 for the chromosome 1. While eight linkage groups were constructed for ‘Adafuel’, only four linkage groups were constructed for ‘Flordaguard’, given the low heterozygosity of this genotype. High synteny and co-linearity was observed between obtained maps and Peach v2.0. These linkage maps of two phenotypically diverse Prunus rootstocks provide valuable information and will serve as the basis for identification of QTLs and genes relevant for Prunus rootstocks breeding.This work was funded by grants AGL2014-52063-R and INIA RFP 2015-00019, with FEDER and Gobierno de Aragón-A44 cofunding from Spain. It was also funded by CONICYTREGIONAL/GORE O´HIGGINS/CEAF/R08I1001, FONDECYT 3160316 and CONICYT R16F20006 from Chile. Carolina Font i Forcada is beneficiary of a Juan de la Cierva Incorporación 2017 contract.Peer reviewe