ABSTRACT The potential of Turnip mosaic virus (TuMV) to infect and damage cool season crops in th... more ABSTRACT The potential of Turnip mosaic virus (TuMV) to infect and damage cool season crops in the grain belt of New South Wales, Australia, was investigated by serological tests on 24,689 dicot weed, grain, and forage specimens from 1999 to 2007 and infectivity/pathogenicity tests with six isolates. Natural infection by TuMV was common in Brassicaceae weeds. Infected grain crops included mustard (Brassica juncea), field pea (Pisum sativum), chickpea (Cicer arietinum), and coriander (Coriandrum sativum). Forage (tur- nip, Brassica rapa) was also infected. None of 9,816 canola (Brassica napus, at least 19 cultivars) or 1,967 faba bean(Vicia faba, three cultivars) plants were infected. Six isolates from weeds, mustard, and chickpea were inoculated on a range of weed and crop species including four B. napus pathotype differential lines. Inoculated Brassicaceae weeds, mustard, field pea cv. ‘Cressy Blue’, coriander, Chinese cab- bage (B. rapa), and forage turnip (B. rapa) were usually infected. Field pea cv. Dundale and radishes (Raphanus sativus) were infected infrequently. Symptoms were severe in mustard, forage turnip, chickpea, and field pea. The report- edly susceptible canola cv. ‘Outback’ displayed only variable infectivity and mild symptoms for five isolates and no infec- tivity for one isolate. Faba bean, field pea cv. ‘Excell’, and two B. napus differentials appeared to be non-hosts. The results suggest that TuMV strains naturalised in Brassicaceae weeds in NSW in 1999–2007 could damage mustard, field pea, and forage turnip, but not canola or faba bean. These NSW strains appeared to be distinct from strains that damage canola in Europe, North America, and Asia.
DNA research : an international journal for rapid publication of reports on genes and genomes, 2015
Improved knowledge of genome composition, especially of its repetitive component, generates impor... more Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR's divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs...
Retrotransposons are an ubiquitous component of plant genomes, especially abundant in species wit... more Retrotransposons are an ubiquitous component of plant genomes, especially abundant in species with large genomes. Populus trichocarpa has a relatively small genome, which was entirely sequenced; however, studies focused on poplar retrotransposons dynamics are rare. With the aim to study the retrotransposon component of the poplar genome, we have scanned the complete genome sequence searching full-length long-terminal repeat (LTR) retrotransposons,
ABSTRACT Poplar interspecific hybrids are one of the most important forest crops. In order to obt... more ABSTRACT Poplar interspecific hybrids are one of the most important forest crops. In order to obtain data on molecular responses of forest trees to drought, Illumina sequencing technology was used to determine the sequence of most gene transcripts. This approach identified genes that contribute to tolerance to water-limiting environments, contributing to the long-term aim of developing strategies to improve plant productivity under drought. We generated 72,197,113 sequence reads, each 51 nt in length, encompassing 3.68 Gb of sequence from 12 cDNA libraries obtained from leaves of plants of a hybrid between Populus deltoides and Populus nigra subjected or not to moderate or severe drought. The expression of 41,335 poplar genes included in the Populus trichocarpa Phytozome database was studied by mapping Illumina cDNA reads on poplar unigene models. Expressed genes were characterised by gene ontology and by determining the metabolic pathway to which they belong. Most genes detected were expressed in control and drought-treated plants; however, a number of genes that were observed were significantly induced or repressed by drought. Induction or repression of most genes was more common after severe (relative water content around 55–60 %) than after moderate water deficit (around 85 %) even for genes that usually respond promptly to changes in environmental conditions, such as those encoding transcription factors. The dataset of expression profiles will be useful for future studies on responses to other stimula and for crop improvement of poplar.
ABSTRACT The potential of Turnip mosaic virus (TuMV) to infect and damage cool season crops in th... more ABSTRACT The potential of Turnip mosaic virus (TuMV) to infect and damage cool season crops in the grain belt of New South Wales, Australia, was investigated by serological tests on 24,689 dicot weed, grain, and forage specimens from 1999 to 2007 and infectivity/pathogenicity tests with six isolates. Natural infection by TuMV was common in Brassicaceae weeds. Infected grain crops included mustard (Brassica juncea), field pea (Pisum sativum), chickpea (Cicer arietinum), and coriander (Coriandrum sativum). Forage (tur- nip, Brassica rapa) was also infected. None of 9,816 canola (Brassica napus, at least 19 cultivars) or 1,967 faba bean(Vicia faba, three cultivars) plants were infected. Six isolates from weeds, mustard, and chickpea were inoculated on a range of weed and crop species including four B. napus pathotype differential lines. Inoculated Brassicaceae weeds, mustard, field pea cv. ‘Cressy Blue’, coriander, Chinese cab- bage (B. rapa), and forage turnip (B. rapa) were usually infected. Field pea cv. Dundale and radishes (Raphanus sativus) were infected infrequently. Symptoms were severe in mustard, forage turnip, chickpea, and field pea. The report- edly susceptible canola cv. ‘Outback’ displayed only variable infectivity and mild symptoms for five isolates and no infec- tivity for one isolate. Faba bean, field pea cv. ‘Excell’, and two B. napus differentials appeared to be non-hosts. The results suggest that TuMV strains naturalised in Brassicaceae weeds in NSW in 1999–2007 could damage mustard, field pea, and forage turnip, but not canola or faba bean. These NSW strains appeared to be distinct from strains that damage canola in Europe, North America, and Asia.
DNA research : an international journal for rapid publication of reports on genes and genomes, 2015
Improved knowledge of genome composition, especially of its repetitive component, generates impor... more Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR's divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs...
Retrotransposons are an ubiquitous component of plant genomes, especially abundant in species wit... more Retrotransposons are an ubiquitous component of plant genomes, especially abundant in species with large genomes. Populus trichocarpa has a relatively small genome, which was entirely sequenced; however, studies focused on poplar retrotransposons dynamics are rare. With the aim to study the retrotransposon component of the poplar genome, we have scanned the complete genome sequence searching full-length long-terminal repeat (LTR) retrotransposons,
ABSTRACT Poplar interspecific hybrids are one of the most important forest crops. In order to obt... more ABSTRACT Poplar interspecific hybrids are one of the most important forest crops. In order to obtain data on molecular responses of forest trees to drought, Illumina sequencing technology was used to determine the sequence of most gene transcripts. This approach identified genes that contribute to tolerance to water-limiting environments, contributing to the long-term aim of developing strategies to improve plant productivity under drought. We generated 72,197,113 sequence reads, each 51 nt in length, encompassing 3.68 Gb of sequence from 12 cDNA libraries obtained from leaves of plants of a hybrid between Populus deltoides and Populus nigra subjected or not to moderate or severe drought. The expression of 41,335 poplar genes included in the Populus trichocarpa Phytozome database was studied by mapping Illumina cDNA reads on poplar unigene models. Expressed genes were characterised by gene ontology and by determining the metabolic pathway to which they belong. Most genes detected were expressed in control and drought-treated plants; however, a number of genes that were observed were significantly induced or repressed by drought. Induction or repression of most genes was more common after severe (relative water content around 55–60 %) than after moderate water deficit (around 85 %) even for genes that usually respond promptly to changes in environmental conditions, such as those encoding transcription factors. The dataset of expression profiles will be useful for future studies on responses to other stimula and for crop improvement of poplar.
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Papers by Rosa M Cossu