Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae)

<p>Abstract</p> <p>Background</p> <p>The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, <it>i.e</it>. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (<it>Cichorium intybus </it>L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae.</p> <p>Findings</p> <p>Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from <it>Hin</it>dIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and <it>S</it>₂<it>S</it>₂for the <it>S</it>-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and <it>S</it>₁<it>S</it>₄. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers.</p> <p>Conclusions</p> <p>This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the <it>S</it>-locus in this Asteraceae species.</p

Author Correction: A chickpea genetic variation map based on the sequencing of 3,366 genomes

In Extended Data Fig. 1 of this Article, the labels ‘Market class’ and ‘Biological status’ were inadvertently swapped. In the corresponding figure legend, “Track 1: Biological status; Track 2: Market class;” should have been “Track 1: Market class; Track 2: Biological status;”. The original Article has been corrected online

HACRE1, a recently inserted copia-like retrotransposon of sunflower (Helianthus annuus L.)

n this paper we report on the isolation and characterization, for the first time, of a complete 6511 bp retrotransposon of sunflower. Considering its protein domain order and sequence similarity to other copia elements of dicotyledons, this retrotransposon was assigned to the copia retrotransposon superfamily and named HACRE1 (Helianthus annuus copia-like retroelement 1). HACRE1 carries 5′ and 3′ long terminal repeats (LTRs) flanking an internal region of 4661 bp. The LTRs are identical in their sequence except for two deletions of 7 and 5 nucleotides in the 5′ LTR. Based on the sequence identity of the LTRs, HACRE1 was estimated to have inserted within the last 84 000 years. The isolated sequence contains a complete open reading frame with only one complete reading frame. The absence of nonsense mutations agrees with the very high sequence identity between LTRs, confirming that HACRE1 insertion is recent. The haploid genome of sunflower (inbred line HCM) contains about 160 copies of HACRE1. This retrotransposon is expressed in leaflets from 7-day-old plantlets under different light conditions, probably in relation to the occurrence of many putative light-related regulatory cis-elements in the LTRs. However, sequenced cDNAs show less variability than HACRE1 genomic sequences, indicating that only a subset of this family is expressed under these conditions

HACRE1, a recently inserted copia-like retrotransposon of sunflower (Helianthus annuus L.)

In this paper we report on the isolation and characterization, for the first time, of a complete 6511 bp retrotransposon of sunflower. Considering its protein domain order and sequence similarity to other copia elements of dicotyledons, this retrotransposon was assigned to the copia retrotransposon superfamily and named HACRE1 (Helianthus annuus copia-like retroelement 1). HACRE1 carries 5' and 3' long terminal repeats (LTRs) flanking an internal region of 4661 bp. The LTRs are identical in their sequence except for two deletions of 7 and 5 nucleotides in the 5' LTR. Based on the sequence identity of the LTRs, HACRE1 was estimated to have inserted within the last approximately 84 000 years. The isolated sequence contains a complete open reading frame with only one complete reading frame. The absence of nonsense mutations agrees with the very high sequence identity between LTRs, confirming that HACRE1 insertion is recent. The haploid genome of sunflower (inbred line HCM) contains about 160 copies of HACRE1. This retrotransposon is expressed in leaflets from 7-day-old plantlets under different light conditions, probably in relation to the occurrence of many putative light-related regulatory cis-elements in the LTRs. However, sequenced cDNAs show less variability than HACRE1 genomic sequences, indicating that only a subset of this family is expressed under these conditions.In this paper we report on the isolation and characterization, for the first time, of a complete 6511 bp retrotransposon of sunflower. Considering its protein domain order and sequence similarity to other copia elements of dicotyledons, this retrotransposon was assigned to the copia retrotransposon superfamily and named HACRE1 (Helianthus annuus copia-like retroelement 1). HACRE1 carries 5′ and 3′ long terminal repeats (LTRs) flanking an internal region of 4661 bp. The LTRs are identical in their sequence except for two deletions of 7 and 5 nucleotides in the 5′ LTR. Based on the sequence identity of the LTRs, HACRE1 was estimated to have inserted within the last ~84000 years. The isolated sequence contains a complete open reading frame with only one complete reading frame. The absence of nonsense mutations agrees with the very high sequence identity between LTRs, confirming that HACRE1 insertion is recent. The haploid genome of sunflower (inbred line HCM) contains about 160 copies of HACRE1. This retrotransposon is expressed in leaflets from 7-day-old plantlets under different light conditions, probably in relation to the occurrence of many putative light-related regulatory cis-elements in the LTRs. However, sequenced cDNAs show less variability than HACRE1 genomic sequences, indicating that only a subset of this family is expressed under these conditions

Functional traits diversity and fitness evaluation in response to salt stress in some annual Medicago spp wild populations

Salt-affected soils are naturally present in all climates, and the global warming will increase salinity impact particularly in arid and semi-arid regions. Medicago genus, mostly composed by annual species, is of a real interest in improving soil fertility and maintaining pastures for livestock, and as a ubiquitous component of species assemblage around the Mediterranean Basin. It is present in various environments, where the populations of these species have to cope with diverse biotic and abiotic factors at their site of origin. Thus, we assessed the response to salt stress of adaptive traits in 40 populations of six annual Medicago species originating from contrasted environments.A common garden trial was performed in saline and non-saline soils, and functional and fitness-related traits were recorded. Only M. ciliaris populations survived in the saline soil (SS), highlighting its negative effect at plant emergence. ANOVA and PCA revealed that salt tolerance affected the percentage of emerged plants, proxy of plant size and proxy of fitness.The response to salt stress was further studied by analyzing germination capacities of 37 populations under five NaCl concentrations from 0 to 200 mM, during seven days. Kaplan-Meier survivor curves and Cox PH models indicated that depending on the species and the population, time to 50% germination, germinability and germination synchrony are differently affected by the increase of salts. The variation in germination response to NaCl and the significant role of environmental variables and seed weight may be considered as an adaptation at germination. Local adaptation may partly explain the patterns of salt tolerance, as no differences appeared between the different populations in the SS. M. ciliaris is the most tolerant species, with a relatively high level of intraspecific variability. Finally, this multi-species study may help to develop strategies to protect and restore agro- or ecosystems vulnerable to salinity