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91.
A high quality draft consensus sequence of the genome of a heterozygous grapevine variety 总被引:7,自引:0,他引:7
Velasco R Zharkikh A Troggio M Cartwright DA Cestaro A Pruss D Pindo M Fitzgerald LM Vezzulli S Reid J Malacarne G Iliev D Coppola G Wardell B Micheletti D Macalma T Facci M Mitchell JT Perazzolli M Eldredge G Gatto P Oyzerski R Moretto M Gutin N Stefanini M Chen Y Segala C Davenport C Demattè L Mraz A Battilana J Stormo K Costa F Tao Q Si-Ammour A Harkins T Lackey A Perbost C Taillon B Stella A Solovyev V Fawcett JA Sterck L Vandepoele K Grando SM Toppo S Moser C Lanchbury J Bogden R 《PloS one》2007,2(12):e1326
Background
Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented.Principal Findings
We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before).Conclusions
Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape. 相似文献92.
Does sexual selection shape sex differences in longevity and senescence patterns across vertebrates? A review and new insights from captive ruminants 下载免费PDF全文
Morgane Tidière Jean‐Michel Gaillard Dennis W. H. Müller Laurie Bingaman Lackey Olivier Gimenez Marcus Clauss Jean‐François Lemaître 《Evolution; international journal of organic evolution》2015,69(12):3123-3140
In most mammals, both sexes display different survival patterns, often involving faster senescence in males. Being under intense sexual competition to secure mating opportunities, males of polygynous species allocate resources to costly behaviors and conspicuous sexual traits, which might explain these observed differences in longevity and senescence patterns. However, comparative studies performed to date have led to conflicting results. We aimed to resolve this problem by first reviewing case studies of the relationship between the strength of sexual selection and age‐specific survival metrics. Then, we performed a comprehensive comparative analysis to test whether such relationships exist among species of captive ruminants. We found that the strength of sexual selection negatively influenced the onset of actuarial senescence in males, with males senescing earlier in polygynous than in monogamous species, which led to reduced male longevity in polygynous species. Moreover, males of territorial species senesced earlier but slower, and have a shorter longevity than males of species displaying other mating tactics. We detected little influence of the strength of sexual selection on the rate of actuarial senescence. Our findings demonstrate that the onset of actuarial senescence, rather than its rate, is a side effect of physiological mechanisms linked to sexual selection, and potentially accounts for observed differences in longevity. 相似文献
93.
94.
Levels of oestrogens in plasma of mature fall-spawning rainbow trout Salmo gairdneri were determined using a radio-immunoassay. No significant difference was found in oestrogen concentration between the sexes (male =2.5 ng/ml; female =4.4 ng/ml); between individual variability was great. Four blood samplings over a 24-h period via cardiac puncture of males revealed no diel variation or change in estrogen levels due to the stress of bleedings. Although no gonado-somatic index-estrogen relationship could be demonstrated for either sex, there was correlation between oestrogen and androgen levels in the female. 相似文献
95.
Avery A. Lane Michelle K. McGuire Mark A. McGuire Janet E. Williams Kimberly A. Lackey Edward H. Hagen Abhishek Kaul Debela Gindola Dubale Gebeyehu Katherine E. Flores James A. Foster Daniel W. Sellen Elizabeth W. Kamau-Mbuthia Egidioh W. Kamundia Samwel Mbugua Sophie E. Moore Andrew M. Prentice Linda J. Kvist Gloria E. Otoo Juan M. Rodríguez Lorena Ruiz Rossina G. Pareja Lars Bode William J. Price Courtney L. Meehan 《American journal of physical anthropology》2019,169(3):526-539
96.
97.
E.Arthur Bell James A. Lackey Roger M. Polhill 《Biochemical Systematics and Ecology》1978,6(3):201-212
Canavanine is a nitrogen-rich non-protein amino acid, with a supposedly dual role of food storage and defence in seeds and seedlings. It seems to be unique to Leguminosae subfamily Papilionoideae although it does not occur in all species or genera. This report extends the previous surveys for canavanine to 1200 species in 240 genera (including first records for 70 genera) and assesses the systematic and ecological significance of its distribution. 相似文献
98.
We critically compared Marcusenius specimens from the mouth of the Cunene River on the Namibia/Angola border, a harsh desert environment on the Atlantic Ocean coast virtually devoid of aerial insects with aquatic larvae which are an important food item, with Marcusenius multisquamatus Kramer & Wink, 2013 from the escarpment region of that same river, in a relatively rich and productive subtropical savannah environment. River mouth specimens were differentiated in morphology and electric organ discharges, as determined by ANOVA/MANOVA comparisons, principal component and discriminant analyses on morphological and electrophysiological characters, and genetics, including sequences of the mitochondrial cytochrome b gene, indicating reproductive isolation. Specimens from the river mouth differed from M. multisquamatus, their closest relatives, by having a shorter snout, a smaller eye diameter, and smaller nares separation. River mouth specimens were also differentiated from other, increasingly less-close relatives, such as M. altisambesi Kramer et al., 2007 from the Okavango River, Botswana, and from M. krameri Maake et al., 2014 from the Limpopo System, South Africa. We therefore designate the new species Marcusenius desertus sp. nov. for the Cunene River mouth population. 相似文献
99.
Jeremy G. Wideman Sebastian W. K. Lackey Martin A. Srayko Kacie A. Norton Frank E. Nargang 《PloS one》2013,8(8)
The endoplasmic reticulum mitochondria encounter structure (ERMES) tethers the ER to mitochondria and contains four structural components: Mmm1, Mdm12, Mdm10, and Mmm2 (Mdm34). The Gem1 protein may play a role in regulating ERMES function. Saccharomyces cerevisiae and Neurospora crassa strains lacking any of Mmm1, Mdm12, or Mdm10 are known to show a variety of phenotypic defects including altered mitochondrial morphology and defects in the assembly of β-barrel proteins into the mitochondrial outer membrane. Here we examine ERMES complex components in N. crassa and show that Mmm1 is an ER membrane protein containing a Cys residue near its N-terminus that is conserved in the class Sordariomycetes. The residue occurs in the ER-lumen domain of the protein and is involved in the formation of disulphide bonds that give rise to Mmm1 dimers. Dimer formation is required for efficient assembly of Tom40 into the TOM complex. However, no effects are seen on porin assembly or mitochondrial morphology. This demonstrates a specificity of function and suggests a direct role for Mmm1 in Tom40 assembly. Mutation of a highly conserved region in the cytosolic domain of Mmm1 results in moderate defects in Tom40 and porin assembly, as well as a slight morphological phenotype. Previous reports have not examined the role of Mmm2 with respect to mitochondrial protein import and assembly. Here we show that absence of Mmm2 affects assembly of β-barrel proteins and that lack of any ERMES structural component results in defects in Tom22 assembly. Loss of N. crassa Gem1 has no effect on the assembly of these proteins but does affect mitochondrial morphology. 相似文献
100.
Allison M. Land Emily K. Law Michael A. Carpenter Lela Lackey William L. Brown Reuben S. Harris 《The Journal of biological chemistry》2013,288(24):17253-17260
APOBEC3A (A3A) is a myeloid lineage-specific DNA cytosine deaminase with a role in innate immunity to foreign DNA. Previous studies have shown that heterologously expressed A3A is genotoxic, suggesting that monocytes may have a mechanism to regulate this enzyme. Indeed, we observed no significant cytotoxicity when interferon was used to induce the expression of endogenous A3A in CD14+-enriched primary cells or the monocytic cell line THP-1. In contrast, doxycycline-induced A3A in HEK293 cells caused major cytotoxicity at protein levels lower than those observed when CD14+ cells were stimulated with interferon. Immunofluorescent microscopy of interferon-stimulated CD14+ and THP-1 cells revealed that endogenous A3A is cytoplasmic, in stark contrast to stably or transiently transfected A3A, which has a cell-wide localization. A3A constructs engineered to be cytoplasmic are also nontoxic in HEK293 cells. These data combine to suggest that monocytic cells use a cytoplasmic retention mechanism to control A3A and avert genotoxicity during innate immune responses. 相似文献