Abstract:
:Although the hemipterans (Aphididae) are comprised of roughly 50,000 extant insect species, only four have sequenced genomes that are publically available, namely Acyrthosiphon pisum (pea aphid), Rhodnius prolixus (Kissing bug), Myzus persicae (Green peach aphid) and Diuraphis noxia (Russian wheat aphid). As a significant proportion of agricultural pests are phloem feeding aphids, it is crucial for sustained global food security that a greater understanding of the genomic and molecular functioning of this family be elucidated. Recently, the genome of US D. noxia biotype US2 was sequenced but its assembly only incorporated ~ 32% of produced reads and contained a surprisingly low gene count when compared to that of the model/first sequenced aphid, A. pisum. To this end, we present here the genomes of two South African Diuraphis noxia (Kurdjumov, Hemiptera: Aphididae) biotypes (SA1 and SAM), obtained after sequencing the genomes of the only two D. noxia biotypes with documented linked genealogy. To better understand overall targets and patterns of heterozygosity, we also sequenced a pooled sample of 9 geographically separated D. noxia populations (MixIX). We assembled a 399 Mb reference genome (PRJNA297165, representing 64% of the projected genome size 623 Mb) using ± 28 Gb of 101 bp paired-end HiSeq2000 reads from the D. noxia biotype SAM, whilst ± 13 Gb 101 bp paired-end HiSeq2000 reads from the D. noxia biotype SA1 were generated to facilitate genomic comparisons between the two biotypes. Sequencing the MixIX sample yielded ±26 Gb 50 bp paired-end SOLiD reads which facilitated SNP detection when compared to the D. noxia biotype SAM assembly. Ab initio gene calling produced a total of 31,885 protein coding genes from the assembled contigs spanning ~ 399 Mb (GCA_001465515.1).
journal_name
Stand Genomic Scijournal_title
Standards in genomic sciencesauthors
Burger NFV,Botha AMdoi
10.1186/s40793-017-0307-6subject
Has Abstractpub_date
2017-12-28 00:00:00pages
90issn
1944-3277pii
307journal_volume
12pub_type
abstract::The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a publ...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2205004
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journal_title:Standards in genomic sciences
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doi:10.1186/s40793-017-0225-7
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journal_title:Standards in genomic sciences
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doi:10.1186/s40793-017-0242-6
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journal_title:Standards in genomic sciences
pub_type: 杂志文章
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journal_title:Standards in genomic sciences
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doi:10.1186/s40793-017-0249-z
更新日期:2017-07-27 00:00:00
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journal_title:Standards in genomic sciences
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doi:10.1186/s40793-016-0219-x
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journal_title:Standards in genomic sciences
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journal_title:Standards in genomic sciences
pub_type: 杂志文章
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journal_title:Standards in genomic sciences
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doi:10.1186/s40793-018-0337-8
更新日期:2018-11-28 00:00:00
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journal_title:Standards in genomic sciences
pub_type: 杂志文章
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journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-018-0309-z
更新日期:2018-04-11 00:00:00
abstract::The Roseophages, a group of marine viruses that uniquely infect the Roseobacter clade of bacteria, play a significant role in marine ecosystems. Here we present a complete genomic sequence of an N4 phage 'vB_DshP-R1', which infects Dinoroseobacter shibae DFL12, together with its structural and genomic features. vB_Dsh...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/1944-3277-10-6
更新日期:2015-01-21 00:00:00
abstract::Phage ST0 lysing Escherichia coli H8 was isolated from wastewater and sequenced using an Illumina HiSeq system. Genomic analyses revealed that it was virulent phages and contained a circular double-stranded DNA genome, consisting of 170,496 nucleotides with an average G + C content of 37.67%. This study may provide po...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0304-9
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journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0306-7
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abstract::Strain CCMM B554, also known as FSM-MA, is a soil dwelling and nodule forming, nitrogen-fixing bacterium isolated from the nodules of the legume Medicago arborea L. in the Maamora Forest, Morocco. The strain forms effective nitrogen fixing nodules on species of the Medicago, Melilotus and Trigonella genera and is exce...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0298-3
更新日期:2017-12-13 00:00:00
abstract::A strain of a hyperthermophilic filamentous archaeon was isolated from a sample of Kamchatka hot spring sediment. Isolate 1807-2 grew optimally at 85 °C, pH 6.0-6.5, the parameters being close to those at the sampling site. 16S rRNA gene sequence analysis placed the novel isolate in the crenarchaeal genus Thermofilum;...
journal_title:Standards in genomic sciences
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doi:10.1186/s40793-015-0105-y
更新日期:2015-12-09 00:00:00
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journal_title:Standards in genomic sciences
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doi:10.1186/s40793-016-0174-6
更新日期:2016-08-24 00:00:00
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journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0037-6
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journal_title:Standards in genomic sciences
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doi:10.1186/s40793-017-0263-1
更新日期:2017-08-31 00:00:00
abstract::Methanoplanus petrolearius Ollivier et al. 1998 is the type strain of the genus Methanoplanus. The strain was originally isolated from an offshore oil field from the Gulf of Guinea. Members of the genus Methanoplanus are of interest because they play an important role in the carbon cycle and also because of their sign...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
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journal_title:Standards in genomic sciences
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journal_title:Standards in genomic sciences
pub_type: 杂志文章
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journal_title:Standards in genomic sciences
pub_type:
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journal_title:Standards in genomic sciences
pub_type: 杂志文章
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journal_title:Standards in genomic sciences
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journal_title:Standards in genomic sciences
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doi:10.1186/s40793-016-0217-z
更新日期:2017-01-05 00:00:00
abstract::Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and p...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/1944-3277-10-17
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abstract::Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales, class Bacilli and phylum Firmicutes. The increasing relevance of S. cohnii to human health prompted us to determine the genomic sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a multidrug-resistant isolat...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
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更新日期:2014-03-15 00:00:00