Abstract:
BACKGROUND:Sugarcane is an economically important crop contributing to about 80% of the world sugar production. Increasing efforts in molecular biological studies have been performed for improving the sugar yield and other relevant important agronomic traits. However, due to sugarcane's complicated genomes, it is still challenging to study the genetic basis of traits, such as sucrose accumulation. Sucrose transporters (SUTs) are critical for both phloem loading in source tissue and sucrose uptaking in sink tissue, and are considered to be the control points for regulating sucrose storage. However, no genomic study for sugarcane sucrose transporter (SsSUT) families has been reported up to date. RESULTS:By using comparative genomics and bacterial artificial chromosomes (BACs), six SUT genes were identified and characterized in S. spontaenum. Phylogenetic analyses revealed that the two pairs SsSUTs (SsSUT1/SsSUT3 and SsSUT5/SsSUT6) could be clustered together into two separate monocot specific SUT groups, while SsSUT2 and SsSUT4 were separated into the other two groups, with members from both dicot and monocot species. Gene structure comparison demonstrated that the number and position of exons/introns in SUTs were highly conserved among the close orthologs; in contrast, there were variations among the paralogous SUTs in Sacchuarm. Though with the high polyploidy level, gene allelic haplotype comparative analysis showed that the examined four SsSUT members exhibited conservations of gene structures and amino acid sequences among the allelic haplotypes accompanied by variations of intron sizes. Gene expression analyses were performed for tissues from seedlings under drought stress and mature plants of three Saccharum species (S.officinarnum, S.spotaneum and S.robustum). Both SUT1 and SUT4 expressed abundantly at different conditions. SUT2 had similar expression level in all of the examined tissues, but SUT3 was undetectable. Both of SUT5 and SUT6 had lower expression level than other gene member, and expressed stronger in source leaves and are likely to play roles in phloem loading. In the seeding plant leave under water stress, four genes SUT1, SUT2, SUT4 and SUT5 were detectable. In these detectable genes, SUT1 and SUT4 were down regulated, while, SUT2 and SUT5 were up regulated. CONCLUSIONS:In this study, we presented the first comprehensive genomic study for a whole gene family, the SUT family, in Saccharum. We speculated that there were six SUT members in the S. spotaneum genome. Out of the six members, SsSUTs, SsSUT5 and SsSUT6 were recent duplication genes accompanied by rapid evolution, while, SsSUT2 and SsSUT4 were the ancient members in the families. Despite the high polypoidy genome, functional redundancy may not exist among the SUTs allelic haplotypes supported by the evidence of strong purifying selection of the gene allele. SUT3 could be a low active member in the family because it is undetectable in our study, but it might not be a pseudogene because it harbored integrated gene structure. SUT1 and SUT4 were the main members for the sucrose transporter, while, these SUTs had sub-functional divergence in response to sucrose accumulation and plant development in Saccharum.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Zhang Q,Hu W,Zhu F,Wang L,Yu Q,Ming R,Zhang Jdoi
10.1186/s12864-016-2419-6subject
Has Abstractpub_date
2016-02-01 00:00:00pages
88issn
1471-2164pii
10.1186/s12864-016-2419-6journal_volume
17pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Helicobacter pylori is presumed to be co-evolved with its human host and is a highly diverse gastric pathogen at genetic levels. Ancient origins of H. pylori in the New World are still debatable. It is not clear how different waves of human migrations in South America contributed to the evolution of strain d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-191
更新日期:2006-07-27 00:00:00
abstract:BACKGROUND:Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation. RESULTS:Draft mitochondrial genomes of 16 Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data. Mitochondri...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06846-x
更新日期:2020-06-24 00:00:00
abstract:BACKGROUND:On a single strand of genomic DNA the number of As is usually about equal to the number of Ts (and similarly for Gs and Cs), but deviations have been noted for transcribed regions and origins of replication. RESULTS:The mouse genome is shown to have a segmented structure defined by strand bias. Transcriptio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-16
更新日期:2008-01-14 00:00:00
abstract:BACKGROUND:High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequenc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-16
更新日期:2014-01-10 00:00:00
abstract:BACKGROUND:Host genetics is one of several factors known to shape human gut microbiome composition, however, the physiological processes underlying the heritability are largely unknown. Inter-individual differences in host factors secreted into the gut lumen may lead to variation in microbiome composition. One such fac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3290-1
更新日期:2016-11-21 00:00:00
abstract:BACKGROUND:Pancreatic cancer is a deadly disease with a five-year survival of less than 5%. A better understanding of the underlying biology may suggest novel therapeutic targets. Recent surveys of the pancreatic cancer genome have uncovered numerous new alterations; yet systematic functional characterization of candid...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-624
更新日期:2013-09-16 00:00:00
abstract:BACKGROUND:The Lundehund is a highly specialized breed characterized by a unique flexibility of the joints and polydactyly in all four limbs. The extremely small population size and high inbreeding has promoted a high frequency of diseased dogs affected by the Lundehund syndrome (LS), a severe gastro-enteropathic disea...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2844-6
更新日期:2016-08-02 00:00:00
abstract:BACKGROUND:Protein structure comparison and classification is an effective method for exploring protein structure-function relations. This problem is computationally challenging. Many different computational approaches for protein structure comparison apply the secondary structure elements (SSEs) representation of prot...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-S2-S1
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:Finger millet (Eleusine coracana (L.) Gaertn.) is an important staple food crop widely grown in Africa and South Asia. Among the millets, finger millet has high amount of calcium, methionine, tryptophan, fiber, and sulphur containing amino acids. In addition, it has C4 photosynthetic carbon assimilation mech...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3850-z
更新日期:2017-06-15 00:00:00
abstract:BACKGROUND:After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. However, relatively little is known about...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-63
更新日期:2011-01-26 00:00:00
abstract:BACKGROUND:The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4570-8
更新日期:2018-03-06 00:00:00
abstract:BACKGROUND:The hard clam or northern quahog, Mercenaria mercenaria, is one of the most valuable seafood products in the United States representing the first marine resource in some Northeastern states. Severe episodes of hard clam mortality have been consistently associated with infections caused by a thraustochytrid p...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-245
更新日期:2014-03-28 00:00:00
abstract:BACKGROUND:The advance of high-throughput sequencing has made it possible to obtain new transcriptomes and study splicing mechanisms in non-model organisms. In these studies, there is often a need to investigate the transcriptomes of two related organisms at the same time in order to find the similarities and differenc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S11-S5
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Genomic approaches provide unique opportunities to study interactions of insects with their pathogens. We developed a cDNA microarray to analyze the gene transcription profile of the lepidopteran pest Spodoptera frugiperda in response to injection of the polydnavirus HdIV associated with the ichneumonid wasp...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-160
更新日期:2006-06-21 00:00:00
abstract:BACKGROUND:Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and thre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6619-8
更新日期:2020-03-04 00:00:00
abstract:BACKGROUND:Lipoxygenases (LOXs), a type of non-haem iron-containing dioxygenase, are ubiquitous enzymes in plants and participate in the formation of fruit aroma which is a very important aspect of fruit quality. Amongst the various aroma volatiles, saturated and unsaturated alcohols and aldehydes provide the character...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-444
更新日期:2014-06-07 00:00:00
abstract:BACKGROUND:Genetic resistance in cattle is considered a suitable way to control tick burden and its consequent losses for livestock production. Exploring tick-resistant (R) and tick-susceptible (S) hosts, we investigated the genetic mechanisms underlying the variation of Braford resistance to tick infestation. Skin bio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6360-3
更新日期:2019-12-19 00:00:00
abstract:BACKGROUND:Oxidative stress is a consequence of normal and abnormal cellular metabolism and is linked to the development of human diseases. The effective functioning of the pathway responding to oxidative stress protects the cellular DNA against oxidative damage; conversely the failure of the oxidative stress response ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S6-S4
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:The molecular mechanisms that determine the organism's response to a variety of doses and modalities of stress factors are not well understood. RESULTS:We studied effects of ionizing radiation (144, 360 and 864 Gy), entomopathogenic fungus (10 and 100 CFU), starvation (16 h), and cold shock (+4, 0 and -4°C)...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S13-S8
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS:To overcome these limitations, we developed a novel RoV capture and genome sequencing method combin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3714-6
更新日期:2017-04-24 00:00:00
abstract:BACKGROUND:The packaging of DNA into chromatin regulates transcription from initiation through 3' end processing. One aspect of transcription in which chromatin plays a poorly understood role is the co-transcriptional splicing of pre-mRNA. RESULTS:Here we provide evidence that H2B monoubiquitylation (H2BK123ub1) marks...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-627
更新日期:2011-12-22 00:00:00
abstract:BACKGROUND:Matricaria recutita (German chamomile) and Chamaemelum nobile (Roman chamomile) belong to the botanical family Asteraceae. These two herbs are not only morphologically distinguishable, but their secondary metabolites - especially the essential oils present in flowers are also different, especially the terpen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6579-z
更新日期:2020-02-18 00:00:00
abstract:BACKGROUND:S. aureus is one of the main pathogens responsible for the intra-mammary infection in dairy ruminants. Although much work has been carried out to understand the complex physiological and cellular events that occur in the mammary gland in response to S. aureus, the protective mechanisms are still poorly under...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-540
更新日期:2012-10-09 00:00:00
abstract:BACKGROUND:Petal nectar spurs, which facilitate pollination through animal attraction and pollen placement, represent a key innovation promoting diversification in the genus Aquilegia (Ranunculaceae). Identifying the genetic components that contribute to the development of these three-dimensional structures will inform...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6002-9
更新日期:2019-08-22 00:00:00
abstract:BACKGROUND:Mitochondrial genomes (mtDNA) of multicellular animals (Metazoa) with bilateral symmetry (Bilateria) are compact and usually carry 13 protein-coding genes for subunits of three respiratory complexes and ATP synthase. However, occasionally reported exceptions to this typical mtDNA organization prompted specul...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3626-5
更新日期:2017-03-31 00:00:00
abstract:BACKGROUND:Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-720
更新日期:2012-12-22 00:00:00
abstract:BACKGROUND:Low iron bioavailability is a common feature of ocean surface water and therefore micro-algae developed original strategies to optimize iron uptake and metabolism. The marine picoeukaryotic green alga Ostreococcus tauri is a very good model for studying physiological and genetic aspects of the adaptation of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2666-6
更新日期:2016-05-03 00:00:00
abstract:BACKGROUND:Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMethylation450 BeadChip (450 K) which has now been replaced by the latest platform, Illumina Methylation...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07168-8
更新日期:2020-10-27 00:00:00
abstract:BACKGROUND:Citrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is made by demonstrating physical blockage of xylem cells that prevents the movement of water. This test ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6339-0
更新日期:2019-12-11 00:00:00
abstract:BACKGROUND:As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolates originated from the natural environments. RESULTS:In this study, comparative genomic analysis ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5975-8
更新日期:2019-07-22 00:00:00