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Marsupial satellite DNA as faithful reflections of long-terminal repeat retroelement structure. 有袋动物卫星DNA作为长端重复逆元结构的忠实反射。
IF 3.1 3区 生物学
Genome Pub Date : 2022-09-01 Epub Date: 2022-08-05 DOI: 10.1139/gen-2022-0039
Sakura Hayashi, Yusuke Honda, Etsuko Kanesaki, Akihiko Koga
{"title":"Marsupial satellite DNA as faithful reflections of long-terminal repeat retroelement structure.","authors":"Sakura Hayashi,&nbsp;Yusuke Honda,&nbsp;Etsuko Kanesaki,&nbsp;Akihiko Koga","doi":"10.1139/gen-2022-0039","DOIUrl":"https://doi.org/10.1139/gen-2022-0039","url":null,"abstract":"<p><p>Long terminal repeat (LTR) retroelements, including endogenous retroviruses, are one of the origins of satellite DNAs. However, the vast majority of satellite DNAs originating from LTR retroelements consists of parts of the element. In addition, they frequently contain sequences unrelated to that element. Here we report a novel marsupial satellite DNA (named walbRep) that contains, and consists solely of, the entire sequence of an LTR retroelement (the <i>walb</i> element). As is common with LTR retroelements, <i>walb</i> copies exhibit length variation. We focused on the abundance of copies of a specific length (2.7 kb) in the genome of the red-necked wallaby. Cloning and analyses of long genomic DNA fragments revealed a satellite DNA in which the LTR sequence (0.4 kb) and the sequence of the internal region of a nonautonomous <i>walb</i> copy (2.3 kb) were repeated alternately. The junctions between these two components exhibited the same end-to-end arrangements as those in the <i>walb</i> element. This satellite organization could be accounted for by a simple formation model that includes slippage during chromosome pairing followed by homologous recombination but does not invoke any other types of rearrangements. We discuss the possible reasons why satellite DNAs having such structures are rarely found in mammals.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40584689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Enriched tandem repeats in chromosomal fusion points of Rineloricaria latirostris (Boulenger, 1900) (Siluriformes: Loricariidae). 在染色体融合点上富集串联重复序列(Boulenger, 1900)(蛭形目:蛭形螨科)。
IF 3.1 3区 生物学
Genome Pub Date : 2022-09-01 Epub Date: 2022-08-08 DOI: 10.1139/gen-2022-0043
Larissa Glugoski, Viviane Nogaroto, Geize Aparecida Deon, Matheus Azambuja, Orlando Moreira-Filho, Marcelo Ricardo Vicari
{"title":"Enriched tandem repeats in chromosomal fusion points of <i>Rineloricaria latirostris</i> (Boulenger, 1900) (Siluriformes: Loricariidae).","authors":"Larissa Glugoski,&nbsp;Viviane Nogaroto,&nbsp;Geize Aparecida Deon,&nbsp;Matheus Azambuja,&nbsp;Orlando Moreira-Filho,&nbsp;Marcelo Ricardo Vicari","doi":"10.1139/gen-2022-0043","DOIUrl":"https://doi.org/10.1139/gen-2022-0043","url":null,"abstract":"<p><p>Cytogenetic data showed the enrichment of repetitive DNAs in chromosomal rearrangement points between closely related species in armored catfishes. Still, few studies integrated cytogenetic and genomic data aiming to identify their prone-to-break DNA sites. Here, we aimed to obtain the repetitive fraction in <i>Rineloricaria latirostris</i> to recognize the microsatellite and homopolymers flanking the regions previously described as chromosomal fusion points. The results indicated that repetitive DNAs in <i>R. latirostris</i> are predominantly DNA transposons, and considering the microsatellite and homopolymers, A/T-rich expansions were the most abundant. The in situ localization demonstrated the A/T-rich repetitive sequences were scattered on the chromosomes, while A/G-rich microsatellite units were accumulated in some regions. The DNA transposon <i>hAT</i>, the 5S rDNA, and 45S rDNA (previously identified in Robertsonian fusion points in <i>R. latirostris</i>) were clusterized with some microsatellites, especially (CA)<i><sub>n</sub></i>, (GA)<i><sub>n</sub></i>, and poly-A, which were also enriched in regions of chromosomal fusions. Our findings demonstrated that repetitive sequences such as rDNAs, <i>hAT</i> transposons, and microsatellite units flank probable evolutionary breakpoint regions in <i>R. latirostris</i>. However, due to the sequence unit homologies in different chromosomal sites, these repeat DNAs only may facilitate chromosome fusion events in <i>R. latirostris</i> rather than working as a double-strand breakpoint site.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40595209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Analysis and evaluation of different sequencing depths from 5 to 20 million reads in shotgun metagenomic sequencing, with optimal minimum depth being recommended. 霰弹枪宏基因组测序中5 ~ 2000万reads不同测序深度的分析与评价,推荐最佳最小深度。
IF 3.1 3区 生物学
Genome Pub Date : 2022-09-01 Epub Date: 2022-09-06 DOI: 10.1139/gen-2021-0120
Jin Liu, Xiaokai Wang, Hailiang Xie, Qinghua Zhong, Yan Xia
{"title":"Analysis and evaluation of different sequencing depths from 5 to 20 million reads in shotgun metagenomic sequencing, with optimal minimum depth being recommended.","authors":"Jin Liu,&nbsp;Xiaokai Wang,&nbsp;Hailiang Xie,&nbsp;Qinghua Zhong,&nbsp;Yan Xia","doi":"10.1139/gen-2021-0120","DOIUrl":"https://doi.org/10.1139/gen-2021-0120","url":null,"abstract":"<p><p>Our study was to analyze and evaluate the impact of different shotgun metagenomic sequencing depths from 5 to 20 million in metagenome-wide association studies (MWASs), and to determine the optimal minimum sequencing depth. We included a set of 200 previously published gut microbial shotgun metagenomic sequencing data on obesity (100 obese vs. 100 non-obese). The reads with original sequencing depths >20 million were downsized into seven experimental groups with depths from 5 to 20 million (interval 2.5 million). Using both integrated gene cluster (IGC) and metagenomic phylogenetic analysis 2 (MetaPhlAn2), we obtained and analyzed the read matching rates, gene count, species richness and abundance, diversity, and clinical biomarkers of the experimental groups with the original depth as the control group. An additional set of 100 published data from a colorectal cancer (CRC) study was included for validation (50 CRC vs. 50 CRC-free). Our results showed that more genes and species were identified following the increase in sequencing depths. When it reached 15 million or higher, the species richness became more stable with changing rate of 5% or lower, and the species composition more stable with ICC intraclass correlation coefficient (ICC) higher than 0.75. In terms of species abundance, 81% and 97% of species showed significant differences in IGC and MetaPhlAn2 among all groups with <i>p</i> < 0.05. Diversity showed significant differences across all groups, with decreasing differences of diversity between the experimental and the control groups following the increase in sequencing depth. The area under a receiver operating characteristic curve, AUC, of the obesity classifier for running the obesity testing samples showed an increasing trend following the increase in sequencing depth (<i>τ</i> = 0.29). The validation results were consistent with the above results. Our study found that the higher the sequencing depth is, the more the microbial information in structure and composition it provides. We also found that when sequencing depth was 15 million or higher, we obtained more stable species compositions and disease classifiers with good performance. Therefore, we recommend 15 million as the optimal minimum sequencing depth for an MWAS.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40595207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Assessing population genetic structure of three New Zealand stream insects using mitochondrial and nuclear DNA markers. 利用线粒体和核DNA标记评估三种新西兰溪流昆虫的种群遗传结构。
IF 3.1 3区 生物学
Genome Pub Date : 2022-08-01 Epub Date: 2022-07-04 DOI: 10.1139/gen-2022-0021
Vanessa de Araujo Barbosa, S Elizabeth Graham, Brian J Smith, Ian D Hogg, Angela McGaughran
{"title":"Assessing population genetic structure of three New Zealand stream insects using mitochondrial and nuclear DNA markers.","authors":"Vanessa de Araujo Barbosa,&nbsp;S Elizabeth Graham,&nbsp;Brian J Smith,&nbsp;Ian D Hogg,&nbsp;Angela McGaughran","doi":"10.1139/gen-2022-0021","DOIUrl":"https://doi.org/10.1139/gen-2022-0021","url":null,"abstract":"<p><p>Assessing genetic differentiation among natural populations can aid understanding of dispersal patterns and connectivity among habitats. Several molecular markers have become increasingly popular in determining population genetic structure for this purpose. Here, we compared the resolution of mitochondrial cytochrome <i>c</i> oxidase subunit I (COI) and nuclear single nucleotide polymorphism (SNP) markers for detecting population structure among stream insects at small spatial scales. Individuals of three endemic taxa-<i>Coloburiscus humeralis</i> (Ephemeroptera), <i>Zelandobius confusus</i> (Plecoptera), and <i>Hydropsyche fimbriata</i> (Trichoptera)-were collected from forested streams that flow across open pasture in the North Island of New Zealand. Both COI and SNP data indicated limited population structure across the study area, and small differences observed among these species were likely related to their putative dispersal abilities. For example, fine-scale genetic differentiation between and among neighbouring stream populations for <i>H. fimbriata</i> suggests that gene flow, and hence dispersal, may be more limited for this species relative to the others. Based on the generally similar results provided by both types of markers, we suggest that either COI or SNP markers can provide suitable initial estimates of fine-scale population genetic differentiation in stream insects.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40470260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
The construction of a high-density consensus genetic map for soybean based on SNP markers derived from genotyping-by-sequencing. 基于基因分型测序(GBS) SNP标记的大豆高密度一致遗传图谱的构建
IF 3.1 3区 生物学
Genome Pub Date : 2022-08-01 Epub Date: 2022-06-03 DOI: 10.1139/gen-2021-0054
Manel Fallah, Martine Jean, Vincent-Thomas Boucher St-Amour, Louise O'Donoughue, François Belzile
{"title":"The construction of a high-density consensus genetic map for soybean based on SNP markers derived from genotyping-by-sequencing.","authors":"Manel Fallah, Martine Jean, Vincent-Thomas Boucher St-Amour, Louise O'Donoughue, François Belzile","doi":"10.1139/gen-2021-0054","DOIUrl":"10.1139/gen-2021-0054","url":null,"abstract":"<p><p>Genetic linkage maps are used to localize markers on the genome based on the recombination frequency. Most often, these maps are based on the segregation observed within a single biparental population of limited size (<i>n</i> < 300) where relatively few recombination events are sampled and in which some genomic regions are monomorphic because both parents carry the same alleles. Together, these two limitations affect both the resolution and extent of genome coverage of such maps. Consensus genetic maps overcome the limitations of individual genetic maps by merging the information from multiple segregating populations derived from a greater diversity of parental combinations, thus increasing the number of recombination events and reducing the number of monomorphic regions. The aim of this study was to construct a high-density consensus genetic map for single nucleotide polymorphism (SNP) markers obtained through a genotyping-by-sequencing (GBS) approach. Individual genetic maps were generated from six F<sub>4:5</sub> mapping populations (<i>n</i> = 278-365), totaling 1857 individuals. The six linkage maps were then merged to produce a consensus map comprising a total of 16 311 mapped SNPs that jointly cover 99.5% of the soybean genome with only two gaps larger than 10 cM. Compared to previous soybean consensus maps, it offers a more extensive and uniform coverage.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43436702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Patterns of genome size variation in caridean shrimps: new estimates for non-gambarelloides Synalpheus species. caridian对虾基因组大小变异模式:对非gambarelloides Synalpheus物种的新估计。
IF 3.1 3区 生物学
Genome Pub Date : 2022-08-01 Epub Date: 2022-08-02 DOI: 10.1139/gen-2022-0015
Isabela R R Moraes, Luis Miguel Pardo, Cristian Araya-Jaime, Milena Regina Wolf, George Shigueki Yasui, Jaiber J Solano-Iguaran, Graziela Gorete Romagnoli, Kaio Cesar Chaboli Alevi, Antonio Leão Castilho
{"title":"Patterns of genome size variation in caridean shrimps: new estimates for non-gambarelloides <i>Synalpheus</i> species.","authors":"Isabela R R Moraes,&nbsp;Luis Miguel Pardo,&nbsp;Cristian Araya-Jaime,&nbsp;Milena Regina Wolf,&nbsp;George Shigueki Yasui,&nbsp;Jaiber J Solano-Iguaran,&nbsp;Graziela Gorete Romagnoli,&nbsp;Kaio Cesar Chaboli Alevi,&nbsp;Antonio Leão Castilho","doi":"10.1139/gen-2022-0015","DOIUrl":"https://doi.org/10.1139/gen-2022-0015","url":null,"abstract":"<p><p>Genome size (GS) or DNA nuclear content is considered a useful index for making inferences about evolutionary models and life history in animals, including taxonomic, biogeographical, and ecological scenarios. However, patterns of GS variation and their causes in crustaceans are still poorly understood. This study aimed to describe the GS of five Neotropical <i>Synalpheus</i> non-gambarelloides shrimps (<i>S. apioceros, S. minus, S. brevicarpus, S. fritzmueller</i>, and <i>S. scaphoceris</i>) and compare the C-values of all Caridea infraorder in terms of geography and phylogenetics. All animals were sampled in the coast of São Paulo State, Brazil, and GS was assessed by flow cytometry analysis (FCA). The C-values ranged from 7.89 pg in <i>S. apioceros</i> to 12.24 pg in <i>S. scaphoceris</i>. Caridean shrimps had higher GS than other Decapoda crustaceans. The results reveal a tendency of obtaining larger genomes in species with direct development in <i>Synalpheus</i> shrimps. In addition, a tendency of positive biogeographical (latitudinal) correlation with Caridea infraorder was also observed. This study provides remarkable and new protocol for FCA (using gating strategy for the analysis), which led to the discovery of new information regarding GS of caridean shrimps, especially for Neotropical <i>Synalpheus</i>, which represents the second-largest group in the Caridea infraorder.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40594557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genome-wide investigation and expression analysis of the AP2/ERF family for selection of agarwood-related genes in Aquilaria sinensis (Lour.) Gilg. 沉香相关基因选择的AP2/ERF家族全基因组研究及表达分析Gilg。
IF 3.1 3区 生物学
Genome Pub Date : 2022-08-01 Epub Date: 2022-07-18 DOI: 10.1139/gen-2022-0003
Meng-Jun Xiao, Ya-Nan Feng, Pei-Wen Sun, Yan-Hong Xu, Mei Rong, Yang Liu, Jie-Mei Jiang, Cui-Cui Yu, Zhi-Hui Gao, Jian-He Wei
{"title":"Genome-wide investigation and expression analysis of the AP2/ERF family for selection of agarwood-related genes in <i>Aquilaria sinensis</i> (Lour.) Gilg.","authors":"Meng-Jun Xiao,&nbsp;Ya-Nan Feng,&nbsp;Pei-Wen Sun,&nbsp;Yan-Hong Xu,&nbsp;Mei Rong,&nbsp;Yang Liu,&nbsp;Jie-Mei Jiang,&nbsp;Cui-Cui Yu,&nbsp;Zhi-Hui Gao,&nbsp;Jian-He Wei","doi":"10.1139/gen-2022-0003","DOIUrl":"https://doi.org/10.1139/gen-2022-0003","url":null,"abstract":"<p><p><i>Aquilaria sinensis</i> is an important non-timber tree species for producing high-value agarwood, which is widely used as a traditional medicine and incense. Agarwood is the product of <i>Aquilaria</i> trees in response to injury and fungal infection. The APETALA2/ethylene responsive factor (<i>AP2/ERF</i>) transcription factors (TFs) play important roles in plant stress responses and metabolite biosynthesis. In this study, 119 <i>AsAP2/ERF</i> genes were identified from the <i>A. sinensis</i> genome and divided into ERF, AP2, RAV, and Soloist subfamilies. Their conserved motif, gene structure, chromosomal localization, and subcellular localization were characterized. A stress/defense-related ERF-associated amphiphilic repression (EAR) motif and an EDLL motif were identified. Moreover, 11 genes that were highly expressed in the agarwood layer in response to whole-tree agarwood induction technique (Agar-Wit) treatment were chosen, and their expression levels in response to methyl jasmonate (MeJA), salicylic acid (SA), or salt treatment were further analyzed using the quantitative real time PCR (qRT-PCR). Among the 11 genes, eight belonged to subgroup B-3. All 11 genes were significantly upregulated under salt treatment, while eight genes were significantly induced by both MeJA and SA. In addition, the gene clusters containing these upregulated genes on chromosomes were observed. The results obtained from this research not only provide useful information for understanding the functions of <i>AP2/ERF</i> genes in <i>A. sinensis</i> but also identify candidate genes and gene clusters to dissect their regulatory roles in agarwood formation for future research.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40602843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Genome organization of major tandem repeats and their specificity for heterochromatin of macro- and microchromosomes in Japanese quail. 日本鹌鹑主要串联重复序列的基因组结构及其对宏、微染色体异染色质的特异性。
IF 3.1 3区 生物学
Genome Pub Date : 2022-07-01 DOI: 10.1139/gen-2022-0012
Maria Kulak, Aleksey Komissarov, Valerie Fillon, Kseniya Tsukanova, Alsu Saifitdinova, Svetlana Galkina
{"title":"Genome organization of major tandem repeats and their specificity for heterochromatin of macro- and microchromosomes in Japanese quail.","authors":"Maria Kulak,&nbsp;Aleksey Komissarov,&nbsp;Valerie Fillon,&nbsp;Kseniya Tsukanova,&nbsp;Alsu Saifitdinova,&nbsp;Svetlana Galkina","doi":"10.1139/gen-2022-0012","DOIUrl":"https://doi.org/10.1139/gen-2022-0012","url":null,"abstract":"<p><p>Tandemly repeated DNAs form heterochromatic regions of chromosomes, including the vital centromeric chromatin. Despite the progress in new genomic technologies, tandem repeats remain poorly deciphered and need targeted analysis in the species of interest. The Japanese quail is one of the highest-producing poultry species as well as a model organism. Its genome differs by a noticeable accumulation of heterochromatin, which led to an increase by 1/7 compared to the chicken genome size. Prominent heterochromatin blocks occupy the short arms of acrocentric macrochromosomes and of microchromosomes. We have applied de novo repeat finder approach to unassembled raw reads of the Japanese quail genome. We identified the 20 most common tandem repeats with the abundance >1 Mb, which represent about 4.8% of the genome. We found that tandem repeat <i>Cjap</i>SAT primarily contributes to the centromeric regions of the macrochromosomes CJA1-8. <i>Cjap</i>31B together with previously characterized <i>Bgl</i>II makes up centromere regions of microchromosomes and W chromosome. Other repeats populate heterochromatin of microchromosomal short arms in unequal proportions, as revealed by fluorescence in situ hybridization. The <i>Cjap</i>84A, <i>Cjap</i>408A, and <i>Cjap</i>SAT repeat sequences show similarities to retrotransposon motifs. This suggests that retroelements may have played a crucial role in the distribution of repeats throughout the Japanese quail genome.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40552803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Comparative analysis reveals chromosome number reductions in the evolution of African bermudagrass (Cynodon transvaalensis Burtt-Davy). 比较分析揭示了非洲百慕大草(Cynodon transvaalensis Burtt-Davy)在进化过程中染色体数目的减少。
IF 3.1 3区 生物学
Genome Pub Date : 2022-06-01 Epub Date: 2022-07-19 DOI: 10.1139/gen-2021-0122
Shuhao Yu, Hongxu Dong, Tilin Fang, Yanqi Wu
{"title":"Comparative analysis reveals chromosome number reductions in the evolution of African bermudagrass (<i>Cynodon transvaalensis</i> Burtt-Davy).","authors":"Shuhao Yu,&nbsp;Hongxu Dong,&nbsp;Tilin Fang,&nbsp;Yanqi Wu","doi":"10.1139/gen-2021-0122","DOIUrl":"https://doi.org/10.1139/gen-2021-0122","url":null,"abstract":"<p><p>African bermudagrass (<i>Cynodon transvaalensis</i> Burtt-Davy) (2n = 2x = 18) belongs to the genus <i>Cynodon</i>, tribe Cynodonteae, subfamily Chloridoideae in the grass family Poaceae. The species is frequently crossed with common bermudagrass (<i>Cynodon</i> <i>dactylon</i> Pers.) in developing high-quality hybrid turf cultivars. Molecular resources for <i>C. transvaalensis</i> are scarce; thus, its genomic evolution is unknown. Recently, a linkage map consisting of 1278 markers provided a powerful tool for African bermudagrass genomic research. The objective of this study was to investigate chromosome number reduction events that resulted in the nine haploid chromosomes in this species. Tag sequences of mapped single nucleotide polymorphism markers in <i>C. transvaalensis</i> were compared against genome sequences of <i>Oropetium thomaeum</i> (L.f.) Trin. (2n = 2x = 20), a genomic model in the Cynodonteae tribe. The comparative genomic analyses revealed broad collinearity between the genomes of these two species. The analyses further revealed that two major interchromosomal rearrangements of the paleochromosome ρ12 (ρ1-ρ12-ρ1 and ρ6-ρ12-ρ6) resulted in nine chromosomes in the genome of <i>C. transvaalensis</i>. The findings provide novel information regarding the formation of the initial diploid species in the <i>Cynodon</i> genus.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40605308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Genome-wide association studies identified loci associated with both feed conversion ratio and residual feed intake in Yorkshire pigs. 全基因组关联研究确定了与约克郡猪饲料转化率和剩余采食量相关的位点。
IF 3.1 3区 生物学
Genome Pub Date : 2022-05-20 DOI: 10.1139/gen-2021-0105
Kai Wang, Shujie Wang, Xiang‐Fen Ji, Dong Chen, Qi Shen, Yang Yu, Wei-hang Xiao, Pingxian Wu, G. Tang
{"title":"Genome-wide association studies identified loci associated with both feed conversion ratio and residual feed intake in Yorkshire pigs.","authors":"Kai Wang, Shujie Wang, Xiang‐Fen Ji, Dong Chen, Qi Shen, Yang Yu, Wei-hang Xiao, Pingxian Wu, G. Tang","doi":"10.1139/gen-2021-0105","DOIUrl":"https://doi.org/10.1139/gen-2021-0105","url":null,"abstract":"Feed occupies a significant proportion in the production cost of pigs, and the feed efficiency (FE) in pigs are of utmost economic importance. Hence, the objective of this study is to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with FE related traits, including feed conversion ratio (FCR) and residual feed intake (RFI). A genome-wide association study (GWAS) was conducted for FCR and RFI in 169 Yorkshire pigs using whole-genome sequencing data. A total of 23 and 33 suggestive significant SNPs (P<1×10^(-6)) were detected for FCR and RFI, respectively. However, none of the SNPs achieved the genome-wide significance threshold (P<5×10^(-8)). Importantly, three common SNPs (SSC7:7987268, SSC13:42350250, and SSC13:42551718) were associated with both FCR and RFI. Additionally, the NEDD9 gene related to FCR and RFI traits was overlapped. This study detected novel SNPs on SSC7 and SSC13 common for FCR and RFI. These results provide new insights into the genetic mechanisms and candidate genes of FE-related traits in pigs.","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2022-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46111269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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