DNA Research最新文献_第5页

A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China. 染色体水平的基因组组装揭示了中国黄河流域柽柳的地方适应性。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-08-01 DOI: 10.1093/dnares/dsae021

Shuai Gong, Honghao Gan, Jianmin Chu, Zhaoshan Wang, Jia Sun

{"title":"A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China.","authors":"Shuai Gong, Honghao Gan, Jianmin Chu, Zhaoshan Wang, Jia Sun","doi":"10.1093/dnares/dsae021","DOIUrl":"10.1093/dnares/dsae021","url":null,"abstract":"Tamarix austromongolica is endemic to the Yellow River Basin and has adapted to diverse ecological settings in the region, including the arid areas of northwestern China and the saline soil regions of the Yellow River Delta. However, the genetic basis of its local adaptation remains unclear. We report a chromosome-level assembly of the T. austromongolica genome based on PacBio high-fidelity sequencing and Hi-C technology. The 12 pseudochromosomes cover 98.44% of the 1.32 Gb assembly, with a contig N50 of 52.57 Mb and a BUSCO score of 98.2%. The genome comprises 913.6 Mb (68.83%) of repetitive sequences and 22,374 protein-coding genes. Genome evolution analyses suggest that genes under positive selection and significantly expanded gene families have facilitated T. austromongolica's adaptability to diverse environmental factors and high resistance to diseases. Using genotyping-by-sequencing, we conducted population structure and selection analyses of 114 samples from 15 sites. Two genetic groups were identified, and 114 and 289 candidate genes were assigned to the populations of the northwestern and eastern parts of the Yellow River, respectively. Furthermore, we discovered numerous candidate genes associated with high-altitude adaptability and salt tolerance. This research provides valuable genomic resources for the evolutionary study and genetic breeding of tamarisk.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11306577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A high-quality genome assembly reveals adaptations underlying glossy, wax-coated leaves in the heat-tolerant wild raspberry Rubus leucanthus. 高质量的基因组组装揭示了耐热野生树莓 Rubus leucanthus 叶片光泽和蜡质涂层背后的适应性。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-08-01 DOI: 10.1093/dnares/dsae024

Wei Wu, Longyuan Wang, Weicheng Huang, Xianzhi Zhang, Yongquan Li, Wei Guo

{"title":"A high-quality genome assembly reveals adaptations underlying glossy, wax-coated leaves in the heat-tolerant wild raspberry Rubus leucanthus.","authors":"Wei Wu, Longyuan Wang, Weicheng Huang, Xianzhi Zhang, Yongquan Li, Wei Guo","doi":"10.1093/dnares/dsae024","DOIUrl":"10.1093/dnares/dsae024","url":null,"abstract":"With glossy, wax-coated leaves, Rubus leucanthus is one of the few heat-tolerant wild raspberry trees. To ascertain the underlying mechanism of heat tolerance, we generated a high-quality genome assembly with a genome size of 230.9 Mb and 24,918 protein-coding genes. Significantly expanded gene families were enriched in the flavonoid biosynthesis pathway and the circadian rhythm-plant pathway, enabling survival in subtropical areas by accumulating protective flavonoids and modifying photoperiodic responses. In contrast, plant-pathogen interaction and MAPK signaling involved in response to pathogens were significantly contracted. The well-known heat response elements (HSP70, HSP90, and HSFs) were reduced in R. leucanthus compared to two other heat-intolerant species, R. chingii and R. occidentalis, with transcriptome profiles further demonstrating their dispensable roles in heat stress response. At the same time, three significantly positively selected genes in the pathway of cuticular wax biosynthesis were identified, and may contribute to the glossy, wax-coated leaves of R. leucanthus. The thick, leathery, waxy leaves protect R. leucanthus against pathogens and herbivores, supported by the reduced R gene repertoire in R. leucanthus (355) compared to R. chingii (376) and R. occidentalis (449). Our study provides some insights into adaptive divergence between R. leucanthus and other raspberry species on heat tolerance.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11347754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-level genome assembly and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758). 黑海胆 Arbacia lixula (Linnaeus, 1758) 染色体级基因组组装与注释。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-08-01 DOI: 10.1093/dnares/dsae020

Carles Galià-Camps, Carlos Carreras, Marta Pascual, Carola Greve, Tilman Schell, Xavier Turon, Creu Palacín, Rocío Pérez-Portela, Owen S Wangensteen, Cinta Pegueroles

{"title":"Chromosome-level genome assembly and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758).","authors":"Carles Galià-Camps, Carlos Carreras, Marta Pascual, Carola Greve, Tilman Schell, Xavier Turon, Creu Palacín, Rocío Pérez-Portela, Owen S Wangensteen, Cinta Pegueroles","doi":"10.1093/dnares/dsae020","DOIUrl":"10.1093/dnares/dsae020","url":null,"abstract":"The black sea urchin (Arbacia lixula) is a keystone species inhabiting the coastal shallow waters of the Mediterranean Sea, which is a key driver of littoral communities' structure. Here, we present the first genome assembly and annotation of this species, standing as the first Arbacioida genome, including both nuclear and mitochondrial genomes. To obtain a chromosome-level assembly, we used a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). In addition, we generated a high-quality nuclear annotation of both coding and non-coding genes, by using published RNA-Seq data from several individuals of A. lixula and gene models from closely related species. The nuclear genome assembly has a total span of 607.91 Mb, being consistent with its experimentally estimated genome size. The assembly contains 22 chromosome-scale scaffolds (96.52% of the total length), which coincides with its known karyotype. A total of 72,767 transcripts were predicted from the nuclear genome, 24,171 coding, and 48,596 non-coding that included lncRNA, snoRNA, and tRNAs. The circularized mitochondrial genome had 15,740 bp comprising 13 protein-coding genes, 2 rRNA, and 22 tRNA. This reference genome will enhance ongoing A. lixula studies and benefit the wider sea urchin scientific community.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11310861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus. 高完整性葛根变种叶基因组和种群分析揭示了葛根属的遗传多样性。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-06-01 DOI: 10.1093/dnares/dsae017

Xuan-Zhao Huang, Shao-Da Gong, Xiao-Hong Shang, Min Gao, Bo-Yuan Zhao, Liang Xiao, Ping-Li Shi, Wen-Dan Zeng, Sheng Cao, Zheng-Dan Wu, Jia-Ming Song, Ling-Ling Chen, Hua-Bing Yan

{"title":"High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus.","authors":"Xuan-Zhao Huang, Shao-Da Gong, Xiao-Hong Shang, Min Gao, Bo-Yuan Zhao, Liang Xiao, Ping-Li Shi, Wen-Dan Zeng, Sheng Cao, Zheng-Dan Wu, Jia-Ming Song, Ling-Ling Chen, Hua-Bing Yan","doi":"10.1093/dnares/dsae017","DOIUrl":"10.1093/dnares/dsae017","url":null,"abstract":"Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11149379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea. 揭示 DNA 甲基化景观，解读鹰嘴豆表型多样性的进化足迹。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-06-01 DOI: 10.1093/dnares/dsae013

Anurag Daware, Jitendra K Mohanty, Laxmi Narnoliya, Akansha Singh, Deepanshi Rathore, Virevol Thakro, Aleena Francis, Nagendra Pratap Singh, Philip Francis, Shailesh Tripathi, Debasis Chattopadhyay, Swarup K Parida

{"title":"Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea.","authors":"Anurag Daware, Jitendra K Mohanty, Laxmi Narnoliya, Akansha Singh, Deepanshi Rathore, Virevol Thakro, Aleena Francis, Nagendra Pratap Singh, Philip Francis, Shailesh Tripathi, Debasis Chattopadhyay, Swarup K Parida","doi":"10.1093/dnares/dsae013","DOIUrl":"10.1093/dnares/dsae013","url":null,"abstract":"Genetic diversity and environmental factors are long believed to be the dominant contributors to phenotypic diversity in crop plants. However, it has been recently established that, besides genetic variation, epigenetic variation, especially variation in DNA methylation, plays a significant role in determining phenotypic diversity in crop plants. Therefore, assessing DNA methylation diversity in crop plants becomes vital, especially in the case of crops like chickpea, which has a narrow genetic base. Thus, in the present study, we employed whole-genome bisulfite sequencing to assess DNA methylation diversity in wild and cultivated (desi and kabuli) chickpea. This revealed extensive DNA methylation diversity in both wild and cultivated chickpea. Interestingly, the methylation diversity was found to be significantly higher than genetic diversity, suggesting its potential role in providing vital phenotypic diversity for the evolution and domestication of the Cicer gene pool. The phylogeny based on DNA methylation variation also indicates a potential complementary role of DNA methylation variation in addition to DNA sequence variation in shaping chickpea evolution. Besides, the study also identified diverse epi-alleles of many previously known genes of agronomic importance. The Cicer MethVarMap database developed in this study enables researchers to readily visualize methylation variation within the genes and genomic regions of their interest (http://223.31.159.7/cicer/public/). Therefore, epigenetic variation like DNA methylation variation can potentially explain the paradox of high phenotypic diversity despite the narrow genetic base in chickpea and can potentially be employed for crop improvement.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11149376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of transcriptome changes in saline stress adaptation on Leuciscus merzbacheri using PacBio Iso-Seq and RNA-Seq. 利用 PacBio Iso-Seq 和 RNA-Seq 分析梅氏海鯈鱼盐碱胁迫适应过程中转录组变化的特征。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-06-01 DOI: 10.1093/dnares/dsae019

Dan Yu, Min Zhou, Wenjun Chen, Zufa Ding, Cheng Wang, Yuting Qian, Yang Liu, Shunping He, Liandong Yang

{"title":"Characterization of transcriptome changes in saline stress adaptation on Leuciscus merzbacheri using PacBio Iso-Seq and RNA-Seq.","authors":"Dan Yu, Min Zhou, Wenjun Chen, Zufa Ding, Cheng Wang, Yuting Qian, Yang Liu, Shunping He, Liandong Yang","doi":"10.1093/dnares/dsae019","DOIUrl":"10.1093/dnares/dsae019","url":null,"abstract":"Leuciscus merzbacheri is a native fish species found exclusively in the Junggar Basin in Xinjiang. It exhibits remarkable adaptability, thriving in varying water conditions such as the saline waters, the semi-saline water, and the freshwater. Despite its significant economic and ecological value, the underlying mechanisms of its remarkable salinity tolerance remain elusive. Our study marks the first time the full-length transcriptome of L. merzbacheri has been reported, utilizing RNA-Seq and PacBio Iso-Seq technologies. We found that the average length of the full-length transcriptome is 1,780 bp, with an N50 length of 2,358 bp. We collected RNA-Seq data from gill, liver, and kidney tissues of L. merzbacheri from both saline water and freshwater environments and conducted comparative analyses across these tissues. Further analysis revealed significant enrichment in several key functional gene categories and signalling pathways related to stress response and environmental adaptation. The findings provide a valuable genetic resource for further investigation into saline-responsive candidate genes, which will deepen our understanding of teleost adaptation to extreme environmental stress. This knowledge is crucial for the future breeding and conservation of native fish species.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11161863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

High-quality chromosome-level genome assembly of the Northern Pacific sea star Asterias amurensis. 北太平洋海星 Asterias amurensis 的高质量染色体级基因组组装。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-04-01 DOI: 10.1093/dnares/dsae007

Zhichao Huang, Qi Liu, Xiaoqi Zeng, Gang Ni

{"title":"High-quality chromosome-level genome assembly of the Northern Pacific sea star Asterias amurensis.","authors":"Zhichao Huang, Qi Liu, Xiaoqi Zeng, Gang Ni","doi":"10.1093/dnares/dsae007","DOIUrl":"10.1093/dnares/dsae007","url":null,"abstract":"Asterias amurensis, a starfish species that is native to countries such as China and Japan, as well as non-native regions like Australia, has raised serious concerns in terms of its impact on ecology and economy. To gain a better understanding of its population genomics and dynamics, we successfully assembled a high-quality chromosome-level genome of A. amurensis using PacBio and Hi-C sequencing technologies. A total of 87 scaffolds assembly with contig N50 length of 10.85 Mb and scaffold N50 length of 23.34 Mb were obtained, with over 98.80% (0.48 Gb) of them anchored to 22 pseudochromosomes. We predicted 16,673 protein-coding genes, 95.19% of which were functionally annotated. Our phylogenetic analysis revealed that A. amurensis and Asterias rubens formed a clade, and their divergence time was estimated ~ 28 million years ago (Mya). The significantly enriched pathways and Gene Ontology terms related to the amplified gene family were mainly associated with immune response and energy metabolism, suggesting that these factors might have contributed to the adaptability of A. amurensis to its environment. This study provides valuable genomic resources for comprehending the genetics, dynamics, and evolution of A. amurensis, especially when population outbreaks or invasions occur.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139984453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome assembly of Genji firefly (Nipponoluciola cruciata) reveals novel luciferase-like luminescent proteins without peroxisome targeting signal. 元氏萤火虫（Nipponoluciola cruciata）基因组组装揭示了新型荧光素酶样发光蛋白，但没有过氧化物酶体靶向信号。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-04-01 DOI: 10.1093/dnares/dsae006

Kentaro Fukuta, Dai-Ichiro Kato, Juri Maeda, Atsuhiro Tsuruta, Hirobumi Suzuki, Yukio Nagano, Hisao Tsukamoto, Kazuki Niwa, Makoto Terauchi, Atsushi Toyoda, Asao Fujiyama, Hideki Noguchi

{"title":"Genome assembly of Genji firefly (Nipponoluciola cruciata) reveals novel luciferase-like luminescent proteins without peroxisome targeting signal.","authors":"Kentaro Fukuta, Dai-Ichiro Kato, Juri Maeda, Atsuhiro Tsuruta, Hirobumi Suzuki, Yukio Nagano, Hisao Tsukamoto, Kazuki Niwa, Makoto Terauchi, Atsushi Toyoda, Asao Fujiyama, Hideki Noguchi","doi":"10.1093/dnares/dsae006","DOIUrl":"10.1093/dnares/dsae006","url":null,"abstract":"The Genji firefly, Nipponoluciola cruciata, is an aquatic firefly endemic to Japan, inhabiting a wide area of the Japanese archipelago. The luminescence of fireflies is a scientifically interesting phenomenon, and many studies have evaluated this species in Japan. In this study, we sequenced the whole genome of male N. cruciata and constructed a high-quality genome assembly of 662 Mb with a BUSCO completeness of 99.1% in the genome mode. Using the detected set of 15,169 protein-coding genes, the genomic structures and genetic background of luminescence-related genes were also investigated. We found four new firefly luciferase-like genes in the genome. The highest bioluminescent activity was observed for LLa2, which originated from ancestral PDGY, a mitochondrial acyl-CoA synthetase. A thioesterase candidate, NcruACOT1, which is involved in d-luciferin biosynthesis, was expressed in the lantern. Two opsins were also detected and the absorption wavelength of the UV-type opsin candidate shifted from UV to blue. These findings provide an important resource for unravelling the adaptive evolution of fireflies in terms of luminescence and vision.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"31 2","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140144533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology. 太平洋秋刀鱼基因组的染色体 DNA 序列：渔业科学和比较生物学的多功能资源。

IF 3.9 2区生物学

DNA Research Pub Date : 2024-04-01 DOI: 10.1093/dnares/dsae004

Mana Sato, Kazuya Fukuda, Mitsutaka Kadota, Hatsune Makino-Itou, Kaori Tatsumi, Shinya Yamauchi, Shigehiro Kuraku

{"title":"Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology.","authors":"Mana Sato, Kazuya Fukuda, Mitsutaka Kadota, Hatsune Makino-Itou, Kaori Tatsumi, Shinya Yamauchi, Shigehiro Kuraku","doi":"10.1093/dnares/dsae004","DOIUrl":"10.1093/dnares/dsae004","url":null,"abstract":"Pacific saury (Cololabis saira) is a commercially important small pelagic fish species in Asia. In this study, we conducted the first-ever whole genome sequencing of this species, with single molecule, real-time (SMRT) sequencing technology. The obtained high-fidelity (HiFi) long-read sequence data, which amount to ~30-folds of its haploid genome size that was measured with quantitative PCR (1.17 Gb), were assembled into contigs. Scaffolding with Hi-C reads yielded a whole genome assembly containing 24 chromosome-scale sequences, with a scaffold N50 length of 47.7 Mb. Screening of repetitive elements including telomeric repeats was performed to characterize possible factors that need to be resolved towards 'telomere-to-telomere' sequencing. The larger genome size than in medaka, a close relative in Beloniformes, is at least partly explained by larger repetitive element quantity, which is reflected in more abundant tRNAs, in the Pacific saury genome. Protein-coding regions were predicted using transcriptome data, which resulted in 22,274 components. Retrieval of Pacific saury homologs of aquaporin (AQP) genes known from other teleost fishes validated high completeness and continuity of the genome assembly. These resources are available at https://treethinkers.nig.ac.jp/saira/ and will assist various molecular-level studies in fishery science and comparative biology.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":"31 2","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140061158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig. 基于转座子介导的猪基因组多态性的种群遗传分析。

IF 4.1 2区生物学

DNA Research Pub Date : 2024-04-01 DOI: 10.1093/dnares/dsae008

Wencheng Zong, Runze Zhao, Xiaoyan Wang, Chenyu Zhou, Jinbu Wang, Cai Chen, Naiqi Niu, Yao Zheng, Li Chen, Xin Liu, Xinhua Hou, Fuping Zhao, Ligang Wang, Lixian Wang, Chengyi Song, Longchao Zhang

{"title":"Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig.","authors":"Wencheng Zong, Runze Zhao, Xiaoyan Wang, Chenyu Zhou, Jinbu Wang, Cai Chen, Naiqi Niu, Yao Zheng, Li Chen, Xin Liu, Xinhua Hou, Fuping Zhao, Ligang Wang, Lixian Wang, Chengyi Song, Longchao Zhang","doi":"10.1093/dnares/dsae008","DOIUrl":"10.1093/dnares/dsae008","url":null,"abstract":"Transposable elements (TEs) mobility is capable of generating a large number of structural variants (SVs), which can have considerable potential as molecular markers for genetic analysis and molecular breeding in livestock. Our results showed that the pig genome contains mainly TE-SVs generated by short interspersed nuclear elements (51,873/76.49%), followed by long interspersed nuclear elements (11,131/16.41%), and more than 84% of the common TE-SVs (Minor allele frequency, MAF > 0.10) were validated to be polymorphic. Subsequently, we utilized the identified TE-SVs to gain insights into the population structure, resulting in clear differentiation among the three pig groups and facilitating the identification of relationships within Chinese local pig breeds. In addition, we investigated the frequencies of TEs in the gene coding regions of different pig groups and annotated the respective TE types, related genes, and functional pathways. Through genome-wide comparisons of Large White pigs and Chinese local pigs utilizing the Beijing Black pigs, we identified TE-mediated SVs associated with quantitative trait loci and observed that they were mainly involved in carcass traits and meat quality traits. Lastly, we present the first documented evidence of TE transduction in the pig genome.","PeriodicalId":51014,"journal":{"name":"DNA Research","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140050934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0