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Utilitarian selection signatures co-localized with copy number variation regions in Indian goat breeds revealed through whole-genome re-sequencing. 通过全基因组重测序发现印度山羊品种的功利选择特征与拷贝数变异区共定位。
IF 1.7 3区 生物学
Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0029
Nidhi Sukhija, Indrajit Ganguly, K K Kanaka, S P Dixit, Sanjeev Singh, Avnish Bhatia, Rangasai Chandra Goli, Pallavi Rathi
{"title":"Utilitarian selection signatures co-localized with copy number variation regions in Indian goat breeds revealed through whole-genome re-sequencing.","authors":"Nidhi Sukhija, Indrajit Ganguly, K K Kanaka, S P Dixit, Sanjeev Singh, Avnish Bhatia, Rangasai Chandra Goli, Pallavi Rathi","doi":"10.1139/gen-2025-0029","DOIUrl":"10.1139/gen-2025-0029","url":null,"abstract":"<p><p>This study investigates the selection signatures of 11 Indigenous goat breeds from diverse eco-topographies of India, using whole-genome re-sequencing data from 103 individuals. We identified population-wide copy number variation regions (as well as selection signatures through a variance-stabilizing transformation approach for utility traits. A total of 32 711 polymorphic sites were analyzed, revealing 327 significant and 32 highly significant signatures under selection. Key genes identified in selection signatures include GHR, PLAG1, and MTOR, which play crucial roles in growth, development, and reproductive traits across different utility groups. Notable reproduction-related genes such as ITPR3, ESRRG, and SOX6 were found to be associated with fertility, hormone regulation, and reproductive system. Network analysis revealed ESR1 as a central hub gene forming significant interactions with RUNX2, HDAC2, and BCL2, indicating its vital role in muscle development and metabolism. The MTOR signaling pathway emerged as another crucial hub, connecting with DEPDC5 and SESN1, suggesting its importance in nutrient sensing and metabolic regulation for production traits. Gene ontology analysis of the selection signatures revealed pathways for functional categories between meat, milk, and fiber-producing breeds, reflecting the genetic architecture underlying their specialized phenotypes. Identified selection signatures and hub genes can be used in marker-assisted and genomic selection to improve growth, reproduction, and adaptability in indigenous goats, aiding precision breeding and conservation programs.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145307740","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
The mitochondrial genome of pequi tree (Caryocar brasiliense Cambess.): genome structure, gene transfers, and evolutionary insights within Malpighiales. pequi树(Caryocar brasiliense Cambess.)的线粒体基因组:基因组结构、基因转移和马尔皮亚目动物的进化见解。
IF 1.9 3区 生物学
Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0097
Larissa R Carvalho, Leonardo C J Corvalán, Renata O Dias, Ramilla S Braga-Ferreira, Cintia P Targueta, José Alexandre F Diniz-Filho, Mariana P C Telles, Rhewter Nunes
{"title":"The mitochondrial genome of pequi tree (<i>Caryocar brasiliense</i> Cambess.): genome structure, gene transfers, and evolutionary insights within Malpighiales.","authors":"Larissa R Carvalho, Leonardo C J Corvalán, Renata O Dias, Ramilla S Braga-Ferreira, Cintia P Targueta, José Alexandre F Diniz-Filho, Mariana P C Telles, Rhewter Nunes","doi":"10.1139/gen-2025-0097","DOIUrl":"10.1139/gen-2025-0097","url":null,"abstract":"<p><p>The complete mitochondrial genome of <i>Caryocar brasiliense</i> (Caryocaraceae), an ecologically and economically important species native to the Brazilian savannas, was assembled and annotated. Using a hybrid assembly approach combining Oxford Nanopore and Illumina sequencing data, we assembled a 533 641 bp bipartite mitogenome organized into two circular chromosomes. A high density of dispersed repeats and simple sequence repeats was detected, along with extensive DNA transfers from the chloroplast and nuclear genomes (MTPTs and NUMTs). The variation of mitogenome size is positively correlated with the number of dispersed repeats (<i>R</i><sup>2</sup> = 0.88). Genome annotation revealed 74 protein-coding genes, including sequences derived from both mitochondrial and chloroplast origins, as well as 376 predicted RNA editing sites, particularly concentrated in energy metabolism genes such as <i>ccm</i> and <i>nad</i> gene family. Comparative analysis across 10 Malpighiales species identified conserved core mitochondrial genes and revealed topological differences between mitochondrial and plastid phylogenies. These findings offer new insights into the structural and evolutionary dynamics of angiosperm mitochondrial genomes and provide a foundational resource for future genetic, evolutionary, and conservation studies in <i>Caryocar brasiliense</i> and related taxa.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-14"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147941160","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
Classical and molecular cytogenetics of Ponerinae ants reveal evolutionary and taxonomic insights. 蚂蚁的经典和分子细胞遗传学揭示了进化和分类学的见解。
IF 1.9 3区 生物学
Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0056
Emilly Camila Soares Nobre, Gisele Amaro Teixeira, Linda Inês Silveira, Natália Martins Travenzoli, Luísa Antônia Campos Barros, Hilton Jeferson Alves Cardoso de Aguiar
{"title":"Classical and molecular cytogenetics of Ponerinae ants reveal evolutionary and taxonomic insights.","authors":"Emilly Camila Soares Nobre, Gisele Amaro Teixeira, Linda Inês Silveira, Natália Martins Travenzoli, Luísa Antônia Campos Barros, Hilton Jeferson Alves Cardoso de Aguiar","doi":"10.1139/gen-2025-0056","DOIUrl":"10.1139/gen-2025-0056","url":null,"abstract":"<p><p>Eleven species of Ponerinae ants belonging to six distinct genera from the Amazon and Atlantic rainforests were characterized by karyotype, distribution of ribosomal genes, microsatellites (GA)<sub><i>n</i></sub>, and telomeric sequences (TTAGG)<sub><i>n</i></sub>. This is the first study mapping microsatellites in Ponerinae ants. The karyotypes ranged from 2<i>n</i> = 12 to 2<i>n</i> = 94. Colonies of <i>Neoponera verenae</i> from the Amazon (<i>n</i> = 31) and Atlantic (2<i>n</i> = 40) rainforests reinforce the hypothesis of a species complex within this taxon. <i>Neoponera globularia</i> workers had a 2<i>n</i> = 21 karyotype, including an unpaired, large metacentric chromosome. <i>Neoponera unidentata</i> workers had 2<i>n</i> = 12 chromosomes, all metacentric, or 2<i>n</i> = 13 chromosomes, with two acrocentric and one unpaired metacentric chromosome. The rearrangements involved are discussed using telomeric (TTAGG)<sub><i>n</i></sub> data. All the analyzed species had a single pair of rDNA clusters mostly located in the pericentromeric region. The distribution of (GA)<sub><i>n</i></sub> microsatellites contrasted with that of AT-rich chromatin and supported the occurrence of chromosome fissions and the subsequent expansion of constitutive heterochromatin in Ponerinae, in addition to inversions in some species. The chromosomal rearrangements discussed herein contribute to our understanding of the mechanisms underlying the karyotypic evolution of Ponerinae. This study underscores the importance of cytogenetics in unraveling the taxonomic characteristics of complex groups.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-16"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289578","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
Two satellite repeats reveal B chromosome structural diversity in Atractylodes lancea. 两个卫星重复序列揭示了苍术B染色体结构的多样性。
IF 1.9 3区 生物学
Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0025
Kazuya Hara, Takahiro Tsusaka, Miki Sakurai, Kenta Shirasawa, Sachiko Isobe, Shinji Kikuchi
{"title":"Two satellite repeats reveal B chromosome structural diversity in <i>Atractylodes lancea</i>.","authors":"Kazuya Hara, Takahiro Tsusaka, Miki Sakurai, Kenta Shirasawa, Sachiko Isobe, Shinji Kikuchi","doi":"10.1139/gen-2026-0025","DOIUrl":"10.1139/gen-2026-0025","url":null,"abstract":"<p><p><i>Atractylodes lancea</i> in the family Asteraceae is an important plant in traditional herbal medicine. Although its genome has been reported, this species harbors B chromosomes whose DNA composition and biological significance remain largely unexplored. Here, we dissect the origin, structure, and diversification of <i>A. lancea</i> B chromosomes, using an integrated genomic and cytogenetic approach. Illumina sequencing of bulk samples and RepeatExplorer2 analysis identified two satellite repeats as major components of B chromosomes: CL2, a centromeric and pericentromeric repeat shared with A chromosomes, and CL47/59, a B chromosome-specific repeat localized to the interstitial region of B chromosomes. Fluorescence in situ hybridization uncovered striking variation among B chromosomes in repeat distribution, as well as in length and the arm ratio. CL47/59 abundance was positively correlated with B chromosome length, implicating its amplification during B chromosome enlargement. Integrating these genomic and cytological observations, we propose a model for B chromosome diversification in <i>A. lancea</i>, involving a pericentric inversion and the differential accumulation of CL2 and CL47/59 repeats.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-10"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148381988","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
CRISPR-Cas9-induced genetic mosaicism in three species of the microcrustacean Daphnia. crispr - cas9诱导的三种小甲壳动物水蚤的遗传镶嵌现象。
IF 1.9 3区 生物学
Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0049
Sen Xu, Swatantra Neupane, Li Wang
{"title":"CRISPR-Cas9-induced genetic mosaicism in three species of the microcrustacean <i>Daphnia</i>.","authors":"Sen Xu, Swatantra Neupane, Li Wang","doi":"10.1139/gen-2026-0049","DOIUrl":"10.1139/gen-2026-0049","url":null,"abstract":"<p><p>Genetic mosaicism can arise from in vivo CRISPR-Cas9 gene editing, especially in the embryos. This study evaluates the extent of genetic mosaicism resulted from CRISPR-Cas9-mediated knockout for 11 genes in the freshwater microcrustacean <i>Daphnia magna, Daphnia pulex</i>, and <i>Daphnia sinensis</i>. Based on extensive genotyping data of the asexually produced progenies of successfully edited females, we find strong evidence of mosaicism in 9 of these genes. The genotyping data also suggest that the gene editing activity can take place as early as the one-cell embryo stage and extends into the 32-cell and later stages. This study establishes genetic mosaicism as an important feature of Cas9-mediated gene editing in <i>Daphnia</i>.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-7"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148792293","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
DNA barcoding of the Amazon Continental Shelf ichthyoplankton: fish larvae assemblages inside and outside of the Amazon River plume. 亚马逊大陆架浮游鱼的DNA条形码:亚马逊河羽流内外的鱼苗组合。
IF 1.9 3区 生物学
Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0015
Jéssica Dos Santos Lima Pantoja, Lucas da Conceição Corrêa, Xiomara Franchesca García Díaz, Nuno Filipe Alves Correia de Melo, Igor Guerreiro Hamoy, Paula Nepomuceno Campos, Jean-Dominique Durand, André Luiz Alves de Sá
{"title":"DNA barcoding of the Amazon Continental Shelf ichthyoplankton: fish larvae assemblages inside and outside of the Amazon River plume.","authors":"Jéssica Dos Santos Lima Pantoja, Lucas da Conceição Corrêa, Xiomara Franchesca García Díaz, Nuno Filipe Alves Correia de Melo, Igor Guerreiro Hamoy, Paula Nepomuceno Campos, Jean-Dominique Durand, André Luiz Alves de Sá","doi":"10.1139/gen-2026-0015","DOIUrl":"10.1139/gen-2026-0015","url":null,"abstract":"<p><p>The Amazon River plume (ARP) impacts the Amazon Continental Shelf's (ACS) marine ecosystem, but its effect on fish larvae remains uninvestigated. To investigate the influence of the ARP on the ichthyoplankton community, MIDI Multinet net integrative tows were carried in the ACS (September 2021) and samples were identified and separated into morphotypes for molecular analysis. Morphological assessment of 343 fish larvae initially suggested 30 families, but subsequent DNA barcoding revealed a 42% discrepancy, highlighting the limitations of traditional taxonomy for larvae identification. Eighty-three fish larvae, representatives of identified morphotypes were successfully assigned to 58 Barcode Index Numbers, including sequences new to global databases and possibly five new occurrences in the region. The assemblage displayed a heterogeneous mix of neritic, oceanic, and estuarine taxa. However, no clear pattern emerged between species life-history traits and their distribution across the plume-generated hydrographic habitats. Although species composition varied across the plume's influence gradient, our sampling design cannot identify the underlying environmental drivers, underscoring the need for broader seasonal and spatial surveys in the region. These findings reveal the complexity of the ACS ecosystem and demonstrate the necessity of integrating molecular tools to accurately characterize biodiversity gaps and support conservation strategies in this dynamic region.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535798","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
Identification and functional validation of key enzymes related to polysaccharide biosynthesis in Platycodon grandiflorus. 桔梗多糖生物合成关键酶的鉴定及功能验证。
IF 1.9 3区 生物学
Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0086
Hui Wang, Sijia Wang, Hanwen Yu, Xiao Liang, Liangping Zha, Shuangying Gui
{"title":"Identification and functional validation of key enzymes related to polysaccharide biosynthesis in <i>Platycodon grandiflorus</i>.","authors":"Hui Wang, Sijia Wang, Hanwen Yu, Xiao Liang, Liangping Zha, Shuangying Gui","doi":"10.1139/gen-2025-0086","DOIUrl":"10.1139/gen-2025-0086","url":null,"abstract":"<p><p><i>Platycodon grandiflorus</i> (Jacq.) A. DC., a herbaceous plant belonging to the Campanulaceae family, is recognized for its substantial medicinal properties, attributed to its rich composition of bioactive compounds, including polysaccharides, saponins, and flavonoids. The polysaccharide components have been shown to exhibit significant anti-obesity effects. However, there is a notable lack of research on the biosynthesis of polysaccharides in <i>P. grandiflorus</i>. This study aimed to identify and functionally validate key enzymes involved in the polysaccharide biosynthetic pathway of <i>P. grandiflorus</i>. Based on transcriptomic data, the researchers identified four genes associated with the polysaccharide biosynthetic pathway in <i>P. grandiflorus</i>, specifically including one phosphomannose isomerase gene (<i>PgPMI</i>), one phosphoglucose isomerase gene (<i>PgGPI1</i>), and two phosphomannose mutase genes (<i>PgPMM1</i> and <i>PgPMM2</i>). The enzymatic activity of genes was verified in <i>Escherichia coli</i>, demonstrating that the recombinant <i>PgPMI</i> protein catalyzes the interconversion of mannose-6-phosphate and fructose-6-phosphate. Additionally, the recombinant <i>PgPMM1</i> and <i>PgPMM2</i> proteins were shown to catalyze the interconversion of mannose-1-phosphate and mannose-6-phosphate, while the recombinant <i>PgGPI1</i> protein is capable of catalyzing the conversion of glucose-6-phosphate to fructose-6-phosphate. This study enhances knowledge of the polysaccharide biosynthetic pathway and underpins subsequent molecular research on polysaccharide metabolism and related physiology.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-11"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146029407","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
Sex and genetic variation interact to modify the response of Drosophila melanogaster to metal stress. 性别和遗传变异相互作用,改变果蝇对金属应激的反应。
IF 1.9 3区 生物学
Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0099
Allie K Hutchings, Mitchell R Slobodian, Joshua W R Keeping, Jesse D Petahtegoose, Athena L Wallis, Thomas J S Merritt
{"title":"Sex and genetic variation interact to modify the response of <i>Drosophila melanogaster</i> to metal stress.","authors":"Allie K Hutchings, Mitchell R Slobodian, Joshua W R Keeping, Jesse D Petahtegoose, Athena L Wallis, Thomas J S Merritt","doi":"10.1139/gen-2025-0099","DOIUrl":"10.1139/gen-2025-0099","url":null,"abstract":"<p><p>Organisms are under nearly continuous stress from anthropogenic contaminants, but the molecular response mechanisms, particularly the variation in these responses, are not well understood. Nickel (Ni) contamination, often associated with mining activity, is known to cause a series of health effects, but surprisingly little is known about individual variation in Ni response. In this study, we quantified the mortality response of <i>Drosophila melanogaster</i> to environmental Ni across a series of lines and both sexes and compared it with that of copper (Cu), a well-characterized metal contaminant. Ni exposure had substantial negative effects that were significantly modified by sex, line, and interactions between the two. Strikingly, these trends in differential responses between the sexes and lines were mirrored in both Ni and Cu. Variation in Ni-driven mortality was correlated with starvation resistance, but not with Ni body burden. This contrast suggests a possible role of starvation resistance, but not body burden, in differential mortality. Across all experiments, sex and line effects were not independent; the level of sexual dimorphism varied significantly and substantially across lines, and line effects differed between the sexes. Overall, the results of this study highlight the fact that an understanding of biology requires examination of both sexes and multiple lines.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-8"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289652","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
Highly conserved complete organellar genomes of Bangia atropurpurea (Bangiales, Rhodophyta) revealed by refined annotation. 通过精细注释揭示了Bangia atropurpurea (Bangiales, Rhodophyta)高度保守的完整细胞器基因组。
IF 1.9 3区 生物学
Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0067
Jie Wang, Yan-De Wang, Yu-Lian Li, Chuan-Ming Hu, Jing Chen, Li-En Yang
{"title":"Highly conserved complete organellar genomes of <i>Bangia atropurpurea</i> (Bangiales, Rhodophyta) revealed by refined annotation.","authors":"Jie Wang, Yan-De Wang, Yu-Lian Li, Chuan-Ming Hu, Jing Chen, Li-En Yang","doi":"10.1139/gen-2025-0067","DOIUrl":"10.1139/gen-2025-0067","url":null,"abstract":"<p><p><i>Bangia atropurpurea</i> is the only freshwater species in the ancient order Bangiales, which dates back to approximately 1047 Mya. It was speculated that <i>B. atropurpurea</i> originated from a marine ancestor. However, the timing and mechanism by which this species transitioned from the marine to the freshwater environment remain unclear. Genomic data could shed light on these problems. We provided the complete organellar genomes of a sample of <i>B. atropurpurea</i> from China in the present study. The gene content, genomic organization, tRNA secondary structures and codon usage of the organellar genomes were analyzed. The gene annotations were manually refined. Comparative genomics revealed that the chloroplast genomes in Bangiaceae are highly conserved, whereas the mitochondrial genomes are relatively less conserved. The factors and probable mechanisms that affect the genome were discussed. Genes unique to freshwater or filamentous species could be interesting candidates for the next step of adaptive evolution research. The phylogeny based on genomic data provides solid evidence to split <i>Pyropia</i> into four genera.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289633","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
Uneven DNA barcode representation among tree communities and regions in tropical South America. 南美洲热带树木群落和地区的DNA条形码表示不均匀。
IF 1.7 3区 生物学
Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0123
Marcella Baroni de Resende Costa, Danilo Rafael Mesquita Neves, Fernanda Antunes Carvalho
{"title":"Uneven DNA barcode representation among tree communities and regions in tropical South America.","authors":"Marcella Baroni de Resende Costa, Danilo Rafael Mesquita Neves, Fernanda Antunes Carvalho","doi":"10.1139/gen-2025-0123","DOIUrl":"10.1139/gen-2025-0123","url":null,"abstract":"<p><p>DNA barcode has become an important tool for identifying species, accelerating biodiversity assessments. However, most species still lack barcode data, especially in tropical biomes. We used a comprehensive DNA barcode library for South American tree species and identified geographic and phylogenetic gaps in DNA sequences. We compiled distribution data for 11 525 tree species across 3283 sites in four ecoregions: Amazônia, Caatinga, Cerrado, and Mata Atlântica, and searched GenBank for the main plant DNA barcodes: ITS2, <i>matk</i>, <i>rbcL</i>, and <i>trnH-psbA</i>. To assess phylogenetic diversity gaps, we used a dated molecular phylogeny of 1100 angiosperm genera found in tropical South America. Only around 25% of species have sequences available in GenBank for the selected DNA markers. Most species lacking sequences occur in the Mata Atlântica and Amazônia ecoregions. Moreover, missing species on GenBank are not randomly distributed across the angiosperm phylogeny, leading to large phylogenetic gaps. By calculating phylogenetic endemism, we identified new priority sites for future fieldwork, highlighting the importance of biodiversity metrics beyond species richness. This work revealed major geographic and phylogenetic gaps in DNA barcode data for tropical tree species in South America, helping to guide targeted sampling and improve conservation planning based on biodiversity and evolutionary analyses.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147941184","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
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