IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0093

Nureyev F Rodrigues, Maria Eguiluz, Frank Guzman, Mateus Dias-Oliveira, Rogerio Margis

{"title":"Abiotic stress-responsive tRNA-derived fragments in pitanga (Eugenia uniflora L.): regulatory roles in drought and salinity adaptation.","authors":"Nureyev F Rodrigues, Maria Eguiluz, Frank Guzman, Mateus Dias-Oliveira, Rogerio Margis","doi":"10.1139/gen-2025-0093","DOIUrl":"10.1139/gen-2025-0093","url":null,"abstract":"The tRNA-derived RNA fragments (tRFs) have emerged as pivotal regulators of eukaryotic stress responses. These small non-coding RNAs are implicated in various biological domains. This study investigates the expression and functions of plant tRFs in response to abiotic stress with focus on Eugenia uniflora L. In silico analysis identified a diverse set of small RNAs originating from 73 conserved tRNAs. High-throughput analysis of small RNA (sRNA) libraries revealed a prevalence of 5'tRFs, with 51 947 sRNAs. RT-qPCR analysis unveiled predominant tRFs, such as those derived from tRNA-Arg-CCT. Among the 11 tRFs examined, six displayed notable differences in expression levels under high salt and osmotic stress triggered by NaCl and polyethylene glycol. Notably, 5'tRF ArgTCG and 5'tRF GlyTCC were positively regulated under both saline and water stress conditions. Additionally, we demonstrated that some previously identified targets of these tRFs showed reduced expression following both types of stress. Our findings suggest that abiotic stress-related tRFs interact with various signaling and metabolic pathways. Alterations in the expression of three tRFs and their target genes in both stress conditions highlight the potential significance of tRF changes in E. uniflora adaptation to drought and salinity.","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":"148257685","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

Development and application of new chromosome-specific oligonucleotide probes for Thinopyrum elongatum. 一种新的染色体特异寡核苷酸探针的研制与应用。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0009

Jianing Zhao, Xiangqian Chen, Hao Wang, Xiaofang Cheng, Zi Wang, Yue Guan, Fantao Liu, Zuchun Li, Tingdong Li, Chunhuan Chen, Jixin Zhao, Changyou Wang, Xinlun Liu, TingTing Li, Pingchuan Deng, Wanquan Ji

{"title":"Development and application of new chromosome-specific oligonucleotide probes for Thinopyrum elongatum.","authors":"Jianing Zhao, Xiangqian Chen, Hao Wang, Xiaofang Cheng, Zi Wang, Yue Guan, Fantao Liu, Zuchun Li, Tingdong Li, Chunhuan Chen, Jixin Zhao, Changyou Wang, Xinlun Liu, TingTing Li, Pingchuan Deng, Wanquan Ji","doi":"10.1139/gen-2025-0009","DOIUrl":"10.1139/gen-2025-0009","url":null,"abstract":"The E genome of Thinopyrum elongatum is an important alien genetic resource for the breeding of Triticum aestivum. The purpose of this study was to develop chromosome-specific oligonucleotide probes for Th. elongatum. Based on the Th. elongatum reference genome, 1 522 611 tandem repeats were identified using bioinformatics methods. By further merging tandem repeats using bedtools in sliding windows of 10 kb, we obtained 15 500 high-copy sequences with a copy number exceeding 100. We identified 1609 unique high-copy tandem repeats of Th. elongatum as candidate sequences by comparing them with the wheat reference genome. Based on their chromosome specificity and distribution sites, 19 Th. elongatum oligonucleotide probes were developed and applied to material identification. The results showed that the Oligo-7ES-2 probe produced a clear and stable in situ hybridization signal on the chromosome of the CS-7E addition line material, located on the long arm of 7E chromosome. The Oligo-7ES-2 probe developed in this study can help the traditional E genome GISH probe for mapping chromosomes or chromosome fragments of 7E and 7EL derived lines of wheat and Th. elongatum. This lays a foundation for the efficient identification of exogenous chromosomes of Th. elongatum in wheat genetic improvement.","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":"146018296","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

Chromosomal dynamics and evidence of differentiation of the proto-sex chromosomes XY in Farlowella oxyrryncha (Loricariidae; Loricariinae). 法罗蝇科原性染色体XY的染色体动力学和分化证据。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0079

Leandro Marajó, Patrik Ferreira Viana, Alex Matheus Viana Ferreira, Victoria Tura, Eliana Feldberg

{"title":"Chromosomal dynamics and evidence of differentiation of the proto-sex chromosomes XY in Farlowella oxyrryncha (Loricariidae; Loricariinae).","authors":"Leandro Marajó, Patrik Ferreira Viana, Alex Matheus Viana Ferreira, Victoria Tura, Eliana Feldberg","doi":"10.1139/gen-2025-0079","DOIUrl":"10.1139/gen-2025-0079","url":null,"abstract":"Farlowella is the second most species-rich genus within Loricariinae; however, cytogenetic data for its species remain scarce. In this study, we employed conventional and molecular cytogenetic procedures on Farlowella oxyrryncha, a species widely distributed across the Amazon and Orinoco River basins. Karyotypic analysis revealed a conserved diploid number (2n = 58), with 12m+22sm+18st+6a, in addition to notable structural variation compared to other species of the genus. The pattern of constitutive heterochromatin (CH) facilitated the characterization of chromosome pairs. Furthermore, a conspicuous sex-linked heteromorphism was detected in chromosome pair 27, suggesting the presence of an XY sex chromosome system. Fluorescence in situ hybridization identified single site of 18S and 5S ribosomal DNA, with 18S colocalizing with U2 small nuclear DNA, simple sequence repeats, and CH. Interstitial telomeric sequences (ITSs) were found in five pairs, with dimorphic ITS patterns in pair 27, suggesting its role as a proto-sexual pair. The colocalization of repetitive sequences in pair 27 suggests that repetitive DNA plays a key role in the early differentiation of sex chromosomes. These findings indicate that F. oxyrryncha is a structurally dynamic lineage and provide new insights into karyotype evolution and sex chromosome differentiation in Loricariidae.","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":"146040859","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 genome sequence of the açaí berry (Euterpe oleracea Mart.) and RNA-Seq analysis of the fruit ripening. açaí浆果（Euterpe oleracea Mart.）基因组序列及果实成熟的RNA-Seq分析。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0105

Maria Silvanira Ribeiro Barbosa, Sávio de Souza Costa, Davi Josué Marcon, Adan Rodrigues de Oliveira, Lucas da Silva E Silva, Maria Paula Cruz Schneider, Juarez Antônio Simões Quaresma, Diego Assis das Graças, Adonney Allan de Oliveira Veras, Maria do Socorro Padilha de Oliveira, Simone de Miranda Rodrigues, Elisa Ferreira Moura, Artur Silva, Rafael Azevedo Baraúna

{"title":"The genome sequence of the açaí berry (Euterpe oleracea Mart.) and RNA-Seq analysis of the fruit ripening.","authors":"Maria Silvanira Ribeiro Barbosa, Sávio de Souza Costa, Davi Josué Marcon, Adan Rodrigues de Oliveira, Lucas da Silva E Silva, Maria Paula Cruz Schneider, Juarez Antônio Simões Quaresma, Diego Assis das Graças, Adonney Allan de Oliveira Veras, Maria do Socorro Padilha de Oliveira, Simone de Miranda Rodrigues, Elisa Ferreira Moura, Artur Silva, Rafael Azevedo Baraúna","doi":"10.1139/gen-2025-0105","DOIUrl":"10.1139/gen-2025-0105","url":null,"abstract":"Euterpe oleracea Mart. is a perennial wetland palm native to the eastern Amazon that produces a fruit called açaí, which is used to prepare a beverage of great social and economic importance to the region. We have sequenced the açaí genome using Oxford Nanopore long-read platform, and we have evaluated the gene expression of the fruit during the ripening process in both the white and purple varieties via RNA-Seq analysis. The assembled genome had a size of 3 066 969 163 bp, with the longest contig displaying 430 834 bp, an N50 of 54 646, and a GC content of 49.97%. The transcriptome analysis identified crucial genes that regulate the production of anthocyanins in purple açaí. For example, the upregulation of the flavonoid 3'5'-hydroxylase enzyme plays a crucial role in the synthesis of purple anthocyanins, such as delphinidin 3-glucoside, between 70 and 130 days after flowering. In contrast, a general downregulation of the enzymes responsible for the initial stages of the anthocyanin synthesis was observed in the white variety. Our findings provide a valuable contribution to the understanding of the molecular mechanisms that regulate the ripening process of açaí fruits and present the first genome of E. oleracea.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-14"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147941237","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

From lab bench to public voice: how to incorporate science communication into your research program. 从实验室工作台到公众声音：如何将科学传播纳入你的研究计划。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0003

Allie Hutchings, Owen W Allard, Konan Blaise Koko, Cameron daCosta, Emma Salvati, Chongwen Mika Zhao, Thomas J S Merritt

引用次数: 0

Cytogenetic characterization and phylogenetic analysis in two Tyranninae species (Aves: Passeriformes): the leading edge of chromosome evolution in Passeriformes. 两个暴龙科物种的细胞遗传学特征和系统发育分析：暴龙科染色体进化的前沿。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0055

Benilson Silva Rodrigues, Ivanete de Oliveira Furo, Ricardo José Gunski, Analía Del Valle Garnero, Patrícia O'Brien, Malcolm Ferguson-Smith, Rafael Kretschmer, Edivaldo Herculano Correa de Oliveira

{"title":"Cytogenetic characterization and phylogenetic analysis in two Tyranninae species (Aves: Passeriformes): the leading edge of chromosome evolution in Passeriformes.","authors":"Benilson Silva Rodrigues, Ivanete de Oliveira Furo, Ricardo José Gunski, Analía Del Valle Garnero, Patrícia O'Brien, Malcolm Ferguson-Smith, Rafael Kretschmer, Edivaldo Herculano Correa de Oliveira","doi":"10.1139/gen-2025-0055","DOIUrl":"10.1139/gen-2025-0055","url":null,"abstract":"Chromosome painting has proven to be an essential tool for elucidating the evolutionary mechanisms underlying avian karyotype diversification and for identifying key synapomorphies that enhance our understanding of avian phylogenetic relationships. In the Neotropical region, the family Tyrannidae exhibits the greatest species diversity, providing valuable opportunities to investigate chromosomal evolution among closely related taxa. To contribute to our understanding of chromosomal evolution within Tyrannidae, we analyzed the karyotypes of two representative species, Myiozetetes cayanensis and Lathrotriccus euleri, combining classical cytogenetic techniques with fluorescence in situ hybridization. We employed whole-chromosome probes from Gallus gallus (GGA) and Leucopternis albicollis (LAL), as well as 18S rDNA and telomeric repeats (TTAGGG)n probes. Our results revealed the conserved karyotypic structure characteristic of Passeriformes (approximately 80 chromosomes), with M. cayanensis exhibiting 2n = 80 and Lathrotriccus euleri 2n = 78. In both species, the karyotypes are predominantly composed of acrocentric chromosomes. Telomeric probes produced signals restricted to terminal chromosomal regions, while 18S rDNA probes hybridized to a single pair of microchromosomes. Probes from GGA and LAL revealed chromosomal fissions and inversions in both species. Similar rearrangements have been observed in other tyrannid species from the subfamilies Fluvicolinae, Tyranninae, and Elaeniinae, suggesting a possible shared evolutionary pattern within Tyrannidae.","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":"147289575","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

Concordance and divergence between self-declared ancestry and genome-derived ancestry composition in 10 250 participants from the HostSeq cohort. 来自HostSeq队列的10,250名参与者自我声明的祖先和基因组衍生的祖先组成之间的一致性和差异

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0022

René L Warren, Lauren Coombe, Inanc Birol

{"title":"Concordance and divergence between self-declared ancestry and genome-derived ancestry composition in 10 250 participants from the HostSeq cohort.","authors":"René L Warren, Lauren Coombe, Inanc Birol","doi":"10.1139/gen-2026-0022","DOIUrl":"10.1139/gen-2026-0022","url":null,"abstract":"Accurate characterization of human genetic diversity is essential for robust genomic analyses. We compared self-declared and genome-derived ancestry composition in 10 250 participants from the pan-Canadian HostSeq cohort using whole-genome sequencing data. Global and local ancestry were inferred at the continental super-population level using the alignment-free ntRoot algorithm and evaluated through both hard-label concordance and multiclass Brier score analyses incorporating full ancestry fraction profiles. Strong agreement was observed among East Asian / Pacific Islander (mean Brier score ± SD: 0.012 ± 0.052), Black (0.013 ± 0.042), White (0.055 ± 0.022), and South Asian (0.057 ± 0.098) participants, whereas higher scores among Hispanic (0.083 ± 0.060) and Middle Eastern or Central Asian (0.122 ± 0.034) participants reflected broader and more admixed ancestry profiles. Principal component analysis of centered log-ratio-transformed ancestry fractions revealed overlapping ancestry gradients rather than discrete continental groupings. Entropy- and dominance margin-based analyses further indicated that many discordant cases reflected diffuse admixture rather than categorical mismatch. Together, these findings support representing ancestry as a continuous compositional spectrum rather than discrete categories. Genome-derived ancestry estimates describe patterns of genomic variation and should not be interpreted as proxies for race.","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":"148578320","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

Systematic evaluation of rDNA ITS2 as a DNA barcode for molecular identification of cyclorrhapha flies in China. rDNA ITS2作为环裂蝇分子鉴定DNA条形码的系统评价。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0070

Rong Peng, Yaxu Dong, Yuhan Wang, Keyi Hou, Zihan Zhao, Yiyou Wang, Pan Liu, Li Hu, Yae Zhao

{"title":"Systematic evaluation of rDNA ITS2 as a DNA barcode for molecular identification of cyclorrhapha flies in China.","authors":"Rong Peng, Yaxu Dong, Yuhan Wang, Keyi Hou, Zihan Zhao, Yiyou Wang, Pan Liu, Li Hu, Yae Zhao","doi":"10.1139/gen-2026-0070","DOIUrl":"https://doi.org/10.1139/gen-2026-0070","url":null,"abstract":"Morphological identification of medically important flies is often hindered by incomplete or damaged specimens, cryptic species, and morphological conservatism among closely related species. In this study, common fly species were collected from 15 cities across 10 provinces in China to evaluate rDNA internal transcribed spacer 2 (ITS2) as a potential DNA barcode for molecular identification. A total of 1252 fly specimens were collected, of which 933 were morphologically classified into 19 species, 15 genera, 9 families, and 3 superfamilies; 319 remained unidentified due to the loss of key morphological characters. Seventeen mitochondrial and ribosomal candidates were evaluated using sequences retrieved from GenBank across Cyclorrhapha. ITS2 was selected based on its relatively low intraspecific divergence, higher interspecific divergence, and conserved flanking regions suitable for universal primer design. The designed ITS2 primers successfully amplified and sequenced all 144 tested specimens, including morphologically damaged samples. Integrating morphological and molecular data, 27 fly species were identified. Barcode gap analyses indicated clear interspecific discrimination in the genera of Muscidae, Calliphoridae, and Sarcophagidae. Phylogenetic analyses further supported species-level identification and revealed ITS2 sequence diversity within Musca domestica specimens. These results demonstrate that ITS2 is a promising candidate DNA barcode for Cyclorrhapha flies, particularly for specimens with ambiguous or damaged morphology.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"69 ","pages":"1-15"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149016822","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

Detecting bumble bees in the wild using environmental DNA: development and validation of a qPCR assay for the endangered Franklin's bumble bee (Bombus franklini). 利用环境DNA检测野生大黄蜂：濒危富兰克林大黄蜂（Bombus franklini） qPCR检测的开发和验证。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0006

Michaela R Grossklaus, David S Pilliod, Stephen F Spear, Matthew B Laramie, Akhil Kholwadwala, Amanda J Boone, Yer Lor, Marissa Kaminski, Jeffrey G Everett

{"title":"Detecting bumble bees in the wild using environmental DNA: development and validation of a qPCR assay for the endangered Franklin's bumble bee (Bombus franklini).","authors":"Michaela R Grossklaus, David S Pilliod, Stephen F Spear, Matthew B Laramie, Akhil Kholwadwala, Amanda J Boone, Yer Lor, Marissa Kaminski, Jeffrey G Everett","doi":"10.1139/gen-2025-0006","DOIUrl":"10.1139/gen-2025-0006","url":null,"abstract":"Environmental DNA (eDNA) sampling is a noninvasive alternative to conventional methods of surveying insects that may be particularly useful for detecting pollinators. We developed a quantitative polymerase chain reaction (qPCR) assay to detect the DNA of Franklin's bumble bee (Bombus franklini) from flower samples and conducted an initial test of the assay using samples collected within and around the historical range of the species. We further analyzed all samples using metabarcoding. Our qPCR assay successfully amplified B. franklini DNA and exhibited no cross-reactivity with nontarget bumble bee DNA during in silico and in vitro testing. We did not detect B. franklini DNA from field-collected flower samples using either qPCR or metabarcoding. However, metabarcoding analysis revealed DNA of at least 16 other bumble bee species. This finding underscores the potential utility of eDNA sampling for surveying bumble bees. Nondetection of B. franklini from field-collected flower samples may be due to the extreme rarity of the species; B. franklini is endangered and has not been observed in the wild since 2006. Our B. franklini assay is among the first bee-specific qPCR assays ever developed and provides proof of concept for additional assays that may improve detection rates of rare and endangered bees.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"69 ","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":"147638545","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

Filling DNA barcode gaps in Central European Auchenorrhyncha: a new reference library and Oxford Nanopore Technologies-based species identification. 填补中欧桃金娘的DNA条形码空白：一个新的参考库和基于牛津纳米孔技术的物种鉴定。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0009

Sandra Schallhart, Jacqueline Grimm, Werner E Holzinger, Elisabeth Huber, Nadine Klar, Gernot Kunz, Sylvia Schäffer, Lydia Schlosser, Bettina Thalinger, Stephan Koblmüller

{"title":"Filling DNA barcode gaps in Central European Auchenorrhyncha: a new reference library and Oxford Nanopore Technologies-based species identification.","authors":"Sandra Schallhart, Jacqueline Grimm, Werner E Holzinger, Elisabeth Huber, Nadine Klar, Gernot Kunz, Sylvia Schäffer, Lydia Schlosser, Bettina Thalinger, Stephan Koblmüller","doi":"10.1139/gen-2026-0009","DOIUrl":"10.1139/gen-2026-0009","url":null,"abstract":"Terrestrial arthropods are declining in most ecosystems, creating a need for efficient and scalable biodiversity monitoring tools. DNA-barcoding enables high-throughput species identification but is constrained by incomplete reference libraries for many taxa. Here, we expand the DNA barcode database for Austrian Auchenorrhyncha by combining morphological identification with Sanger-sequenced cytochrome c oxidase I (COI) barcodes. A total of 1304 specimens representing 394 species were successfully barcoded, resulting in 384 Barcode Index Numbers (BINs), including 73 newly established BINs. Elevated intraspecific COI divergence and BIN discordance in several taxa reveal species complexes and missing barcode gaps. The expanded reference library was applied to Auchenorrhyncha from Malaise trap samples collected at an agricultural lowland and an alpine site and analyzed using a high-throughput Oxford Nanopore Technologies (ONTs) workflow. The improved reference library substantially increased assignment success and taxonomic resolution. Finally, we compared the ONT barcoding results from Malaise trap catches with morphology-based identifications from single-event suction sampling. Both approaches detected similar proportions of species, and differences in species composition likely reflect sampling- and method-specific biases. Overall, this study advances the development of a comprehensive DNA barcode reference library for Central European Auchenorrhyncha and underscores the importance of regionally curated databases and complementary approaches for biodiversity assessments.","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":"148764372","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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