Erin R Voss, Merly Escalona, Krzysztof M Kozak, William Seligmann, Colin W Fairbairn, Oanh Nguyen, Mohan P A Marimuthu, Chris J Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman
{"title":"De novo genome assembly of a Geomyid rodent, Botta's pocket gopher (Thomomys bottae bottae).","authors":"Erin R Voss, Merly Escalona, Krzysztof M Kozak, William Seligmann, Colin W Fairbairn, Oanh Nguyen, Mohan P A Marimuthu, Chris J Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman","doi":"10.1093/jhered/esae045","DOIUrl":"10.1093/jhered/esae045","url":null,"abstract":"<p><p>Botta's pocket gopher (Thomomys bottae) is a common and widespread subterranean rodent of the North American West. The species has been of great interest to evolutionary biologists due to the phenotypic diversity and unusual levels of variation in chromosome number and composition observed across its range. Here, we present a high-quality reference genome from a male T. b. bottae individual captured in the San Francisco Bay Area. The assembly is comprised of 2,792 scaffolds, with a scaffold N50 value of 23.6 Mb and a BUSCO completeness score of 91.0%. This genome helps fill a significant taxonomic sampling gap in rodent genome resources. With this reference genome, we envision new opportunities to investigate questions regarding the genomics of adaptation to the belowground niche. Further, we can begin to explore the impact of associated life history traits, such as limited dispersal and low population connectivity, on intraspecific genetic and phenotypic variation, genome evolution, speciation, and phylogenetic relationships across the Geomyoidea.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"513-523"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12277567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074570","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}
Linjing Lan, Xin Zhang, Shanxiu Yang, Xiuguang Mao, Ji Dong
{"title":"Chromosome-level genome assembly of the king horseshoe bat (Rhinolophus rex) provides insights into its conservation status and chromosomal evolution of Rhinolophus.","authors":"Linjing Lan, Xin Zhang, Shanxiu Yang, Xiuguang Mao, Ji Dong","doi":"10.1093/jhered/esae077","DOIUrl":"10.1093/jhered/esae077","url":null,"abstract":"<p><p>A high-quality reference genome is quite valuable in assessing the conservation status of a rare species when adequate data from other sources are unavailable. Bats comprise almost a fifth of all mammals and contribute greatly to the ecosystem. However, due to the nocturnal and elusive habits, it is difficult to obtain the accurate census population size of a rare bat species and assess its conservation status. Here, we generate a chromosome-level genome assembly for the king horseshoe bat (Rhinolophus rex) and assess its conservation status by comparing the genome-wide summary statistics with other related species. The genome assembly size was 2.1 Gb (contig N50: 75.26 Mb) and 99.9% of the total sequences were anchored onto 30 autosomes, X and Y chromosomes. Despite lower genome-wide heterozygosity and recent inbreeding, R. rex did not exhibit a higher genetic load compared with the other two Rhinolophus species. Historical demography analysis revealed that R. rex maintained a long-term (~2 million years) stable population size (~150,000). In the future, whole-genome sequencing data from more individuals will be needed to comprehensively assess the conservation status at recent timescales. We also reconstructed the ancestral karyotype of Rhinolophus as 2n = 54 and found that Robertsonian fissions and fusions were the main mechanisms of chromosomal rearrangements in this genus. Overall, our study shows important implications of reference-quality genomes in both conservation genomics and comparative genomics.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"499-512"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andrey Tomarovsky, Ruqayya Khan, Olga Dudchenko, Azamat Totikov, Natalia A Serdyukova, David Weisz, Nadejda V Vorobieva, Tatiana Bulyonkova, Alexei V Abramov, Wenhui Nie, Jinhuan Wang, Svetlana A Romanenko, Anastasiya A Proskuryakova, Nikolay Cherkasov, Malcolm A Ferguson-Smith, Fengtang Yang, Elena Balanovskaya, M Thomas P Gilbert, Alexander S Graphodatsky, Erez Lieberman Aiden, Roger Powell, Klaus-Peter Koepfli, Polina L Perelman, Sergei Kliver
{"title":"Chromosome-length genome assembly of the stone marten (Martes foina, Mustelidae): A new view on one of the cornerstones in carnivore cytogenetics.","authors":"Andrey Tomarovsky, Ruqayya Khan, Olga Dudchenko, Azamat Totikov, Natalia A Serdyukova, David Weisz, Nadejda V Vorobieva, Tatiana Bulyonkova, Alexei V Abramov, Wenhui Nie, Jinhuan Wang, Svetlana A Romanenko, Anastasiya A Proskuryakova, Nikolay Cherkasov, Malcolm A Ferguson-Smith, Fengtang Yang, Elena Balanovskaya, M Thomas P Gilbert, Alexander S Graphodatsky, Erez Lieberman Aiden, Roger Powell, Klaus-Peter Koepfli, Polina L Perelman, Sergei Kliver","doi":"10.1093/jhered/esaf001","DOIUrl":"10.1093/jhered/esaf001","url":null,"abstract":"<p><p>The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n = 38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long runs of homozygosity require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large-scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"548-557"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Terrence Sylvester, Richard Adams, Robert F Mitchell, Ann M Ray, Rongrong Shen, Na Ra Shin, Kasuni C Daundasekara, Duane D McKenna
{"title":"Insights into longhorn beetle (Cerambycidae) evolution from comparative analyses of the red-headed ash borer (Neoclytus acuminatus acuminatus) genome.","authors":"Terrence Sylvester, Richard Adams, Robert F Mitchell, Ann M Ray, Rongrong Shen, Na Ra Shin, Kasuni C Daundasekara, Duane D McKenna","doi":"10.1093/jhered/esaf016","DOIUrl":"10.1093/jhered/esaf016","url":null,"abstract":"<p><p>Neoclytus acuminatus acuminatus, the red-headed ash borer, is a wood-boring longhorn beetle (Cerambycidae: Cerambycinae) native to North America and introduced in Eurasia and South America. Its larvae develop in dying or recently dead hardwood trees, including ecologically and economically significant species of ash, hickory, and oak. We sequenced, assembled, and annotated the genome of a female N. acuminatus and compared it to the publicly available genomes of other cerambycid species. The 508 Mb N. acuminatus genome assembly spanned 20 contigs (19 nuclear + 1 mitochondrial), with an N50 of 52.59 Mb and largest contig of 61.20 Mb. A moderately high fraction of the genome (62.63%) comprised repetitive sequences, with nearly all (99.4%) expected single-copy orthologous genes (BUSCOs) present and fully assembled. We identified 2 contigs as fragments of the N. acuminatus sex chromosome. Genome annotation identified 12,899 genes, including 109 putative horizontally transferred loci. Synteny analysis identified well-conserved blocks of collinearity between the N. acuminatus genome and other Cerambycidae. The genome contains a similar number of genes encoding putative plant cell wall degrading enzymes as other Cerambycidae. The N. acuminatus genome provides new insights into genome evolution in the family Cerambycidae, known for its rich diversity of xylophagous species, and provides a new viewpoint from which to study the evolution and genomic basis of traits such as wood-feeding and olfaction in beetles and other insects.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"558-567"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Veronica Z Radice, Johanna C Gijsbers, Silvia Vimercati, Daniel J Barshis
{"title":"First reference genomes for two mesophotic, reef-building coral species: Leptoseris cf. scabra and Montipora cf. grisea.","authors":"Veronica Z Radice, Johanna C Gijsbers, Silvia Vimercati, Daniel J Barshis","doi":"10.1093/jhered/esaf010","DOIUrl":"10.1093/jhered/esaf010","url":null,"abstract":"<p><p>Coral mortality is occurring worldwide at an alarming rate. Despite the immense and underestimated biodiversity of reef-building corals, very few genomes are available. Further, almost all genomic resources originate from shallow water corals even though photosynthetic, symbiotic corals occur at mesophotic depths deeper than 30 m and even >100 m. We present annotated, de novo genomes for two mesophotic, scleractinian (reef-building) corals Montipora cf. grisea and Leptoseris cf. scabra from American Sāmoa, the latter being the first genome for the widespread genus Leptoseris. We used PacBio continuous long reads and Omni-C data to assemble chromosome-level reference genomes. For Montipora cf. grisea, the final genome size was 1.3 Gb with a completeness level (BUSCO) of 99.9% and 97.2% against the eukaryotic and metazoan databases, respectively. The M. cf. grisea genome had a N50 of 50.2 Mb and the annotation predicted 41,981 genes. For Leptoseris cf. scabra, the final genome size was 794 Mb with a BUSCO of 99.2% and 96.1% against the eukaryotic and metazoan databases, respectively. The L. cf. scabra genome had a N50 of 45.2 Mb and 35,741 predicted genes. These genomes serve as critical references for the analysis of coral gene expression responses to climate change such as ocean warming (i.e., coral bleaching) and ocean acidification impacts. The genomes can be used to investigate the genetic diversity and adaptive divergence of shallow vs. mesophotic coral populations to understand reef resilience and guide conservation strategies.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"488-498"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12277568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677419","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}
Guilherme Mota Souza, Jhon Alex Dziechciarz Vidal, Ricardo Utsunomia, Geize Aparecida Deon, Edivaldo Herculano Correa de Oliveira, Raqueli Teresinha Franca, Fabio Porto-Foresti, Thomas Liehr, Fernando Henrique Santos de Souza, Rafael Kretschmer, Marcelo de Bello Cioffi
{"title":"Cytogenomic analysis in Seriemas (Cariamidae): Insights into an atypical avian karyotype.","authors":"Guilherme Mota Souza, Jhon Alex Dziechciarz Vidal, Ricardo Utsunomia, Geize Aparecida Deon, Edivaldo Herculano Correa de Oliveira, Raqueli Teresinha Franca, Fabio Porto-Foresti, Thomas Liehr, Fernando Henrique Santos de Souza, Rafael Kretschmer, Marcelo de Bello Cioffi","doi":"10.1093/jhered/esaf012","DOIUrl":"10.1093/jhered/esaf012","url":null,"abstract":"<p><p>Contrasting with most bird species that present an ancestral-like karyotype (with 2n = 80), the only extant Cariamidae birds, the Red-legged (Cariama cristata) and Black-legged (Chunga burmeisteri) Seriemas, have high 2n and atypically large Z chromosomes. This study combined cytogenetic, bioinformatic, and genomic analyses to examine the distinctive characteristics of an unusual bird karyotype, with a focus on repetitive elements and sex chromosomes. Whole-genome alignments and chromosomal painting with a Z-chromosome-specific probe were also performed against the emu (a species with an ancestral-like karyotype). The satellitomes of C. cristata and C. burmeisteri were composed of only four and 6 long satDNAs, respectively. These satDNAs showed similarity with other repetitive sequences, mostly transposable elements, and were mapped in the pericentromeric regions of several chromosome pairs. CcrSat02-1104 mostly covered the Z and W sex chromosomes, besides being spread throughout additional chromosomes. Interstitial telomeric sites were not detected, even in the Z chromosome, and none of the 16 microsatellites tested showed positive signals on the C. cristata chromosomes. The genome alignments showed that the karyotype evolution that occurred in C. cristata may have involved significant chromosomal reshuffling, particularly fissions. Notwithstanding certain internal inversions, the Z chromosome retained homology with that of the emu. However, repetitive sequences also accumulated on the Z chromosome, contributing to its enlargement relative to the pattern observed in ancestral avian groups.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"441-452"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eamon C Corbett, Andre E Moncrieff, Robb T Brumfield, Brant C Faircloth
{"title":"A reference genome for boat-tailed grackles (Quiscalus major).","authors":"Eamon C Corbett, Andre E Moncrieff, Robb T Brumfield, Brant C Faircloth","doi":"10.1093/jhered/esaf019","DOIUrl":"10.1093/jhered/esaf019","url":null,"abstract":"<p><p>Boat-tailed Grackles (Quiscalus major) are marsh-dwelling blackbirds that are endemic to the eastern United States. Various aspects of their biology have been studied extensively, including their mating system, plumage and molt patterns, diet, and interspecific interactions. Boat-tailed Grackles are also interesting because they exhibit variation in their iris color that is associated with geography. However, resources that enable genomic studies of Boat-tailed Grackles and other related grackle species are few. Here, we combined Pacific Biosciences long-read, HiFi data with short-read Illumina data from a HiC library to produce haplotype-phased, chromosome-scale genome assemblies for Boat-tailed Grackles. The final version of the assembly, bQuiMaj1, includes two, contiguous haplotypes with total lengths of ~1 Gbp, N50s of ~70 Mbp, and L50s of 5-6. BUSCO and merqury analyses suggest both haplotypes are also relatively complete (95-99%) with respect to gene and k-mer content. The resulting assemblies will significantly enhance our understanding of Boat-tailed Grackle biology and physiology, as well as contribute to the growing number of genomes representing species belonging to the taxonomic family Icteridae (the New World blackbirds).</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"540-547"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143991633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Linette Umbrello, Rujiporn Thavornkanlapachai, Shelley McArthur, Diana Prada, Chris Knuckey, Robyn Shaw, Peter B S Spencer, Kym Ottewell
{"title":"Noninvasive sampling reveals landscape genetic structure in the threatened ghost bat (Macroderma gigas) in an ore-rich region of Western Australia.","authors":"Linette Umbrello, Rujiporn Thavornkanlapachai, Shelley McArthur, Diana Prada, Chris Knuckey, Robyn Shaw, Peter B S Spencer, Kym Ottewell","doi":"10.1093/jhered/esaf011","DOIUrl":"10.1093/jhered/esaf011","url":null,"abstract":"<p><p>Bat species are expected to exhibit low genetic structuring due to their high mobility. Thus, habitat connectivity is important to maintain gene flow and genetic diversity to retain evolutionary potential. The ghost bat (Macroderma gigas) is a large carnivorous bat endemic to Australia. Listed as Vulnerable, the species has a disjunct distribution across northern Australia and is patchily distributed at local scales due to limited roost habitat availability and anthropogenic impacts. Here, we survey the genetic diversity and structure of M. gigas in the isolated, arid Pilbara bioregion in Western Australia, primarily using noninvasively collected fecal DNA samples obtained from roosts. Fecal and tissue samples, representing 399 individuals, were genotyped using an optimized autosomal marker panel, with a subset also being sequenced at the mitochondrial D-loop region to investigate historical gene flow. Spatially explicit Bayesian clustering analyses of autosomal markers revealed low genetic structure and high levels of gene flow amongst the two Pilbara subregions, with some further structuring evident within the Hamersley Ranges. Mitochondrial DNA sequencing showed strong geographic structuring of haplotypes between the subpopulations, with only a small number of shared haplotypes indicating low levels of maternal gene flow. Such patterns across the two marker types are consistent with maternal philopatry and male-mediated gene flow that has previously been described for this species. Conservation actions for the ghost bat in the Pilbara should therefore recognize maintenance of connectivity between roosts and subregions is important to maintain gene flow for this threatened species in the face of anthropogenic threats.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"453-465"},"PeriodicalIF":3.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12277569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607170","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}
Anna Halpin-McCormick, Robert Thomson, Robert C Clarke, Jeffrey Neyhart, Michael B Kantar
{"title":"Dissecting Genotype-Environment interactions with functional implications for parental selection in Cannabis Breeding.","authors":"Anna Halpin-McCormick, Robert Thomson, Robert C Clarke, Jeffrey Neyhart, Michael B Kantar","doi":"10.1093/jhered/esaf048","DOIUrl":"https://doi.org/10.1093/jhered/esaf048","url":null,"abstract":"<p><p>As climate variability continues to impact agricultural systems, identifying genetic factors that contribute to environmental adaptation will be essential for optimizing breeding strategies for the development of climate resilient varieties. Through human cultivation and naturalization, Cannabis sativa has dispersed globally, adapting to a range of environmental conditions across various climates and latitudes. We combined raw data from multiple public sources to conduct an Environmental Genomic Selection (EGS) analysis on 149 C. sativa samples, to assess how different populations of Cannabis relate to their environmental conditions. Exploring Genomic Estimated Adaptive Values (GEAVs) across bioclimatic variables can facilitate the selection of parental material adapted for a specific condition. We further explore potential mechanisms of local adaptation by characterizing the individual marker effects which underlie these GEAV scores. To facilitate interpretation, we used previously described genetic groupings (Basal, Hemp-type, Drug-type feral, Drug-type). Distinct patterns emerged across population groups with the drug-type (Type I) group showing consistently narrow GEAV ranges, whereas the drug-type feral group showed a broader distribution, often having high GEAVs for precipitation variables. A key climate variable difference was seen in monthly average values, revealing a seasonal response to precipitation in drug-type feral samples. By examining monthly differences in marker effects associated with precipitation, we identify potential genomic mechanisms underlying seasonal environmental responses in drug-type feral samples. As these samples are sourced from geographic regions that have seasonal monsoons, they may have traits conferring flood tolerance (water logging) that could be introgressed into other backgrounds. The basal group also exhibited broad GEAV ranges across several bioclimatic traits, indicating they may be a valuable genetic resource for introgression to enhance environmental resilience. These findings underscore the importance of incorporating diverse germplasm into breeding programs to improve Cannabis resilience to changing environmental conditions. EGS provides a fast method to enable climate-conscious parental selection while gaining mechanistic information. Ultimately, we hope that such a strategy could support the development of climate-resilient Cannabis varieties tailored to both current and future environmental challenges.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"High-quality genome assembly of the endemic, threatened, White-bellied Sholakili Sholicola albiventris (Muscicapidae: Blanford, 1868) from the Shola Sky Islands, India.","authors":"K L Vinay, Chiti Arvind, Naman Goyal, V V Robin","doi":"10.1093/jhered/esaf049","DOIUrl":"https://doi.org/10.1093/jhered/esaf049","url":null,"abstract":"<p><p>The White-bellied Sholakili (Sholicola albiventris) is an endemic, elevationally restricted species occurring in the Shola Sky Islands of the Western Ghats of India. This unique understory bird, with a complex vocal repertoire, exhibits impacts of anthropogenic habitat fragmentation on gene flow. Here, we present the first genome assembly for Sholicola albiventris, which was assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.083 Gbp, consisting of 975 scaffolds with an N50 of 68.64 Mbp and L50 of 6. Our genome assembly's completeness is supported by a number of metrics - high BUSCOs (99.9%), and a total of 4887 ultraconserved element (UCE) loci retrieved. We also report the complete mitochondrial genome comprising 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. We identified 11.82% of the nuclear genome as repetitive and 36,000 putative genes, with 12017 genes functionally annotated. Our assembly showed a great synteny between Taeniopygia guttata and Gallus gallus chromosome level assemblies. This reference will be pivotal for investigating landscape connectivity, sub-population genetics, local adaptation, and conservation genetics of this high-elevation, range-restricted endemic bird species.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}