IF 2.3 3区生物学

Genome Pub Date : 2024-12-01 Epub Date: 2024-10-16 DOI: 10.1139/gen-2024-0030

Hari D Upadhyaya, Lihua Wang, Andrew H Paterson, C L L Gowda, Rajendra Kumar, Jieqin Li, Yi-Hong Wang

引用次数: 0

Stabilizing selection and mitochondrial heteroplasmy in the Canada lynx (Lynx canadensis). 加拿大猞猁（Lynx canadensis）的稳定选择和线粒体异形。

IF 2.3 3区生物学

Genome Pub Date : 2024-12-01 Epub Date: 2024-09-03 DOI: 10.1139/gen-2023-0094

Krystyn J Forbes, McIntyre A Barrera, Karsten Nielsen-Roine, Evan W Hersh, Jasmine K Janes, William L Harrower, Jamieson C Gorrell

{"title":"Stabilizing selection and mitochondrial heteroplasmy in the Canada lynx (Lynx canadensis).","authors":"Krystyn J Forbes, McIntyre A Barrera, Karsten Nielsen-Roine, Evan W Hersh, Jasmine K Janes, William L Harrower, Jamieson C Gorrell","doi":"10.1139/gen-2023-0094","DOIUrl":"10.1139/gen-2023-0094","url":null,"abstract":"Mitochondrial DNA is commonly used in population genetic studies to investigate spatial structure, intraspecific variation, and phylogenetic relationships. The control region is the most rapidly evolving and largest non-coding region, but its analysis can be complicated by heteroplasmic signals of genome duplication in many mammals, including felids. Here, we describe the presence of heteroplasmy in the control region of Canada lynx (Lynx canadensis) through intra-individual sequence variation. Our results demonstrate multiple haplotypes of varying length in each lynx, resulting from different copy numbers of the repetitive sequence RS-2 and suggest possible heteroplasmic single nucleotide polymorphisms in both repetitive sequences RS-2 and RS-3. Intra-individual variation was only observed in the repetitive sequences while inter-individual variation was detected in the flanking regions outside of the repetitive sequences, indicating that heteroplasmic mutations are restricted to these repeat regions. Although each lynx displayed multiple haplotypes of varying length, we found the most common variant contained three complete copies of the RS-2 repeat unit, suggesting copy number is regulated by stabilizing selection. While genome duplication offers potential for increased diversity, heteroplasmy may lead to a selective advantage or detriment in the face of mitochondrial function and disease, which could have significant implications for wildlife populations experiencing decline (e.g., bottlenecks) as a result of habitat modification or climate change.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"493-502"},"PeriodicalIF":2.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125508","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

Linking the spatial and genomic structure of adaptive potential for conservation management: a review. 将适应潜力的空间结构和基因组结构联系起来进行保护管理：综述。

IF 2.3 3区生物学

Genome Pub Date : 2024-11-01 Epub Date: 2024-07-31 DOI: 10.1139/gen-2024-0036

Avneet K Chhina, Niloufar Abhari, Arne Mooers, Jayme M M Lewthwaite

{"title":"Linking the spatial and genomic structure of adaptive potential for conservation management: a review.","authors":"Avneet K Chhina, Niloufar Abhari, Arne Mooers, Jayme M M Lewthwaite","doi":"10.1139/gen-2024-0036","DOIUrl":"10.1139/gen-2024-0036","url":null,"abstract":"We unified the recent literature with the goal to contribute to the discussion on how genetic diversity might best be conserved. We argue that this decision will be guided by how genomic variation is distributed among manageable populations (i.e., its spatial structure), the degree to which adaptive potential is best predicted by variation across the entire genome or the subset of that variation that is identified as putatively adaptive (i.e., its genomic structure), and whether we are managing species as single entities or as collections of diversifying lineages. The distribution of genetic variation and our ultimate goal will have practical implications for on-the-ground management. If adaptive variation is largely polygenic or responsive to change, its spatial structure might be broadly governed by the forces determining genome-wide variation (linked selection, drift, and gene flow), making measurement and prioritization straightforward. If we are managing species as single entities, then population-level prioritization schemes are possible so as to maximize future pooled genetic variation. We outline one such scheme based on the popular Shapley value from cooperative game theory that considers the relative genetic contribution of a population to an unknown future collection of populations.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"403-423"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859522","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 of full-length genes involved in the biosynthesis of β-caryophyllene and lupeol from the leaf transcriptome of Ayapana triplinervis. 从 Ayapana triplinervis 的叶片转录组中鉴定参与β-叶绿素和羽扇豆醇生物合成的全长基因。

IF 2.3 3区生物学

Genome Pub Date : 2024-11-01 Epub Date: 2024-07-12 DOI: 10.1139/gen-2024-0005

Tanuja, Madasamy Parani

{"title":"Identification of full-length genes involved in the biosynthesis of β-caryophyllene and lupeol from the leaf transcriptome of Ayapana triplinervis.","authors":"Tanuja, Madasamy Parani","doi":"10.1139/gen-2024-0005","DOIUrl":"10.1139/gen-2024-0005","url":null,"abstract":"β-Caryophyllene possesses potential anticancer properties against various cancers, including breast, colon, and lung cancer. Therefore, the essential oil of Ayapana triplinervis, which is rich in β-caryophyllene, can be a potential herbal remedy for treating cancer. However, molecular and genomic studies on A. triplinervis are still sparse. In this study, we obtained 14.7 Gb of RNA-Seq data from A. triplinervis leaf RNA and assembled 137 554 transcripts with an N50 value of 1437 bp. We annotated 72 436 (52.7%) transcripts and mapped 10 640 transcripts to 156 biochemical pathways. Among them, 218 were related to terpenoid backbone biosynthesis, while 27 were linked to sesquiterpenoid and triterpenoid pathways. Ninety-four transcripts were annotated in the β-caryophyllene and lupeol pathways. From these transcripts, for the first time, we identified 25 full-length genes encoding all the 17 enzymes involved in β-caryophyllene biosynthesis and an additional five genes involved in lupeol biosynthesis. These genes will be useful for the metabolic engineering of β-caryophyllene and lupeol biosynthesis, not just in A. triplinervis but also in other species.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"440-444"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141599108","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

An analysis of the gaps in the South African DNA barcoding library of ticks of veterinary and public health importance. 分析南非兽医和公共卫生重要蜱虫 DNA 条形码库中的空白。

IF 2.3 3区生物学

Genome Pub Date : 2024-11-01 Epub Date: 2024-07-17 DOI: 10.1139/gen-2024-0052

Nozipho Khumalo, Mamohale Chaisi, Rebecca Magoro, Monica Mwale

{"title":"An analysis of the gaps in the South African DNA barcoding library of ticks of veterinary and public health importance.","authors":"Nozipho Khumalo, Mamohale Chaisi, Rebecca Magoro, Monica Mwale","doi":"10.1139/gen-2024-0052","DOIUrl":"10.1139/gen-2024-0052","url":null,"abstract":"Ticks transmit pathogens of veterinary and public health importance. Understanding their diversity is critical as infestations lead to significant economic losses globally. To date, over 90 species across three families have been identified in South Africa. However, the taxonomy of most species has not been resolved due to morphological identification challenges. DNA barcoding through the Barcode of Life Data Systems (BOLD) is therefore a valuable tool for species verifications for biodiversity assessments. This study conducted an analysis of South African tick COI barcodes on BOLD by verifying species on checklists, literature, and other sequence databases. The compiled list represented 97 species, including indigenous (59), endemics (27), introduced (2), invasives (1), and eight that could not be classified. Analyses indicated that 31 species (32%) from 11 genera have verified COI barcodes. These are distributed across all nine provinces with the Eastern Cape having the highest species diversity, followed by Limpopo, with KwaZulu-Natal having the least diversity. Rhipicephalus, Hyalomma, and Argas species had multiple barcode index numbers, suggesting cryptic diversity or unresolved taxonomy. We identified 21 species of veterinary or zoonotic importance from the Argasidae and Ixodidae families that should be prioritised for barcoding. Coordinating studies and defining barcoding targets is necessary to ensure that tick checklists are updated to support decision-making for the control of vector-borne diseases and alien invasives.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"392-402"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141633203","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

Comparative genomic and phylogenetic analysis of the complete mitochondrial genome of Cricula trifenestrata (Helfer) among lepidopteran insects. 鳞翅目昆虫中 Cricula trifenestrata (Helfer) 完整线粒体基因组的比较基因组学和系统发生学分析。

IF 2.3 3区生物学

Genome Pub Date : 2024-11-01 Epub Date: 2024-07-24 DOI: 10.1139/gen-2023-0037

Deepika Singh, Ponnala Vimal Mosahari, Pragya Sharma, Kartik Neog, Utpal Bora

{"title":"Comparative genomic and phylogenetic analysis of the complete mitochondrial genome of Cricula trifenestrata (Helfer) among lepidopteran insects.","authors":"Deepika Singh, Ponnala Vimal Mosahari, Pragya Sharma, Kartik Neog, Utpal Bora","doi":"10.1139/gen-2023-0037","DOIUrl":"10.1139/gen-2023-0037","url":null,"abstract":"Cricula trifenestrata Helfer (commonly known as Amphutukoni muga/Cricula silkworm), a wild sericigenous insect produces golden yellow silk similar to Antheraea assamensis (muga silkworm), with significant potential as a natural fiber and biomaterial. Cricula is considered as a pest as it competes for food with muga, which produces the prized golden silk. This study focuses on decoding the mitochondrial genome of C. trifenestrata using next-generation sequencing technology and includes comparative analysis with Bombycoids and other lepidopteran insects. We found that the Cricula mitogenome spans 15 425 bp and exhibits typical gene content and arrangement consistent with other Saturniids and lepidopterans. All protein-coding genes were found to undergo purifying selection, with the highest and lowest conservation observed in the cox1 and atp8 gene, respectively, indicating their potential role in future evolutionary events. We identified two types of mismatches: 23 \"G-U\" and 6 \"U-U\" pairs, similar to those found in Actias selene among the Saturniids. Additionally, our study uncovered the presence of two 33 bp repeat units and a \"TTAGA\" motif in the control region, in contrast to the typical \"ATAGA\" motif, suggesting functional similarity with evolving sequences. Furthermore, phylogenetic analysis supports the close relationship of Cricula with other species within the Saturniidae family.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"424-439"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758265","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

Reduced representation bisulfite sequencing (RRBS) analysis reveals variation in distribution and levels of DNA methylation in white birch (Betula papyrifera) exposed to nickel. 还原表征亚硫酸氢盐测序（RRBS）分析揭示了暴露于镍的白桦树（Betula papyrifera）DNA甲基化分布和水平的变化。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-01 Epub Date: 2024-09-03 DOI: 10.1139/gen-2024-0019

Kabwe Nkongolo, Paul Michael

{"title":"Reduced representation bisulfite sequencing (RRBS) analysis reveals variation in distribution and levels of DNA methylation in white birch (Betula papyrifera) exposed to nickel.","authors":"Kabwe Nkongolo, Paul Michael","doi":"10.1139/gen-2024-0019","DOIUrl":"10.1139/gen-2024-0019","url":null,"abstract":"Research in understanding the role of genetics and epigenetics in plant adaptations to environmental stressors such as metals is still in its infancy. The objective of the present study is to assess the effect of nickel on DNA methylation level and distribution in white birch (Betula papyrifera Marshall) using reduced representation bisulfite sequencing (RRBS). The distribution of methylated C sites of each sample revealed that the level of methylation was much higher in CG context varying between 54% and 65%, followed by CHG (24%-31.5%), and then CHH with the methylation rate between 3.3% and 5.2%. The analysis of differentially methylated regions (DMR) revealed that nickel induced both hypermethylation and hypomethylation when compared to water. Detailed analysis showed for the first time that nickel induced a higher level of hypermethylation compared to controls, while potassium triggers a higher level of hypomethylation compared to nickel. Surprisingly, the analysis of the distribution of DMRs revealed that 38%-42% were located in gene bodies, 20%-24% in exon, 19%-20% in intron, 16%-17% in promoters, and 0.03%-0.04% in transcription start site. RRBS was successful in detecting and mapping DMR in plants exposed to nickel.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"351-367"},"PeriodicalIF":2.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125507","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

Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems. 不同性染色体系统鱼类可转座元件动态对比分析

IF 2.3 3区生物学

Genome Pub Date : 2024-10-01 Epub Date: 2024-05-13 DOI: 10.1139/gen-2023-0134

Carolina Crepaldi, Diogo Cavalcanti Cabral-de-Mello, Patricia Pasquali Parise-Maltempi

{"title":"Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems.","authors":"Carolina Crepaldi, Diogo Cavalcanti Cabral-de-Mello, Patricia Pasquali Parise-Maltempi","doi":"10.1139/gen-2023-0134","DOIUrl":"10.1139/gen-2023-0134","url":null,"abstract":"Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: Megaleporinus elongatus (Z1Z1Z2Z2/Z1W1Z2W2), Megaleporinus macrocephalus (ZZ/ZW) (both with highly differentiated W sex chromosomes), and Leporinus friderici (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with L. friderici having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both Megaleporinus recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, L. friderici showed the opposite pattern. Therefore, despite having similar TE compositions, Megaleporinus and Leporinus exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"339-350"},"PeriodicalIF":2.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140915974","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 southern African mammal species and construction of a reference library for forensic application. 南部非洲哺乳动物物种的 DNA 条形码和法医应用参考文献库的构建。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-01 Epub Date: 2024-07-12 DOI: 10.1139/gen-2023-0050

J R Baxter, A Kotze, M de Bruyn, K Matlou, K Labuschagne, M Mwale

{"title":"DNA barcoding of southern African mammal species and construction of a reference library for forensic application.","authors":"J R Baxter, A Kotze, M de Bruyn, K Matlou, K Labuschagne, M Mwale","doi":"10.1139/gen-2023-0050","DOIUrl":"10.1139/gen-2023-0050","url":null,"abstract":"Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"378-391"},"PeriodicalIF":2.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141599107","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

Specific amino acid changes correlate with pathogenic flavobacteria. 特定氨基酸的变化与致病性黄杆菌有关。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-01 Epub Date: 2022-09-05 DOI: 10.1139/gen-2024-0018

Vincent Gélinas, Valérie E Paquet, Maude F Paquet, Steve J Charette, Antony T Vincent

{"title":"Specific amino acid changes correlate with pathogenic flavobacteria.","authors":"Vincent Gélinas, Valérie E Paquet, Maude F Paquet, Steve J Charette, Antony T Vincent","doi":"10.1139/gen-2024-0018","DOIUrl":"10.1139/gen-2024-0018","url":null,"abstract":"Flavobacterium is a genus of microorganisms living in a variety of hosts and habitats across the globe. Some species are found in fish organs, and only a few, such as Flavobacterium psychrophilum and Flavobacterium columnare, cause severe disease and losses in fish farms. The evolution of flavobacteria that are pathogenic to fish is unknown, and the protein changes accountable for the selection of their colonization to fish have yet to be determined. A phylogenetic tree was constructed with the complete genomic sequences of 208 species of the Flavobacterium genus using 861 softcore genes. This phylogenetic analysis revealed clade CII comprising nine species, including five pathogenic species, and containing the most species that colonize fish. Thirteen specific amino acid changes were found to be conserved across 11 proteins within the CII clade compared with other clades, and these proteins were enriched in functions related to replication, recombination, and repair. Several of these proteins are known to be involved in pathogenicity and fitness adaptation in other bacteria. Some of the observed amino acid changes can be explained by preferential selection for certain codons and tRNA frequency. These results could help explain how species belonging to the CII clade adapt to fish environments.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"67 10","pages":"368-377"},"PeriodicalIF":2.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345157","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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