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

Peroxisome inter-organelle cooperation in Drosophila. 果蝇的过氧物酶体细胞器间合作

IF 2.3 3区生物学

Genome Pub Date : 2024-10-29 DOI: 10.1139/gen-2024-0082

Andy Y Cheng, Andrew J Simmonds

{"title":"Peroxisome inter-organelle cooperation in Drosophila.","authors":"Andy Y Cheng, Andrew J Simmonds","doi":"10.1139/gen-2024-0082","DOIUrl":"10.1139/gen-2024-0082","url":null,"abstract":"Many cellular functions are compartmentalized within the optimized environments of organelles. However, processing or storage of metabolites from the same pathway can occur in multiple organelles. Thus, spatially separated organelles need to cooperate functionally. Coordination between organelles in different specialized cells is also needed, with shared metabolites passed via circulation. Peroxisomes are membrane-bounded organelles responsible for cellular redox and lipid metabolism in eukaryotic cells. Peroxisomes coordinate with other organelles including mitochondria, endoplasmic reticulum, lysosomes, and lipid droplets. This functional coordination requires, or is at least enhanced by, direct contact between peroxisomes and other organelles. Peroxisome dysfunction in humans leads to multiorgan effects including neurological, metabolic, developmental, and age-related diseases. Thus, increased understanding of peroxisome coordination with other organelles, especially cells in various organs is essential. Drosophila melanogaster (fruit fly) has emerged recently as an effective animal model for understanding peroxisomes. Here we review current knowledge of pathways regulating coordination between peroxisomes with other organelles in flies, speculating about analogous roles for conserved Drosophila genes encoding proteins with known organelle coordinating roles in other species.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545118","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

Asp/ASPM phospho-regulation throughout the cell cycle. Asp/ASPM在整个细胞周期中的磷酸化调控。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-29 DOI: 10.1139/gen-2024-0111

Maria C Burns, Lori Borgal

{"title":"Asp/ASPM phospho-regulation throughout the cell cycle.","authors":"Maria C Burns, Lori Borgal","doi":"10.1139/gen-2024-0111","DOIUrl":"10.1139/gen-2024-0111","url":null,"abstract":"In mammals and Drosophila melanogaster, Asp/ASPM proteins contribute to cell proliferation and spindle formation. Recent evidence also suggests interphase roles for Asp/ASPM proteins, but little is known about the regulation allowing distinct roles in different cell cycle phases. In this review, we consider a cross-species comparison of Asp/ASPM protein sequences in light of cyclin-CDK literature, and suggest Asp/ASPM proteins to be prime candidates for cyclin-CDK regulation. Conserved regulatory features include an N-terminal proline directed serine/threonine (S/T-P) \"supershift\" phosphorylation domain common to proteins with bistable interphase and mitotic roles, as well as putative cyclin-binding sites positioned to allow multisite phosphorylation by cyclin-CDK complexes. Human, mouse, and Drosophila Asp/ASPM protein structural predictions show that multisite phosphorylation of the N-term supershift domain could alter the availability of CH-domains and HEAT-motifs, which can contribute to microtubule binding and protein aggregation likely required for spindle formation. Structural predictions of the smallest reported microcephaly patient truncation also emphasize the importance of the arrangement of these motifs. We position this in silico analysis within recent literature to build new hypotheses for Asp/ASPM regulation in interphase and mitosis, as well as de-regulation in microcephaly and cancer. We also highlight the utility of comparing structural/functional differences between human ASPM and Drosophila Asp to gain further insight.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545115","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 satellite DNA mapping in species of the genus Prochilodus (Teleostei, Characiformes) and its evolutionary implications. Prochilodus属（Teleostei，Characiformes）物种的卫星DNA比较图谱及其进化意义。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-29 DOI: 10.1139/gen-2024-0085

Rodrigo Zeni Dos Santos, Caio Augusto Gomes Goes, José Henrique Forte Stornioli, Francisco de Menezes Cavalcante Sassi, Renata Luiza Rosa de Moraes, Jorge Abdala Dergam, Fábio Porto-Foresti, Marcelo de Bello Cioffi, Ricardo Utsunomia

{"title":"Comparative satellite DNA mapping in species of the genus Prochilodus (Teleostei, Characiformes) and its evolutionary implications.","authors":"Rodrigo Zeni Dos Santos, Caio Augusto Gomes Goes, José Henrique Forte Stornioli, Francisco de Menezes Cavalcante Sassi, Renata Luiza Rosa de Moraes, Jorge Abdala Dergam, Fábio Porto-Foresti, Marcelo de Bello Cioffi, Ricardo Utsunomia","doi":"10.1139/gen-2024-0085","DOIUrl":"10.1139/gen-2024-0085","url":null,"abstract":"Satellite DNA (satDNA) sequences are dynamic components of the eukaryotic genome that can play significant roles in species diversification. The Prochilodontidae family, which includes 21 Neotropical fish species, is characterized by a conserved karyotype of 2n = 54 biarmed chromosomes, with variation in some species and populations regarding the presence or absence of B chromosomes. This study aimed to investigate whether the chromosomal distribution of specific satDNA sequences is conserved among three Prochilodus species (Prochilodus lineatus, Prochilodus costatus, and Prochilodus argenteus) regarding organization and number of loci, and to compare their genomes using comparative genomic hybridization (CGH). Our results demonstrated that most satDNA sequences share a similar distribution pattern across the three species, and CGH analysis corroborated that their karyotypes are very similar in terms of repetitive DNA distribution. We also identified a potential CENP-B box sequence within PliSat01, a satDNA located in the pericentromeric region of all analyzed species. In contrast, PliSat04 and PliSat14 displayed differential locations and variations in the number of loci per genome, underscoring the dynamic nature of repetitive sequences even in species with otherwise highly conserved genomes. These findings represent the first evidence of karyotype diversification in Prochilodus, highlighting the evolutionary dynamism of satDNA sequences.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545116","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

Epigenetic factors related to recalcitrance in plant biotechnology. 植物生物技术中与顽抗有关的表观遗传因素。

IF 2.3 3区生物学

Genome Pub Date : 2024-10-29 DOI: 10.1139/gen-2024-0098

Mohsen Hesami, Marco Pepe, Ben Spitzer-Rimon, Milad Eskandari, Andrew Maxwell Phineas Jones

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

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