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.
蜱虫传播对兽医和公共卫生具有重要意义的病原体。了解蜱虫的多样性至关重要,因为蜱虫侵扰会给全球造成重大经济损失。南非已发现三个科约 90 多个物种。然而,由于形态鉴定方面的困难,大多数物种的分类尚未得到解决。因此,通过生命条形码数据系统(BOLD)进行 DNA 条形编码是生物多样性评估中物种验证的重要工具。本研究通过核查核对表、文献和其他序列数据库中的物种,对 BOLD 上的南非蜱 COI 条形码进行了分析。编制的清单上有 97 个物种,包括本土物种(59 个)、特有物种(27 个)、引进物种(2 个)、入侵物种(1 个)和 8 个无法分类的物种。分析表明,11 个属的 31 个物种(32%)已验证了 COI 条形码。这些物种分布在所有九个省份,其中东开普省的物种多样性最高,其次是林波波省,夸祖鲁-纳塔尔省的物种多样性最低。Rhipicephalus、Hyalomma和Argas物种有多个条形码索引号(BINs),这表明存在隐性多样性或未解决的分类问题。我们从 Argasidae 和 Ixodidae 科中确定了 21 个具有兽医或人畜共患病重要性的物种,这些物种应优先进行条形码编码。有必要协调研究工作并确定条形码目标,以确保更新蜱虫检查列表,为控制病媒传播疾病和外来入侵生物的决策提供支持。
{"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":"<p><p>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 <i>COI</i> 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 <i>COI</i> 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. <i>Rhipicephalus, Hyalomma</i>, and <i>Argas</i> 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.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-17","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}
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 1,37,554 transcripts with an N50 value of 1,437 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. Keywords: β-caryophyllene, Eupatorium ayapana, Eupatorium triplinervis, lupeol, transcriptome.
{"title":"Identification of full-length genes involved in the biosynthesis of β-caryophyllene and Lupeol from the leaf transcriptome of Ayapana triplinervis.","authors":"Madasamy Parani, Tanuja Tanuja","doi":"10.1139/gen-2024-0005","DOIUrl":"https://doi.org/10.1139/gen-2024-0005","url":null,"abstract":"<p><p>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 1,37,554 transcripts with an N50 value of 1,437 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. Keywords: β-caryophyllene, Eupatorium ayapana, Eupatorium triplinervis, lupeol, transcriptome.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-12","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}
J R Baxter, A Kotze, M de Bruyn, K Matlou, K Labuschagne, M Mwale
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.
在南非打击野生动物犯罪需要准确识别贸易物种及其产品。在处理标本时,识别物种所需的诊断形态特征往往会丢失,而海关官员又缺乏识别物种的专业知识。作为一种潜在的解决方案,DNA 条形码可用于在法医案件中识别形态上无法区分的标本。然而,条形码识别需要依赖全面、有效的 DNA 条形码参考数据库,而目前这种数据库非常有限。为了克服这一限制,我们构建了一个包含细胞色素 c 氧化酶亚单位 1(COI)和细胞色素 b(Cyt b)序列的条形码库,用于分析南部非洲受威胁和受保护的哺乳动物。此外,我们还纳入了密切相关或形态相似的物种,并评估了数据库准确识别物种的能力。已发表的南部非洲序列被纳入其中,以估计种内和种间变异。邻接树成功区分了 94-95% 的类群。然而,一些分布广泛的物种表现出较高的种内距离(>2%),这表明存在地理亚结构或隐性物种。由于缺乏可靠的已发表数据,无法明确区分某些物种。这项研究强调了 DNA 条形码在物种鉴定方面的功效,尤其是在法医应用方面。它还强调了对某些广泛分布的物种和具有挑战性的属进行重新分类评估的必要性。
{"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":"<p><p>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 <i>cytochrome c oxidase subunit 1</i> and <i>cytochrome b</i> 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.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-12","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}
Pub Date : 2024-07-01Epub Date: 2024-05-14DOI: 10.1139/gen-2023-0096
Suziane Alves Barcellos, Rafael Kretschmer, Marcelo Santos de Souza, Victoria Tura, Luciano Cesar Pozzobon, Thales Renato Ochotorena de Freitas, Darren K Griffin, Rebecca O'Connor, Ricardo José Gunski, Analía Del Valle Garnero
The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species (Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus, and Picumnus nebulosus) was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from Gallus gallus and Taeniopygia guttata. Findings suggest that P. nebulosus (2n = 110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for V. spilogaster (2n = 88) and demonstrated microchromosomal rearrangements involving C. campestris plus a single, unique hitherto undescribed rearrangement in V. spilogaster. This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of M. candidus is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.
啄木鸟的基因组组织有几个显著特点,如不常见的重复序列积累、增大的 Z 染色体和非典型的二倍体数目。尽管啄木鸟的种类繁多,但详细的细胞基因组研究却很少。通过荧光原位杂交技术,利用最初来源于 Gallus gallus 和 Taeniopygia guttata 的细菌人工染色体,确定了四个物种(Colaptes campestris、Veniliornis spilogaster、Melanerpes candidus 和 Picumnus nebulosus)的基因组组织模式以及微染色体形成过程中的进化变化。研究结果表明,首次描述的 P. nebulosus(2n = 110)在本文研究的鹟科物种中具有最基本的核型,可能是鸟类祖先宏染色体裂解的结果。我们为 V. spilogaster 定义了一个新的染色体数目(2n = 88),并展示了涉及 C. campestris 的微染色体重排,以及 V. spilogaster 中一个迄今未被描述的独特重排。这包括祖先微染色体 12(与鸡微染色体 12 同源)融合后的倒位。我们还确定,M. candidus 的低二倍体数与微染色体融合有关。因此,与推测的祖先核型相比,啄木鸟的核型出现了明显的重新排列。
{"title":"Understanding microchromosomal organization and evolution in four representative woodpeckers (Picidae, Piciformes) through BAC-FISH analysis.","authors":"Suziane Alves Barcellos, Rafael Kretschmer, Marcelo Santos de Souza, Victoria Tura, Luciano Cesar Pozzobon, Thales Renato Ochotorena de Freitas, Darren K Griffin, Rebecca O'Connor, Ricardo José Gunski, Analía Del Valle Garnero","doi":"10.1139/gen-2023-0096","DOIUrl":"10.1139/gen-2023-0096","url":null,"abstract":"<p><p>The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species (<i>Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus</i>, and <i>Picumnus nebulosus)</i> was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from <i>Gallus gallus</i> and <i>Taeniopygia guttata</i>. Findings suggest that <i>P. nebulosus</i> (2<i>n</i> = 110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for <i>V. spilogaster</i> (2<i>n</i> = 88) and demonstrated microchromosomal rearrangements involving <i>C. campestris</i> plus a single, unique hitherto undescribed rearrangement in <i>V. spilogaster</i>. This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of <i>M. candidus</i> is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140922037","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}
Pub Date : 2024-07-01Epub Date: 2024-05-06DOI: 10.1139/gen-2023-0126
Sven E Weber, Lennard Roscher-Ehrig, Tobias Kox, Amine Abbadi, Andreas Stahl, Rod J Snowdon
Advances in sequencing technology allow whole plant genomes to be sequenced with high quality. Combining genotypic and phenotypic data in genomic prediction helps breeders to select crossing partners in partially phenotyped populations. In plant breeding programs, the cost of sequencing entire breeding populations still exceeds available genotyping budgets. Hence, the method for genotyping is still mainly single nucleotide polymorphism (SNP) arrays; however, arrays are unable to assess the entire genome- and population-wide diversity. A compromise involves genotyping the entire population using an SNP array and a subset of the population with whole-genome sequencing. Both datasets can then be used to impute markers from whole-genome sequencing onto the entire population. Here, we evaluate whether imputation of whole-genome sequencing data enhances genomic predictions, using data from a nested association mapping population of rapeseed (Brassica napus). Employing two cross-validation schemes that mimic scenarios for the prediction of close and distant relatives, we show that imputed marker data do not significantly improve prediction accuracy, likely due to redundancy in relationship estimates and imputation errors. In simulation studies, only small improvements were observed, further corroborating the findings. We conclude that SNP arrays are already equipped with the information that is added by imputation through relationship and linkage disequilibrium.
测序技术的进步使得高质量的全植物基因组测序成为可能。在基因组预测中结合基因型和表型数据,有助于育种者在部分表型群体中选择杂交伙伴。在植物育种项目中,对整个育种群体进行测序的成本仍然超出了可用的基因分型预算。因此,基因分型的方法仍然主要是单核苷酸多态性(SNP)阵列;然而,阵列无法评估整个基因组和整个群体的多样性。一种折中的方法是使用 SNP 阵列对整个群体进行基因分型,并使用全基因组测序对群体的一个子集进行基因分型。然后,这两个数据集都可用于将全基因组测序的标记推算到整个群体上。在这里,我们利用油菜(Brassica napus)嵌套关联图谱群体的数据,评估了全基因组测序数据的归因是否能增强基因组预测。我们采用了两种交叉验证方案来模拟预测近亲和远亲的情况,结果表明,归因标记数据并不能显著提高预测准确性,这可能是由于关系估计中的冗余和归因误差造成的。在模拟研究中,只观察到很小的改进,这进一步证实了研究结果。我们的结论是,SNP 阵列已经具备了通过关系和连锁不平衡估算所增加的信息。
{"title":"Genomic prediction in <i>Brassica napus</i>: evaluating the benefit of imputed whole-genome sequencing data.","authors":"Sven E Weber, Lennard Roscher-Ehrig, Tobias Kox, Amine Abbadi, Andreas Stahl, Rod J Snowdon","doi":"10.1139/gen-2023-0126","DOIUrl":"10.1139/gen-2023-0126","url":null,"abstract":"<p><p>Advances in sequencing technology allow whole plant genomes to be sequenced with high quality. Combining genotypic and phenotypic data in genomic prediction helps breeders to select crossing partners in partially phenotyped populations. In plant breeding programs, the cost of sequencing entire breeding populations still exceeds available genotyping budgets. Hence, the method for genotyping is still mainly single nucleotide polymorphism (SNP) arrays; however, arrays are unable to assess the entire genome- and population-wide diversity. A compromise involves genotyping the entire population using an SNP array and a subset of the population with whole-genome sequencing. Both datasets can then be used to impute markers from whole-genome sequencing onto the entire population. Here, we evaluate whether imputation of whole-genome sequencing data enhances genomic predictions, using data from a nested association mapping population of rapeseed (<i>Brassica napus</i>). Employing two cross-validation schemes that mimic scenarios for the prediction of close and distant relatives, we show that imputed marker data do not significantly improve prediction accuracy, likely due to redundancy in relationship estimates and imputation errors. In simulation studies, only small improvements were observed, further corroborating the findings. We conclude that SNP arrays are already equipped with the information that is added by imputation through relationship and linkage disequilibrium.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140850004","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}
Pub Date : 2024-06-01Epub Date: 2024-02-12DOI: 10.1139/gen-2023-0101
Rafael Kretschmer, Marcelo Santos de Souza, Ricardo José Gunski, Analía Del Valle Garnero, Thales Renato Ochotorena de Freitas, Edison Zefa, Gustavo Akira Toma, Marcelo de Bello Cioffi, Edivaldo Herculano Corrêa de Oliveira, Rebecca E O'Connor, Darren K Griffin
The Cuculiformes are a family of over 150 species that live in a range of habitats, such as forests, savannas, and deserts. Here, bacterial artificial chromosome (BAC) probes (75 from chicken and 14 from zebra finch macrochromosomes 1-10 +ZW and for microchromosomes 11-28 (except 16)) were used to investigate chromosome homologies between chicken and the squirrel cuckoo (Piaya cayana). In addition, repetitive DNA probes were applied to characterize the chromosome organization and to explore the role of these sequences in the karyotype evolution of P. cayana. We also applied BAC probes for chicken chromosome 17 and Z to the guira cuckoo (Guira guira) to test whether this species has an unusual Robertsonian translocation between a microchromosome and the Z chromosome, recently described in the smooth-billed ani (Crotophaga ani). Our results revealed extensive chromosome reorganization with inter- and intrachromosomal rearrangements in P. cayana, including a conspicuous chromosome size and heterochromatin polymorphism on chromosome pair 20. Furthermore, we confirmed that the Z-autosome Robertsonian translocation found in C. ani is also found in G. guira, not P. cayana. These findings suggest that this translocation occurred prior to the divergence between C. ani and G. guira, but after the divergence with P. cayana.
鹃形目有 150 多个物种,生活在森林、热带草原和沙漠等多种栖息地。本文利用细菌人工染色体(BAC)探针(75个来自鸡,14个来自斑马雀大染色体1-10 +ZW和微染色体11-28(16除外))研究鸡和松鼠杜鹃(Piaya cayana)的染色体同源性。此外,我们还使用了重复 DNA 探针来描述染色体组织的特征,并探索这些序列在松鼠杜鹃核型进化中的作用。我们还在吉拉杜鹃(Guira guira)中应用了鸡第17号染色体和Z染色体的BAC探针,以检验该物种是否存在微染色体与Z染色体之间不寻常的罗伯逊易位(最近在平嘴杜鹃(Crotophaga ani)中描述过)。我们的研究结果表明,P. cayana 的染色体在染色体间和染色体内发生了广泛的重组,包括第 20 对染色体上明显的染色体大小和异染色质多态性。此外,我们证实在 C. ani 中发现的 Z 自体罗伯逊易位也存在于 G. guira 中,而不是 P. cayana 中。这些发现表明,这种易位发生在 C. ani 与 G. guira 的分化之前,而在与 P. cayana 的分化之后。
{"title":"Understanding the chromosomal evolution in cuckoos (Aves, Cuculiformes): a journey through unusual rearrangements.","authors":"Rafael Kretschmer, Marcelo Santos de Souza, Ricardo José Gunski, Analía Del Valle Garnero, Thales Renato Ochotorena de Freitas, Edison Zefa, Gustavo Akira Toma, Marcelo de Bello Cioffi, Edivaldo Herculano Corrêa de Oliveira, Rebecca E O'Connor, Darren K Griffin","doi":"10.1139/gen-2023-0101","DOIUrl":"10.1139/gen-2023-0101","url":null,"abstract":"<p><p>The Cuculiformes are a family of over 150 species that live in a range of habitats, such as forests, savannas, and deserts. Here, bacterial artificial chromosome (BAC) probes (75 from chicken and 14 from zebra finch macrochromosomes 1-10 +ZW and for microchromosomes 11-28 (except 16)) were used to investigate chromosome homologies between chicken and the squirrel cuckoo (<i>Piaya cayana</i>). In addition, repetitive DNA probes were applied to characterize the chromosome organization and to explore the role of these sequences in the karyotype evolution of <i>P</i>. <i>cayana</i>. We also applied BAC probes for chicken chromosome 17 and Z to the guira cuckoo (<i>Guira guira</i>) to test whether this species has an unusual Robertsonian translocation between a microchromosome and the Z chromosome, recently described in the smooth-billed ani (<i>Crotophaga ani</i>). Our results revealed extensive chromosome reorganization with inter- and intrachromosomal rearrangements in <i>P</i>. <i>cayana</i>, including a conspicuous chromosome size and heterochromatin polymorphism on chromosome pair 20. Furthermore, we confirmed that the Z-autosome Robertsonian translocation found in <i>C</i>. <i>ani</i> is also found in <i>G</i>. <i>guira</i>, not <i>P</i>. <i>cayana</i>. These findings suggest that this translocation occurred prior to the divergence between <i>C</i>. <i>ani</i> and <i>G</i>. <i>guira</i>, but after the divergence with <i>P</i>. <i>cayana</i>.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139722300","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}
Pub Date : 2024-06-01Epub Date: 2024-03-01DOI: 10.1139/gen-2023-0041
Monir Poorrashidi, Megan Hitchcock, Jianping Xu
Campylobacter infections are a leading cause of bacterial diarrheal illness worldwide, with increasing reports of outbreaks in both developing and developed countries. Most studies investigating strain genotypes and epidemiology of Campylobacter jejuni examined on a local scale. Using the archived multilocus sequence typing data at seven loci, and associated strain metadata from the PubMLST database, here we investigated the spatial and temporal genetic structure of the global population of C. jejuni. Our analyses revealed evidence for clonal dispersals of multiple sequence types (STs) among countries and continents. However, despite the observed clonal dispersal and that most genetic variations were found within individual geographic subpopulations, both the non-clone-corrected and clone-corrected samples showed evidence of significant genetic differentiation among national and continental subpopulations, with non-clone-corrected samples showing greater differentiation than clone-corrected samples. Phylogenetic incompatibility analyses provided evidence for recombination within each continental subpopulation. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across the samples. Temporally, multiple STs were found to persist across four decades and the five globally most common STs showed relatively stable frequencies over the last two decades. We discussed the implications of our results to food security, disease transmission, and public health management.
{"title":"Meta-analyses of the global multilocus genotypes of the human pathogen <i>Campylobacter jejuni</i>.","authors":"Monir Poorrashidi, Megan Hitchcock, Jianping Xu","doi":"10.1139/gen-2023-0041","DOIUrl":"10.1139/gen-2023-0041","url":null,"abstract":"<p><p><i>Campylobacter</i> infections are a leading cause of bacterial diarrheal illness worldwide, with increasing reports of outbreaks in both developing and developed countries. Most studies investigating strain genotypes and epidemiology of <i>Campylobacter jejuni</i> examined on a local scale. Using the archived multilocus sequence typing data at seven loci, and associated strain metadata from the PubMLST database, here we investigated the spatial and temporal genetic structure of the global population of <i>C. jejuni</i>. Our analyses revealed evidence for clonal dispersals of multiple sequence types (STs) among countries and continents. However, despite the observed clonal dispersal and that most genetic variations were found within individual geographic subpopulations, both the non-clone-corrected and clone-corrected samples showed evidence of significant genetic differentiation among national and continental subpopulations, with non-clone-corrected samples showing greater differentiation than clone-corrected samples. Phylogenetic incompatibility analyses provided evidence for recombination within each continental subpopulation. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across the samples. Temporally, multiple STs were found to persist across four decades and the five globally most common STs showed relatively stable frequencies over the last two decades. We discussed the implications of our results to food security, disease transmission, and public health management.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140012466","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}
For peanut, the lack of stable cytological markers is a barrier to tracking specific chromosomes, elucidating the genetic relationships between genomes and identifying chromosomal variations. Chromosome mapping using single-copy oligonucleotide (oligo) probe libraries has unique advantages for identifying homologous chromosomes and chromosomal rearrangements. In this study, we developed two whole-chromosome single-copy oligo probe libraries, LS-7A and LS-8A, based on the reference genome sequences of chromosomes 7A and 8A of Arachis duranensis. Fluorescence in situ hybridization (FISH) analysis confirmed that the libraries could specifically paint chromosomes 7 and 8. In addition, sequential FISH and electronic localization of LS-7A and LS-8A in A. duranensis (AA) and A. ipaensis (BB) showed that chromosomes 7A and 8A contained translocations and inversions relative to chromosomes 7B and 8B. Analysis of the chromosomes of wild Arachis species using LS-8A confirmed that this library could accurately and effectively identify A genome species. Finally, LS-7A and LS-8A were used to paint the chromosomes of interspecific hybrids and their progenies, which verified the authenticity of the interspecific hybrids and identified a disomic addition line. This study provides a model for developing specific oligo probes to identify the structural variations of other chromosomes in Arachis and demonstrates the practical utility of LS-7A and LS-8A.
{"title":"Development and application of whole-chromosome painting of chromosomes 7A and 8A of <i>Arachis duranensis</i> based on chromosome-specific single-copy oligonucleotides.","authors":"Chenyu Li, Liuyang Fu, Qian Wang, Hua Liu, Guoquan Chen, Feiyan Qi, Maoning Zhang, Yaoguang Jia, Xiaona Li, Bingyan Huang, Wenzhao Dong, Pei Du, Xinyou Zhang","doi":"10.1139/gen-2023-0116","DOIUrl":"10.1139/gen-2023-0116","url":null,"abstract":"<p><p>For peanut, the lack of stable cytological markers is a barrier to tracking specific chromosomes, elucidating the genetic relationships between genomes and identifying chromosomal variations. Chromosome mapping using single-copy oligonucleotide (oligo) probe libraries has unique advantages for identifying homologous chromosomes and chromosomal rearrangements. In this study, we developed two whole-chromosome single-copy oligo probe libraries, LS-7A and LS-8A, based on the reference genome sequences of chromosomes 7A and 8A of <i>Arachis duranensis</i>. Fluorescence in situ hybridization (FISH) analysis confirmed that the libraries could specifically paint chromosomes 7 and 8. In addition, sequential FISH and electronic localization of LS-7A and LS-8A in <i>A. duranensis (</i>AA) and <i>A. ipaensis</i> (BB) showed that chromosomes 7A and 8A contained translocations and inversions relative to chromosomes 7B and 8B. Analysis of the chromosomes of wild <i>Arachis</i> species using LS-8A confirmed that this library could accurately and effectively identify A genome species. Finally, LS-7A and LS-8A were used to paint the chromosomes of interspecific hybrids and their progenies, which verified the authenticity of the interspecific hybrids and identified a disomic addition line. This study provides a model for developing specific oligo probes to identify the structural variations of other chromosomes in <i>Arachis</i> and demonstrates the practical utility of LS-7A and LS-8A.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139939909","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}
Pub Date : 2024-06-01Epub Date: 2024-02-08DOI: 10.1139/gen-2023-0084
Emily L Wynn, A Springer Browne, Michael L Clawson
Mycoplasmopsis bovis is a worldwide economically important pathogen of cattle that can cause or indirectly contribute to bovine respiratory disease. M. bovis is also a primary etiological agent of respiratory disease in bison with high mortality rates. A major challenge in the development of an efficacious M. bovis vaccine is the design of antigens that contain both MHC-1 and MHC-2 T-cell epitopes, and that account for population level diversity within the species. Publicly available genomes and sequence read archive libraries of 381 M. bovis strains isolated from cattle (n = 202) and bison (n = 179) in North America were used to identify a core genome of 575 genes, including 38 that encode either known or predicted secreted or outer membrane proteins. The antigenic potentials of the proteins were characterized by the presence and strength of their T-cell epitopes, and their protein variant diversity at the population-level. The proteins had surprisingly low diversity and varying predictive levels of T-cell antigenicity. These results provide a reference for the selection or design of antigens for vaccine testing against strains infecting North American cattle and bison.
牛支原体是一种具有全球重要经济价值的牛病原体,可引起或间接引起牛呼吸道疾病。牛支原体也是野牛呼吸道疾病的主要病原体,死亡率很高。开发有效的牛海绵状芽孢杆菌疫苗的一大挑战是设计同时包含 MHC-1 和 MHC-2 T 细胞表位的抗原,并考虑到该物种内种群水平的多样性。我们利用从北美牛(202 头)和野牛(179 头)中分离出的 381 株牛海绵状芽孢杆菌的公开基因组和序列读取档案(SRA)文库,确定了包含 575 个基因的核心基因组,其中 38 个基因编码已知或预测的分泌蛋白或外膜蛋白。这些蛋白质的抗原潜能是通过其 T 细胞表位的存在和强度以及在群体水平上的蛋白质变异多样性来描述的。这些蛋白质的多样性出奇地低,T 细胞抗原性的预测水平也各不相同。这些结果为选择或设计针对北美牛和野牛感染菌株的疫苗测试抗原提供了参考。
{"title":"Diversity and antigenic potentials of <i>Mycoplasmopsis bovis</i> secreted and outer membrane proteins within a core genome of strains isolated from North American bison and cattle.","authors":"Emily L Wynn, A Springer Browne, Michael L Clawson","doi":"10.1139/gen-2023-0084","DOIUrl":"10.1139/gen-2023-0084","url":null,"abstract":"<p><p><i>Mycoplasmopsis bovis</i> is a worldwide economically important pathogen of cattle that can cause or indirectly contribute to bovine respiratory disease. <i>M. bovis</i> is also a primary etiological agent of respiratory disease in bison with high mortality rates. A major challenge in the development of an efficacious <i>M. bovis</i> vaccine is the design of antigens that contain both MHC-1 and MHC-2 T-cell epitopes, and that account for population level diversity within the species. Publicly available genomes and sequence read archive libraries of 381 <i>M. bovis</i> strains isolated from cattle (<i>n</i> = 202) and bison (<i>n</i> = 179) in North America were used to identify a core genome of 575 genes, including 38 that encode either known or predicted secreted or outer membrane proteins. The antigenic potentials of the proteins were characterized by the presence and strength of their T-cell epitopes, and their protein variant diversity at the population-level. The proteins had surprisingly low diversity and varying predictive levels of T-cell antigenicity. These results provide a reference for the selection or design of antigens for vaccine testing against strains infecting North American cattle and bison.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139706516","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}
Pub Date : 2024-06-01Epub Date: 2024-02-27DOI: 10.1139/gen-2023-0135
Yina Her, Danielle M Pascual, Zoe Goldstone-Joubert, Paul C Marcogliese
The last decade has been highlighted by the increased use of next-generation DNA sequencing technology to identify novel human disease genes. A critical downstream part of this process is assigning function to a candidate gene variant. Functional studies in Drosophila melanogaster, the common fruit fly, have made a prominent contribution in annotating variant impact in an in vivo system. The use of patient-derived knock-in flies or rescue-based, "humanization", approaches are novel and valuable strategies in variant testing but have been recently widely reviewed. An often-overlooked strategy for determining variant impact has been GAL4/upstream activation sequence-mediated tissue-defined overexpression in Drosophila. This mini-review will summarize the recent contribution of ectopic overexpression of human reference and variant cDNA in Drosophila to assess variant function, interpret the consequence of the variant, and in some cases infer biological mechanisms.
近十年来,越来越多地使用新一代 DNA 测序技术来鉴定新型人类疾病基因。这一过程的一个关键下游环节是为候选基因变异赋予功能。在黑腹果蝇(常见的果蝇)中进行的功能研究,为注释变异基因在体内系统中的影响做出了突出贡献。使用源自患者的基因敲入蝇或基于拯救的 "人源化 "方法是变异测试中既新颖又有价值的策略,但最近已被广泛评述。果蝇中 GAL4/UAS 介导的组织定义过表达是确定变异影响的一种经常被忽视的策略。本微型综述将总结果蝇异位过表达人类参考和变异 cDNA 在评估变异功能、解释变异后果以及在某些情况下推断生物机制方面的最新贡献。
{"title":"Variant functional assessment in <i>Drosophila</i> by overexpression: what can we learn?","authors":"Yina Her, Danielle M Pascual, Zoe Goldstone-Joubert, Paul C Marcogliese","doi":"10.1139/gen-2023-0135","DOIUrl":"10.1139/gen-2023-0135","url":null,"abstract":"<p><p>The last decade has been highlighted by the increased use of next-generation DNA sequencing technology to identify novel human disease genes. A critical downstream part of this process is assigning function to a candidate gene variant. Functional studies in <i>Drosophila melanogaster</i>, the common fruit fly, have made a prominent contribution in annotating variant impact in an in vivo system. The use of patient-derived knock-in flies or rescue-based, \"humanization\", approaches are novel and valuable strategies in variant testing but have been recently widely reviewed. An often-overlooked strategy for determining variant impact has been GAL4/upstream activation sequence-mediated tissue-defined overexpression in <i>Drosophila</i>. This mini-review will summarize the recent contribution of ectopic overexpression of human reference and variant cDNA in <i>Drosophila</i> to assess variant function, interpret the consequence of the variant, and in some cases infer biological mechanisms.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139982802","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}