Genetica最新文献_第4页

Patterns of cytonuclear discordance and divergence between subspecies of the scarlet macaw (Ara macao) in Central America. 中美洲猩红金刚鹦鹉亚种间的细胞核不一致和分化模式。

IF 1.5 4区生物学

Genetica Pub Date : 2023-10-01 Epub Date: 2023-08-23 DOI: 10.1007/s10709-023-00193-x

Matthew L Aardema, Kari L Schmidt, George Amato

{"title":"Patterns of cytonuclear discordance and divergence between subspecies of the scarlet macaw (Ara macao) in Central America.","authors":"Matthew L Aardema, Kari L Schmidt, George Amato","doi":"10.1007/s10709-023-00193-x","DOIUrl":"10.1007/s10709-023-00193-x","url":null,"abstract":"The scarlet macaw, Ara macao, is a neotropical parrot that contains two described subspecies with broadly discrete geographical distributions. One subspecies, A. m. macao, is found from South America north into southwestern Costa Rica, while the second subspecies, A. m. cyanoptera, is found from eastern Costa Rica north into central Mexico. Our previous research using mitochondrial data to examine phylogeographical divergence across the collective range of these two subspecies concluded that they represent distinct evolutionary entities, with minimal contemporary hybridization between them. Here we further examine phylogenetic relationships and patterns of genetic variation between these two subspecies using a dataset of genetic markers derived from their nuclear genomes. Our analyses show clear nuclear divergence between A. m. macao and A. m. cyanoptera in Central America. Collectively however, samples from this region appear genetically more similar to one another than they do to the examined South American (Brazilian) A. m. macao sample. This observation contradicts our previous assessments based on mitochondrial DNA analyses that A. m. macao in Central and South America represent a single phylogeographical group that is evolutionarily distinct from Central American A. m. cyanoptera. Nonetheless, in agreement with our previous findings, ongoing genetic exchange between the two subspecies appears limited. Rather, our analyses indicate that incomplete lineage sorting is the best supported explanation for cytonuclear discordance within these parrots. High-altitude regions in Central America may act as a reproductive barrier, limiting contemporary hybridization between A. m. macao and A. m. cyanoptera. The phylogeographic complexities of scarlet macaw taxa in this region highlight the need for additional evolutionary examinations of these populations.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"281-292"},"PeriodicalIF":1.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10654179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10060369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification. 新热带细尾蛇科鱼类（Ostariophysi，Characiformes）多样化的核型变化的宏观进化后果。

IF 1.5 4区生物学

Genetica Pub Date : 2023-10-01 Epub Date: 2023-08-11 DOI: 10.1007/s10709-023-00191-z

Uedson Pereira Jacobina, Alany Itala Pontes, Lucas Costa, Gustavo Souza

{"title":"Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification.","authors":"Uedson Pereira Jacobina, Alany Itala Pontes, Lucas Costa, Gustavo Souza","doi":"10.1007/s10709-023-00191-z","DOIUrl":"10.1007/s10709-023-00191-z","url":null,"abstract":"In the Neotropical region, one of the most diverse families of freshwater fishes is the monophyletic Serrasalmidae. Karyotypically, the family shows high diversity in chromosome numbers (2n = 54 to 64). However, little is discussed about whether the chromosomal changes are associated with cladogenetic events within this family. In the present study, we evaluated the role of chromosomal changes in the evolutionary diversification of Serrasalmidae. Our phylogenetic sampling included 36 species and revealed three main clades. The ancestral chromosome number reconstruction revealed the basic number 2n = 54 and a high frequency of ascending dysploid events in the most derived lineages. Our biogeographic reconstruction suggests an Amazonian origin of the family at 48-38 Mya, with independent colonization of other basins between 15 and 8 Mya. We did not find specific chromosomal changes or increased diversification rates correlated with the colonization of a new environment. On the other hand, an increase in the diversification rate was detected involving the genus Serrasalmus and Pygocentrus in the Miocene, correlated with the stasis of 2n = 60. Our data demonstrate that chromosomal rearrangements might have played an important evolutionary role in major cladogenetic events in Serrasalmidae, revealing them as a possible evolutionary driver in their diversification.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"311-321"},"PeriodicalIF":1.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10199706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Correction to: Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification. 更正：新热带Serrasalmidae鱼类（Ostariophysi，Characiformes）多样化的核型变化的宏观进化后果。

IF 1.5 4区生物学

Genetica Pub Date : 2023-10-01 DOI: 10.1007/s10709-023-00195-9

Uedson Pereira Jacobina, Alany Itala Pontes, Lucas Costa, Gustavo Souza

引用次数: 0

Chromosome evolution in Iberolacerta, a genus that deviates from the standard karyotype formula of Lacertidae. 偏离了乳虫科标准核型公式的一属——乳虫属的染色体进化。

IF 1.5 4区生物学

Genetica Pub Date : 2023-10-01 Epub Date: 2023-09-01 DOI: 10.1007/s10709-023-00194-w

Horacio Naveira, Verónica Rojo, Iván Gómez-Seoane, Malcolm A Ferguson-Smith, Jorge C Pereira, Andrés Martínez-Lage

{"title":"Chromosome evolution in Iberolacerta, a genus that deviates from the standard karyotype formula of Lacertidae.","authors":"Horacio Naveira, Verónica Rojo, Iván Gómez-Seoane, Malcolm A Ferguson-Smith, Jorge C Pereira, Andrés Martínez-Lage","doi":"10.1007/s10709-023-00194-w","DOIUrl":"10.1007/s10709-023-00194-w","url":null,"abstract":"This paper describes the preparation of flow-sorted chromosome paints from the Iberian Rock lizard Iberolacerta monticola, exemplifying their subsequent use in cross-species comparisons of chromosome painting. We carried out comparative analyses of chromosome evolution in the congeneric species I. galani and I. bonnali, as well as in two other species of Lacertini (Lacerta schreiberi and Timon lepidus) whose sex chromosomes were also studied through comparative genomic hybridization. Most species of Lacertini possess a diplod number of 2n = 38, with 36 acrocentric macrochromosomes and 2 microchromosomes. However, the nine species included in the genus Iberolacerta do not possess microchromosomes. Furthermore, very conspicuous differences from the standard Lacertini karyotype were observed in the three Pyrenean species of this genus, which included several biarmed metacentrics and a Z1Z2W multiple sex-chromosome system. With the possible exception of L. schreiberi, all the species of the family Lacertidae described to date appear to share homologous Z chromosomes, which date back to the last common ancestor of the whole group. We provide conclusive evidence that L. schreiberi should no longer be considered an exception to this rule, and demonstrate that the loss of microchromosomes in Iberolacerta was produced by their fusion to a middle-sized chromosome. Furthermore, we show that the multiple sex-chromosome system of the Pyrenean species of Iberolacerta originated from the fusion of the ancestral W chromosome with one of the shortest autosomes, and provide additional evidence of the fast evolution of DNA sequences linked to the W chromosome in Lacertini.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"267-279"},"PeriodicalIF":1.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10654178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10132619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic survey of MYB gene family in six pearl millet (Pennisetum glaucum) varieties and their response to abiotic stresses. 6个珍珠粟(Pennisetum glaucum)品种MYB基因家族基因组调查及其对非生物胁迫的响应

IF 1.5 4区生物学

Genetica Pub Date : 2023-06-01 DOI: 10.1007/s10709-023-00188-8

Jinhang Lv, Yue Xu, Xuming Dan, Yuchen Yang, Chunli Mao, Xixi Ma, Jie Zhu, Min Sun, Yarong Jin, Linkai Huang

{"title":"Genomic survey of MYB gene family in six pearl millet (Pennisetum glaucum) varieties and their response to abiotic stresses.","authors":"Jinhang Lv, Yue Xu, Xuming Dan, Yuchen Yang, Chunli Mao, Xixi Ma, Jie Zhu, Min Sun, Yarong Jin, Linkai Huang","doi":"10.1007/s10709-023-00188-8","DOIUrl":"https://doi.org/10.1007/s10709-023-00188-8","url":null,"abstract":"In addition to their roles in developmental and metabolic processes, MYB transcription factors play crucial roles in plant defense mechanisms and stress responses. A comprehensive analysis of six pearl millet genomes revealed the presence of 1133 MYB genes, which can be classified into four phylogenetically distinct subgroups. The duplication pattern of MYB genes across the pearl millet genomes demonstrates their conserved and similar evolutionary history. Overall, MYB genes were observed to be involved in drought and heat stress responses, with stronger differential expressed observed in root tissues. Multiple analyses indicated that MYB genes mediate abiotic stress responses by modulating abscisic acid-related pathways, circadian rhythms, and histone modification processes. A substantial number of duplicated genes were determined to exhibit differential expression under abiotic stress. The consistent positive expression trend observed in duplicated gene pairs, such as PMA5G04432.1 and PMA2G00728.1, across various abiotic stresses suggests that duplicated MYB genes plays a key role in the evolution of adaptive responses of pearl millet to abiotic stresses.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"151 3","pages":"251-265"},"PeriodicalIF":1.5,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9693710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 1

SATB2 expression in hematolymphoid neoplasms. SATB2 在血淋巴肿瘤中的表达。

IF 0.6 4区生物学

Genetica Pub Date : 2023-06-01 Epub Date: 2023-04-03 DOI: 10.1007/s12308-023-00543-w

Gerald C Tiu, Yasodha Natkunam, Sebastian Fernandez-Pol

引用次数: 0

Sequence and expression analysis of the spermatogenesis-specific gene cognates, wampa and Prosα6T, in Drosophila suzukii. 苏氏果蝇精子发生特异性同源基因wampa和Prosα6T的序列与表达分析。

IF 1.5 4区生物学

Genetica Pub Date : 2023-06-01 DOI: 10.1007/s10709-023-00189-7

Qinwen Xia, Kaleem Tariq, Daniel A Hahn, Alfred M Handler

{"title":"Sequence and expression analysis of the spermatogenesis-specific gene cognates, wampa and Prosα6T, in Drosophila suzukii.","authors":"Qinwen Xia, Kaleem Tariq, Daniel A Hahn, Alfred M Handler","doi":"10.1007/s10709-023-00189-7","DOIUrl":"https://doi.org/10.1007/s10709-023-00189-7","url":null,"abstract":"The sterile insect technique (SIT) is a highly effective biologically-based method for the population suppression of highly invasive insect pests of medical and agricultural importance. The efficacy of SIT could be significantly enhanced, however, by improved methods of male sterilization that avoid the fitness costs of irradiation. An alternative sterilization method is possible by gene-editing that targets genes essential for sperm maturation and motility, rendering them nonfunctional, similar to the CRISPR-Cas9 targeting of β2-tubulin in the genetic model system, Drosophila melanogaster. However, since genetic strategies for sterility are susceptible to breakdown or resistance in mass-reared populations, alternative targets for sterility are important for redundancy or strain replacement. Here we have identified and characterized the sequence and transcriptional expression of two genes in a Florida strain of Drosophila suzukii, that are cognates of the D. melanogaster spermatocyte-specific genes wampa and Prosalpha6T. Wampa encodes a coiled-coil dynein subunit required for axonemal assembly, and the proteasome subunit gene, Prosalpha6T, is required for spermatid individualization and nuclear maturation. The reading frames of these genes differed from their NCBI database entries derived from a D. suzukii California strain by 44 and 8 nucleotide substitutions/polymorphisms, respectively, though all substitutions were synonymous resulting in identical peptide sequences. Expression of both genes is predominant in the male testis, and they share similar transcriptional profiles in adult males with β2-tubulin. Their amino acid sequences are highly conserved in dipteran species, including pest species subject to SIT control, supporting their potential use in targeted male sterilization strategies.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"151 3","pages":"215-223"},"PeriodicalIF":1.5,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9994512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Molecular evolution of the hemoglobin gene family across vertebrates. 脊椎动物血红蛋白基因家族的分子进化。

IF 1.5 4区生物学

Genetica Pub Date : 2023-06-01 DOI: 10.1007/s10709-023-00187-9

Yang Mao, Taotao Peng, Feng Shao, Qingyuan Zhao, Zuogang Peng

{"title":"Molecular evolution of the hemoglobin gene family across vertebrates.","authors":"Yang Mao, Taotao Peng, Feng Shao, Qingyuan Zhao, Zuogang Peng","doi":"10.1007/s10709-023-00187-9","DOIUrl":"https://doi.org/10.1007/s10709-023-00187-9","url":null,"abstract":"Adaptation to various altitudes and oxygen levels is a major aspect of vertebrate evolution. Hemoglobin is an erythrocyte protein belonging to the globin superfamily, and the α-, β-globin genes of jawed vertebrates encode tetrameric ((α2β2) hemoglobin, which contributes to aerobic metabolism by delivering oxygen from the respiratory exchange surfaces into cells. However, there are various gaps in knowledge regarding hemoglobin gene evolution, including patterns in cartilaginous fish and the roles of gene conversion in various taxa. Hence, we evaluated the evolutionary history of the vertebrate hemoglobin gene family by analyses of 97 species representing all classes of vertebrates. By genome-wide analyses, we extracted 879 hemoglobin sequences. Members of the hemoglobin gene family were conserved in birds and reptiles but variable in mammals, amphibians, and teleosts. Gene motifs, structures, and synteny were relatively well-conserved among vertebrates. Our results revealed that purifying selection contributed substantially to the evolution of all vertebrate hemoglobin genes, with mean dN/dS (ω) values ranging from 0.057 in teleosts to 0.359 in reptiles. In general, after the fish-specific genome duplication, the teleost hemoglobin genes showed variation in rates of evolution, and the β-globin genes showed relatively high ω values after a gene transposition event in amniotes. We also observed that the frequency of gene conversion was high in amniotes, with fewer hemoglobin genes and higher rates of evolution. Collectively, our findings provide detail insight into complex evolutionary processes shaping the vertebrate hemoglobin gene family, involving gene duplication, gene loss, purifying selection, and gene conversion.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"151 3","pages":"201-213"},"PeriodicalIF":1.5,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10008975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Genome-wide identification and expression analysis of the Pisum sativum (L.) APETALA2/ethylene-responsive factor (AP2/ERF) gene family reveals functions in drought and cold stresses. 对豌豆（L.）APETALA2/乙烯反应因子（AP2/ERF）基因家族的全基因组鉴定和表达分析揭示了其在干旱和寒冷胁迫下的功能。

IF 1.5 4区生物学

Genetica Pub Date : 2023-06-01 Epub Date: 2023-06-03 DOI: 10.1007/s10709-023-00190-0

Trishna Jarambasa, Preetom Regon, Sabnoor Yeasrin Jyoti, Divya Gupta, Sanjib Kumar Panda, Bhaben Tanti

{"title":"Genome-wide identification and expression analysis of the Pisum sativum (L.) APETALA2/ethylene-responsive factor (AP2/ERF) gene family reveals functions in drought and cold stresses.","authors":"Trishna Jarambasa, Preetom Regon, Sabnoor Yeasrin Jyoti, Divya Gupta, Sanjib Kumar Panda, Bhaben Tanti","doi":"10.1007/s10709-023-00190-0","DOIUrl":"10.1007/s10709-023-00190-0","url":null,"abstract":"AP2/ERF (APETALA2/Ethylene Response Factor) is a family of transcription factors that play essential roles in regulating gene expression in response to various environmental stimuli, including biotic and abiotic stresses, hormone signaling, and developmental processes. Pisum sativum (L.), commonly known as garden pea, is a winter crop sensitive to high temperatures and can also be affected by extreme cold and drought conditions. This study performed a genome-wide analysis of AP2/ERF genes and identified 153 AP2/ERF genes in P. sativum. Based on the conserved AP2/ERF domain and sequence homology, they were classified into AP2 (APETALA2), ERF (Ethylene Response Factor), DREB (Dehydration responsive element-binding), RAV (Related to Abscisic Acid Insensitive 3/ Viviparous 1) and Soloist subfamily. The DREB and ERF subfamily were further divided into groups A1-6 and B1-B6. Tandem and segmental duplication events were more frequent in the ERF subfamily, which can have important implications for their evolution and functional diversification. Under cold stress, the expression of DREB1A was highly induced in leaves, whereas DREB1B was suppressed. Similarly, the DREB2A, DREB2C, DREB2E, and DREB2F were induced in leaves under drought stress. The putative target genes of AP2/ERF transcription factors are highly diversified, suggesting that they play essential roles in various physiological responses in plants, including responses to biotic and abiotic stresses as well as developmental processes. Thus, this study of AP2/ERF genes and their functions provides valuable insight into how P. sativum responds to different environmental conditions, including cold and drought stresses.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"151 3","pages":"225-239"},"PeriodicalIF":1.5,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9994013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 2

Integrative comparative analysis of avian chromosome evolution by in-silico mapping of the gene ontology of homologous synteny blocks and evolutionary breakpoint regions. 基于同源合成块和进化断点区域基因本体的鸟类染色体进化综合比较分析。

IF 1.5 4区生物学

Genetica Pub Date : 2023-06-01 DOI: 10.1007/s10709-023-00185-x

Jules Claeys, Michael N Romanov, Darren K Griffin

{"title":"Integrative comparative analysis of avian chromosome evolution by in-silico mapping of the gene ontology of homologous synteny blocks and evolutionary breakpoint regions.","authors":"Jules Claeys, Michael N Romanov, Darren K Griffin","doi":"10.1007/s10709-023-00185-x","DOIUrl":"https://doi.org/10.1007/s10709-023-00185-x","url":null,"abstract":"Avian chromosomes undergo more intra- than interchromosomal rearrangements, which either induce or are associated with genome variations among birds. Evolving from a common ancestor with a karyotype not dissimilar from modern chicken, two evolutionary elements characterize evolutionary change: homologous synteny blocks (HSBs) constitute common conserved parts at the sequence level, while evolutionary breakpoint regions (EBRs) occur between HSBs, defining the points where rearrangement occurred. Understanding the link between the structural organization and functionality of HSBs and EBRs provides insight into the mechanistic basis of chromosomal change. Previously, we identified gene ontology (GO) terms associated with both; however, here we revisit our analyses in light of newly developed bioinformatic algorithms and the chicken genome assembly galGal6. We aligned genomes available for six birds and one lizard species, identifying 630 HSBs and 19 EBRs. We demonstrate that HSBs hold vast functionality expressed by GO terms that have been largely conserved through evolution. Particularly, we found that genes within microchromosomal HSBs had specific functionalities relevant to neurons, RNA, cellular transport and embryonic development, and other associations. Our findings suggest that microchromosomes may have conserved throughout evolution due to the specificity of GO terms within their HSBs. The detected EBRs included those found in the genome of the anole lizard, meaning they were shared by all saurian descendants, with others being unique to avian lineages. Our estimate of gene richness in HSBs supported the fact that microchromosomes contain twice as many genes as macrochromosomes.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"151 3","pages":"167-178"},"PeriodicalIF":1.5,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10267005/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9689931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0