scholarly journals Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature

2021 ◽  
Vol 12 ◽  
Author(s):  
Lian-Ying Shen ◽  
Hang Luo ◽  
Xiao-Ling Wang ◽  
Xue-Meng Wang ◽  
Xiao-Jing Qiu ◽  
...  
Keyword(s):  
Population Structure ◽  
Genome Assembly ◽  
Effective Population ◽  
Last Glacial Period ◽  
Population Structure Analysis ◽  
History Of ◽  
Ziziphus Jujuba ◽  
Fruit Flavor ◽  
High Quality Genome ◽  
The Last Glacial

Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes #3 in D1, #1 in D2, and #4 in wild. Genes under the most significant selection on chromosomes #4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals Genome Assembly and Population Resequencing Reveal the Geographical Divergence of 'Shanmei'(Rubus corchorifolius)

2021 ◽  
Author(s):  
Yinqing Yang ◽  
Kang Zhang ◽  
Ya Xiao ◽  
Lingkui Zhang ◽  
Yile Huang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Ancestral Population ◽  
Effective Population ◽  
High Quality ◽  
Local Environments ◽  
Rubus Species ◽  
Rubus Chingii ◽  
Rubus Chingii Hu ◽  
Genomic Regions ◽  
High Quality Genome

Rubus corchorifolius (Shanmei or mountain berry, 2n =14) is widely distributed in China, and its fruit has high nutritional and medicinal values. Here, we report a high-quality chromosome-scale genome assembly of Shanmei, with a size of 215.69 Mb and encompassing 26696 genes. Genome comparisons among Rosaceae species show that Shanmei and Fupenzi(Rubus chingii Hu) are most closely related, and then is blackberry (Rubus occidentalis). Further resequencing of 101 samples of Shanmei collected from four regions in provinces of Yunnan, Hunan, Jiangxi and Sichuan in South China reveals that the Hunan population of Shanmei possesses the highest diversity and may represent the relatively more ancestral population. Moreover, the Yunnan population undergoes strong selection based on nucleotide diversity, linkage disequilibrium and the historical effective population size analyses. Furthermore, genes from candidate genomic regions that show strong divergence are significantly enriched in flavonoid biosynthesis and plant hormone signal transduction, indicating the genetic basis of adaptation of Shanmei to the local environments. The high-quality genome sequences and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

scholarly journals Palaeogeographical And Archaeological Records Of Natural Changes Of The Jordanowo-Niesulice Subglacial Channel Near Lubrza, The Lubusz Lakeland

2015 ◽  
Vol 34 (3) ◽  
pp. 101-116 ◽  
Author(s):  
Magdalena Ratajczak-Szczerba ◽  
Iwona Sobkowiak-Tabaka ◽  
Iwona Okuniewska-Nowaczyk
Keyword(s):  
Late Glacial ◽  
Last Glacial Period ◽  
Geochemical Composition ◽  
Palynological Analysis ◽  
The Holocene ◽  
Ams Radiocarbon Dating ◽  
History Of ◽  
Geomorphological Analysis ◽  
Geological Research ◽  
The Last Glacial

Abstract The region of the Lubusz Lakeland in western Poland where there are a lot of subglacial channels provides opportunity for multi-proxy palaeoenvironmental reconstructions. None of them has not been the object of a specific study. The developmental history of the palaeolakes and their vicinity in the subglacial trough Jordanowo-Niesulice, spanning the Late Glacial and beginning of the Holocene, was investigated using geological research, lithological and geomorphological analysis, geochemical composition, palynological and archaeological research, OSL and AMS-radiocarbon dating. Geological research shows varied morphology of subglacial channel where at least two different reservoirs functioned in the end of the Last Glacial period and at the beginning of the Holocene. Mostly during the Bølling-Allerød interval and at the beginning of the Younger Dryas there took place melting of buried ice-blocks which preserved the analysied course of the Jordanowo-Niesulice trough. The level of water, and especially depth of reservoirs underwent also changes. Palynological analysis shows very diversified course of the Allerød interval.

Pleistocene history of Betula with special reference to the British Isles

1984 ◽  
Vol 85 (1-2) ◽  
pp. 1-11 ◽  
Author(s):  
J. H. Dickson
Keyword(s):  
Special Reference ◽  
Glacial Period ◽  
British Isles ◽  
Last Glacial Period ◽  
Glacial Sediments ◽  
Last Glacial ◽  
History Of ◽  
The Last Glacial

SynopsisBetula is well represented in the Pleistocene deposits of the British Isles; B. nana is often recovered from glacial sediments and tree Betula flourished early and late in the interglacial periods. In western and northern Britain, tree Betula has remained important in the forests since the last glacial period.

scholarly journals Genome Assembly of the Roundjaw Bonefish (Albula glossodonta), a Vulnerable Circumtropical Sportfish

2021 ◽  
Author(s):  
Brandon D. Pickett ◽  
Sheena Talma ◽  
Jessica R. Glass ◽  
Daniel Ence ◽  
Paul D. Cowley ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Indian Ocean ◽  
Genome Assembly ◽  
Anthropogenic Activities ◽  
Western Indian Ocean ◽  
Genetic Connectivity ◽  
High Quality ◽  
Widespread Species ◽  
High Quality Genome

ABSTRACTBackgroundBonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish, Albula glossodonta is the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCN’s Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which – prior to this study – were lacking for Albula species.ResultsWe generated a high-quality genome assembly of an A. glossodonta individual from Hawai‘i, USA. The assembled contigs had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was annotated with 28.3 K protein-coding genes. We then analyzed 66 A. glossodonta individuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow of A. glossodonta populations between Seychelles and Mauritius.ConclusionsQuantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.

Sister species, different histories: comparative phylogeography of two bird species associated with Amazonian open vegetation

2020 ◽  
Vol 132 (1) ◽  
pp. 161-173
Author(s):  
Camila D Ritter ◽  
Laís A Coelho ◽  
João Mg Capurucho ◽  
Sergio H Borges ◽  
Cíntia Cornelius ◽  
...  
Keyword(s):  
Population Structure ◽  
Bird Species ◽  
Population History ◽  
Sister Species ◽  
White Sand ◽  
Migration Rates ◽  
History Of ◽  
The Last Glacial Maximum ◽  
Vegetation Patches ◽  
The Last Glacial

Abstract Although the expansion of open vegetation within Amazonia was the basis for the Forest Refugia hypothesis, studies of Amazonian biota diversification have focussed mostly on forest taxa. Here we compare the phylogeographic patterns and population history of two sister species associated with Amazonian open-vegetation patches, Elaenia cristata and Elaenia ruficeps (Aves: Tyrannidae). We sampled individuals across Amazonia for both species, and in the central Brazilian savannas (Cerrado) for E. cristata. We sequenced one mitochondrial (ND2) and two nuclear (BFib7 and ACO) markers. We tested for population structure, estimated migration rates and elucidated the historical demography of each species. The Amazon River is the strongest barrier for E. ruficeps and the Branco River is a secondary barrier. For the more broadly distributed E. cristata, there was no discernible population structure. Both species attained their current genetic diversity recently and E. cristata has undergone demographic expansion since the Last Glacial Maximum, The results suggest distinct effects of recent landscape change on population history for the two species. E. ruficeps, which only occurs in Amazonian white sand habitats, has been more isolated in open-vegetation patches than E. cristata, which occupies Amazonian savannas, and extends into the Central Brazilian Cerrado.

scholarly journals Evaluation of 14C Ages of Organic Fractions of Paleosols from Loess-Paleosol Sequences Near Xian, China

Radiocarbon ◽  
1989 ◽  
Vol 31 (03) ◽  
pp. 680-695 ◽  
Author(s):  
M J Head ◽  
Weijian Zhou ◽  
Mingfu Zhou
Keyword(s):  
Shaanxi Province ◽  
Agricultural Activity ◽  
Agricultural Activities ◽  
The Loess Plateau ◽  
Last Glacial Period ◽  
Period Analysis ◽  
History Of ◽  
Climatic History ◽  
Organic Fractions ◽  
The Last Glacial

The 14C dating of organic fractions from paleosol layers containing <2% carbon in loess-paleosol sequences from the loess plateau in China has yielded results that are quite often much younger than the true age of the sediments. Percolation of modern organic materials from agricultural activities, and binding of these materials within the weathered clays of the paleosols has meant that conventional pretreatment techniques for 14C dating would not isolate a reliable chemical fraction. The total sequence from Bei Zhuang Cun, in Shaanxi Province, reflects the climatic history of the area for ca 30,000 years, ranging from the interstadial of the last glacial period to the postglacial period. Analysis of solvent extracts of organic material from this site indicates that they are mainly composed of carbohydrate residues originating from the relatively recent agricultural activity. Validity of the humic components for dating will be discussed.

scholarly journals Genetic Variability and Population Structure in the Sardinian Anglo-Arab Horse

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1018 ◽  
Author(s):  
Andrea Giontella ◽  
Francesca Maria Sarti ◽  
Irene Cardinali ◽  
Samira Giovannini ◽  
Raffaele Cherchi ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Iberian Peninsula ◽  
Inbreeding Coefficient ◽  
Historical Background ◽  
Effective Population ◽  
Horse Breed ◽  
Mitochondrial Data ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The Sardinian Anglo Arab (SAA) is a famous horse breed in Italy, with a significant historical background in the island of Sardinia. The aim of the study is to perform an evaluation of genetic variability in SAA using pedigree and mitochondrial data. In the current population, pedigree completeness was observed to be close to 100%, while the inbreeding coefficient and the average relatedness were lower than 3%. The ratio of effective founders/numbers of ancestors was 3.68 for the whole pedigree. The effective population size (Ne) computed by an individual increase in inbreeding (Ne_1) was 456.86, the Ne on equivalent generations (Ne_2) was 184.75, and this value slightly increased to 209.31 when computed by log-regression on equivalent generations (Ne_3). These results suggest the presence of crossbreeding and bottleneck phenomena, and they were compared with other Italian horses (reported in bibliography) to present the SAA among the Italian horse breeds scenario. Furthermore, the noteworthy mitochondrial variability reflects the use of a considerable number of founder mares; the contribution of L lineage was very important, probably because of the re-colonization from the Iberian Peninsula after the Last Glacial Maximum.

scholarly journals A successful habitat reconstruction effort, the short history of the European Bee-eater (Merops apiaster) colony at Albertirsa (Hungary)

2013 ◽  
Vol 21 (2) ◽  
pp. 47-51
Author(s):  
Sándor Urbán ◽  
Katalin Túri ◽  
Zoltán Vas ◽  
Tibor István Fuisz
Keyword(s):  
Glacial Period ◽  
Short History ◽  
Last Glacial Period ◽  
Reconstruction Effort ◽  
Nesting Sites ◽  
History Of ◽  
Merops Apiaster ◽  
Vertical Walls ◽  
Construction Works ◽  
The Last Glacial

Abstract In the Golyófogó Valley near Albertirsa natural erosion created near vertical walls in the loess deposited in the last glacial period, offering natural nesting sites for the European Bee-eater. Later the deeply cut coach roads, the pits of loess extraction and the construction works of the motorway nearby created further man-made banks. Hence by the 1970-ies a well-established colony bred here, but by the beginning of the 21st century, disturbance and the demise of vertical banks led to a serious reduction in the number of breeding pairs. The purchase of 5-hectare loess grassland plot and the adjacent loess bank, and later its reconstruction led to an unprecedented growth in the number of Bee-eaters. From 2010 the number of breeding pairs exceeded 200 every year. Not only the Bee-eater colony, but also the natural vegetation and the botanical values of the area are managed to maintain the population of rare and protected element of the local flora and fauna.

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