A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858)

Solea senegalensis aquaculture production has experienced a great increase in the last decade and, consequently, the genome knowledge of the species is gaining attention. In this sense, obtaining a high-density genome mapping of the species could offer clues to the aquaculture improvement in those aspects not resolved so far. In the present article, a review and new processed data have allowed to obtain a high-density BAC-based cytogenetic map of S. senegalensis beside the analysis of the sequences of such BAC clones to achieve integrative data. A total of 93 BAC clones were used to localize the chromosome complement of the species and 588 genes were annotated, thus almost reaching the 2.5% of the S. senegalensis genome sequences. As a result, important data about its genome organization and evolution were obtained, such as the lesser gene density of the large metacentric pair compared with the other metacentric chromosomes, which supports the theory of a sex proto-chromosome pair. In addition, chromosomes with a high number of linked genes that are conserved, even in distant species, were detected. This kind of result widens the knowledge of this species’ chromosome dynamics and evolution.

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Chromosomal Map of the Model LegumeLotus japonicus

Genetics ◽

10.1093/genetics/161.4.1661 ◽

2002 ◽

Vol 161 (4) ◽

pp. 1661-1672 ◽

Cited By ~ 7

Author(s):

Andrea Pedrosa ◽

Niels Sandal ◽

Jens Stougaard ◽

Dieter Schweizer ◽

Andreas Bachmair

Keyword(s):

Repetitive Sequences ◽

Lotus Japonicus ◽

Chromosome Complement ◽

Linkage Groups ◽

Closely Related Species ◽

F1 Hybrid ◽

Bac Clones ◽

Genomic Regions ◽

Chromosomal Map

AbstractLotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F1 hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

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Ribosomal DNA localization on Lathyrus species chromosomes by FISH

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-020-00075-1 ◽

2020 ◽

Vol 18 (1) ◽

Author(s):

Hoda B. M. Ali ◽

Samira A. Osman

Keyword(s):

Genome Mapping ◽

Chromosome Complement ◽

5S Rdna ◽

Rdna Locus ◽

5S Rrna ◽

Rrna Genes ◽

45S Rdna ◽

Metaphase Chromosomes ◽

Lathyrus Odoratus ◽

5S Rrna Genes

Abstract Background Fluorescence In Situ Hybridization (FISH) played an essential role to locate the ribosomal RNA genes on the chromosomes that offered a new tool to study the chromosome structure and evolution in plant. The 45S and 5S rRNA genes are independent and localized at one or more loci per the chromosome complement, their positions along chromosomes offer useful markers for chromosome discriminations. In the current study FISH has been performed to locate 45S and 5S rRNA genes on the chromosomes of nine Lathyrus species belong to five different sections, all have chromosome number 2n=14, Lathyrus gorgoni Parl, Lathyrus hirsutus L., Lathyrus amphicarpos L., Lathyrus odoratus L., Lathyrus sphaericus Retz, Lathyrus incospicuus L, Lathyrus paranensis Burkart, Lathyrus nissolia L., and Lathyrus articulates L. Results The revealed loci of 45S and 5S rDNA by FISH on metaphase chromosomes of the examined species were as follow: all of the studied species have one 45S rDNA locus and one 5S rDNA locus except L. odoratus L., L. amphicarpos L. and L. sphaericus Retz L. have two loci of 5S rDNA. Three out of the nine examined species have the loci of 45S and 5S rRNA genes on the opposite arms of the same chromosome (L. nissolia L., L. amphicarpos L., and L. incospicuus L.), while L. hirsutus L. has both loci on the same chromosome arm. The other five species showed the loci of the two types of rDNA on different chromosomes. Conclusion The detected 5S and 45S rDNA loci in Lathyrus could be used as chromosomal markers to discriminate the chromosome pairs of the examined species. FISH could discriminate only one chromosome pair out of the seven pairs in three species, in L. hirsutus L., L. nissolia L. and L. incospicuus L., and two chromosome pairs in five species, in L. paranensis Burkart, L. odoratus L., L. amphicarpos L., L. gorgoni Parl. and L. articulatus L., while it could discriminate three chromosome pairs in L. sphaericus Retz. these results could contribute into the physical genome mapping of Lathyrus species and the evolution of rDNA patterns by FISH in the coming studies in future.

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Analysis of the histone cluster in Senegalese sole (Solea senegalensis): evidence for a divergent evolution of two canonical histone clusters

Genome ◽

10.1139/gen-2016-0143 ◽

2017 ◽

Vol 60 (5) ◽

pp. 441-453 ◽

Cited By ~ 7

Author(s):

Manuel Alejandro Merlo ◽

Roger Iziga ◽

Silvia Portela-Bens ◽

Ismael Cross ◽

Nadezda Kosyakova ◽

...

Keyword(s):

Product Diversification ◽

Divergent Evolution ◽

Solea Senegalensis ◽

Senegalese Sole ◽

Bac Clone ◽

Bac Clones ◽

Different Types ◽

Priority Species ◽

First Time ◽

Canonical Histone

The Senegalese sole (Solea senegalensis) is commercially very important and a priority species for aquaculture product diversification. The main histone cluster was identified within two BAC clones. However, two replacement histones (H1.0 and H3.3) were found in another BAC clone. Different types of canonical histones H2A and H2B were found within the same species for the first time. Phylogenetic analysis demonstrated that the different types of H1, H2A, and H2B histones were all more similar to each other than to canonical histones from other species. The canonical histone H3 of S. senegalensis differs from subtypes H3.1 and H3.2 in humans at the site of residue 96, where a serine is found instead of an alanine. This same polymorphism has been found only in Danio rerio. The karyotype of S. senegalensis comprises 21 pairs of chromosomes, distributed in 3 metacentric pairs, 2 submetacentric pairs, 4 subtelocentric pairs, and 12 acrocentric pairs. The two BAC clones that contain the clusters of canonical histones were both mapped on the largest metacentric pair, and mFISH analysis confirmed the co-location with the dmrt1 gene in that pair. Three chromosome markers have been identified which, in addition to those previously described, account for 18 chromosome pairs in S. senegalensis.

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Use of a Mycobacterium tuberculosisH37Rv Bacterial Artificial Chromosome Library for Genome Mapping, Sequencing, and Comparative Genomics

Infection and Immunity ◽

10.1128/iai.66.5.2221-2229.1998 ◽

1998 ◽

Vol 66 (5) ◽

pp. 2221-2229 ◽

Cited By ~ 144

Author(s):

Roland Brosch ◽

Stephen V. Gordon ◽

Alain Billault ◽

Thierry Garnier ◽

Karin Eiglmeier ◽

...

Keyword(s):

Comparative Genomics ◽

Bacterial Artificial Chromosome ◽

Genome Mapping ◽

Sequence Data ◽

Bac Library ◽

Artificial Chromosome ◽

Excellent Correlation ◽

Sequencing Project ◽

Polysaccharide Biosynthesis ◽

Bac Clones

ABSTRACT The bacterial artificial chromosome (BAC) cloning system is capable of stably propagating large, complex DNA inserts in Escherichia coli. As part of the Mycobacterium tuberculosis H37Rv genome sequencing project, a BAC library was constructed in the pBeloBAC11 vector and used for genome mapping, confirmation of sequence assembly, and sequencing. The library contains about 5,000 BAC clones, with inserts ranging in size from 25 to 104 kb, representing theoretically a 70-fold coverage of the M. tuberculosisgenome (4.4 Mb). A total of 840 sequences from the T7 and SP6 termini of 420 BACs were determined and compared to those of a partial genomic database. These sequences showed excellent correlation between the estimated sizes and positions of the BAC clones and the sizes and positions of previously sequenced cosmids and the resulting contigs. Many BAC clones represent linking clones between sequenced cosmids, allowing full coverage of the H37Rv chromosome, and they are now being shotgun sequenced in the framework of the H37Rv sequencing project. Also, no chimeric, deleted, or rearranged BAC clones were detected, which was of major importance for the correct mapping and assembly of the H37Rv sequence. The minimal overlapping set contains 68 unique BAC clones and spans the whole H37Rv chromosome with the exception of a single gap of ∼150 kb. As a postgenomic application, the canonical BAC set was used in a comparative study to reveal chromosomal polymorphisms between M. tuberculosis, M. bovis, and M. bovis BCG Pasteur, and a novel 12.7-kb segment present in M. tuberculosis but absent from M. bovis and M. bovis BCG was characterized. This region contains a set of genes whose products show low similarity to proteins involved in polysaccharide biosynthesis. The H37Rv BAC library therefore provides us with a powerful tool both for the generation and confirmation of sequence data as well as for comparative genomics and other postgenomic applications. It represents a major resource for present and future M. tuberculosis research projects.

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Integrative genetic map of repetitive DNA in the sole Solea senegalensis genome shows a Rex transposon located in a proto-sex chromosome

Scientific Reports ◽

10.1038/s41598-019-53673-6 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Emilio García ◽

Ismael Cross ◽

Silvia Portela-Bens ◽

María E. Rodríguez ◽

Aglaya García-Angulo ◽

...

Keyword(s):

Repetitive Dna ◽

Chromosome Pair ◽

Sex Chromosome ◽

Repetitive Sequences ◽

Class Ii ◽

Average Density ◽

Solea Senegalensis ◽

Fish Analysis ◽

Senegalese Sole ◽

Bac Clones

AbstractRepetitive sequences play an essential role in the structural and functional evolution of the genome, particularly in the sexual chromosomes. The Senegalese sole (Solea senegalensis) is a valuable flatfish in aquaculture albeit few studies have addressed the mapping and characterization of repetitive DNA families. Here we analyzed the Simple Sequence Repeats (SSRs) and Transposable elements (TEs) content from fifty-seven BAC clones (spanning 7.9 Mb) of this species, located in chromosomes by multiple fluorescence in situ hybridization (m-BAC-FISH) technique. The SSR analysis revealed an average density of 675.1 loci per Mb and a high abundance (59.69%) of dinucleotide coverage was observed, being ‘AC’ the most abundant. An SSR-FISH analysis using eleven probes was also carried out and seven of the 11 probes yielded positive signals. ‘AC’ probes were present as large clusters in almost all chromosomes, supporting the bioinformatic analysis. Regarding TEs, DNA transposons (Class II) were the most abundant. In Class I, LINE elements were the most abundant and the hAT family was the most represented in Class II. Rex/Babar subfamily, observed in two BAC clones mapping to chromosome pair 1, showed the longest match. This chromosome pair has been recently reported as a putative sexual proto-chromosome in this species, highlighting the possible role of the Rex element in the evolution of this chromosome. In the Rex1 phylogenetic tree, the Senegalese sole Rex1 retrotransposon could be associated with one of the four major ancient lineages in fish genomes, in which it is included O. latipes.

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Integrated karyotyping of sorghum by in situ hybridization of landed BACs

Genome ◽

10.1139/g01-141 ◽

2002 ◽

Vol 45 (2) ◽

pp. 402-412 ◽

Cited By ~ 58

Author(s):

Jeong-Soon Kim ◽

Kevin L Childs ◽

M Nurul Islam-Faridi ◽

Monica A Menz ◽

Robert R Klein ◽

...

Keyword(s):

In Situ Hybridization ◽

Genetic Manipulation ◽

Artificial Chromosome ◽

Linkage Groups ◽

Cytogenetic Map ◽

Structural Genomic ◽

Bac Clones ◽

Flow Sorting ◽

Fish Signal

The reliability of genome analysis and proficiency of genetic manipulation are increased by assignment of linkage groups to specific chromosomes, placement of centromeres, and orientation with respect to telomeres. We have endeavored to establish means to enable these steps in sorghum (Sorghum bicolor (L.) Moench), the genome of which contains ca. 780 Mbp spread across n = 10 chromosomes. Our approach relies on fluorescence in situ hybridization (FISH) and integrated structural genomic resources, including large-insert genomic clones in bacterial artificial chromosome (BAC) libraries. To develop robust FISH probes, we selected sorghum BACs by association with molecular markers that map near the ends of linkage groups, in regions inferred to be high in recombination. Overall, we selected 22 BACs that encompass the 10 linkage groups. As a prelude to development of a multiprobe FISH cocktail, we evaluated BAC-derived probes individually and in small groups. Biotin- and digoxygenin-labeled probes were made directly from the BAC clones and hybridized in situ to chromosomes without using suppressive unlabelled C0t-1 DNA. Based on FISH-signal strength and the relative degree of background signal, we judged 19 BAC-derived probes to be satisfactory. Based on their relative position, and collective association with all 10 linkage groups, we chose 17 of the 19 BACs to develop a 17-locus probe cocktail for dual-color detection. FISH of the cocktail allowed simultaneous identification of all 10 chromosomes. The results indicate that linkage and physical maps of sorghum allow facile selection of BAC clones according to position and FISH-signal quality. This capability will enable development of a high-quality molecular cytogenetic map and an integrated genomics system for sorghum, without need of chromosome flow sorting or microdissection. Moreover, transgeneric FISH experiments suggest that the sorghum system might be applicable to other Gramineae.Key words: integrated karyotyping, FISH, sorghum, BAC.

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Chromosome Identification and Cytogenetic Map Construction of Zhikong Scallop (Chlamys farreri) Based on Fluorescence in situ Hybridization

Frontiers in Marine Science ◽

10.3389/fmars.2021.741230 ◽

2021 ◽

Vol 8 ◽

Author(s):

Liping Hu ◽

Liming Jiang ◽

Qiang Xing ◽

Zujing Yang ◽

Qiang Zhao ◽

...

Keyword(s):

Molecular Breeding ◽

Repetitive Sequences ◽

Genomic Analysis ◽

Artificial Chromosome ◽

Chlamys Farreri ◽

Cytogenetic Map ◽

Zhikong Scallop ◽

Bac Clones ◽

Map Construction

Zhikong scallop (Chlamys farreri) is a bivalve species with broad economic and biological value, and an essential species of aquaculture in North China. Recently, efforts have been made to improve knowledge of genome, genetics, and cytogenetics, which is devoted to develop the molecular breeding project for the scallop. In this study, we constructed a cytogenetic map and identified all chromosomes of C. farreri using fluorescence in situ hybridization (FISH). A total of 100 Bacterial Artificial Chromosome (BAC) clones and 27 fosmid clones, including 58 microsatellite marker-anchored BAC clones, 4 genes-anchored BAC clones, 38 random BAC clones, 22 repetitive sequences-anchored fosmid clones, and 5 gene-anchored fosmid clones, were tested as probes, and 69 of them produced specific and stable signal on one pair of chromosomes. Then, multiple co-hybridizations were conducted to distinguish all the submetacentric and subtelocentric chromosomes with similar morphology by the abovementioned chromosome-specific markers. On this basis, a cytogenetic map of C. farreri containing 69 clones was constructed by co-hybridization and karyotype analysis. The markers covered all 19 pairs of chromosomes, and the average number of markers on each chromosome was 3.6. The cytogenetic map provides a platform for genetic and genomic analysis of C. farreri, which facilitates the molecular breeding project of C. farreri and promotes the comparative studies of chromosome evolution in scallops and even bivalves.

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Feeding Protocol Modulates the Digestive Process in Senegalese Sole (Solea senegalensis) Juveniles

Frontiers in Marine Science ◽

10.3389/fmars.2021.698403 ◽

2021 ◽

Vol 8 ◽

Author(s):

Neda Gilannejad ◽

Francisco J. Moyano ◽

Gonzalo Martínez-Rodríguez ◽

Manuel Yúfera

Keyword(s):

Clock Genes ◽

Temporal Organization ◽

Solea Senegalensis ◽

Senegalese Sole ◽

Farmed Fish ◽

Average Production ◽

Experimental Treatments ◽

Feeding Protocol ◽

Aquaculture Production

Understanding the daily digestive function could lead to more efficient feeding practices in the farmed fish species. In this work, the effect of several daily feeding protocols was assessed on the daily expression of the genes related to the circadian system (arntl1, clock, per1, and cry1), appetite (cck), nutrients hydrolysis (try1, ctrb1, pga, atp4a, cel, and amy2a), peptides transport (slc15a1), pH, and activity of key digestive (trypsin, chymotrypsin, amylase, 4C- and 7C-like lipases) and absorptive (alkaline phosphatase) enzymes in the gastrointestinal tract (GIT) of Senegalese sole (Solea senegalensis) juveniles. Some of the tested feeding protocols demonstrated a significant influence on the entrainment of the peripheral oscillator. The synchrony of slc15a1 and some digestive proenzymes with per1 in some of the experimental treatments could underline the role of clock genes in the regulation of these biological functions. Unlike gene expression of the digestive proenzymes wherein feeding protocol occasionally affected the temporal organization, the influence of this factor was determinant on the daily average production and/or circadian pattern of their activities. Daily pH was maintained at approximately neutral levels in all the GIT segments, and no pepsin activity was detected. Fish fed a single diurnal meal showed the lowest activity for all the studied enzymes, except for amylase, suggesting an insufficient utilization of the ingested nutrients. Higher amylase activity in this group, on the other hand, implies the possible activation of alternative compensatory metabolic pathways. Overall, our results pointed to the suitability of higher feeding frequencies, especially during dark hours, for the aquaculture production of this species.

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Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.)

Theoretical and Applied Genetics ◽

10.1007/s00122-011-1701-x ◽

2011 ◽

Vol 124 (2) ◽

pp. 249-259 ◽

Cited By ~ 57

Author(s):

Wei-Wei Zhang ◽

Jun-Song Pan ◽

Huan-Le He ◽

Chi Zhang ◽

Zheng Li ◽

...

Keyword(s):

Cucumis Sativus ◽

Genetic Map ◽

High Density ◽

Cucumis Sativus L ◽

Integrated Genetic Map

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Chromosome walking with BAC clones as a method of genome mapping

Plant Soil and Environment ◽

10.17221/2198-pse ◽

2008 ◽

Vol 53 (No. 10) ◽

pp. 447-450

Author(s):

Z. Kubát

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Mapping ◽

Region Of Interest ◽

Genomic Region ◽

Whole Genome ◽

Chromosome Walking ◽

Contig Assembly ◽

Genomic Libraries ◽

Bac Clones

Current sequencing projects are often based on random sequencing of genomic libraries followed by contig assembly by means of bioinformatics tools. This approach is convenient for whole genome sequencing projects. Chromosome walking described here is suitable for mapping and sequencing of short genomic regions in species where whole genome sequencing is not possible or for cloning gene from its closest known marker. This method is based on searching for overlapping BAC clones specific for the genomic region of interest.

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