Cytogenetic Mapping of 35 New Markers in the Alpaca (Vicugna pacos)

Mendoza, Mayra N.; Raudsepp, Terje; More, Manuel; Gutiérrez, Gustavo; León, F. A. Ponce de

doi:10.3390/genes11050522

Cited by 6 publications

(8 citation statements)

References 42 publications

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“…All camelid species are adapted to extreme environments [ 43 , 44 ], present unique and unusual features of the adaptive immune system [ 45 ], and form a basal clade in the Cetartiodactyla phylogenetic tree [ 46 ]. They are also important production species and icons of cultural legacy in their regions of origin [ 47 , 48 ]. These interests are reflected by recently elevated activities in camelid genomics resulting in chromosome-level reference genomes for the alpaca [ 44 ] and dromedary [ 49 ], though providing no information about the Y chromosome because both genomes were derived from female individuals.…”

Section: Introductionmentioning

confidence: 99%

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

Jevit

Davis

Castaneda

et al. 2021

Genes

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The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.

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Section: Introductionmentioning

confidence: 99%

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

Jevit

Davis

Castaneda

et al. 2021

Genes

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“…Unfortunately, there has been no unambiguous numbering and naming for all the chromosomes of C. farreri due to the lack of accurate chromosomal markers. In some species, such as sorghum (Kim et al, 2002(Kim et al, , 2005, silkworm (Yoshido et al, 2005), alpaca (Mendoza et al, 2020), and Senegalese sole (Merlo et al, 2021), all chromosomes could be identified by simultaneous FISH of a cocktail of landed large-insert DNA clones and/or repetitive DNA probes. In this study, we successfully distinguished all the 19 chromosomes of C. farreri through multiple two-color FISH and numbered them based on the chromosome-specific markers aided by the chromosomal morphology and lengths.…”

Section: Discussionmentioning

confidence: 99%

“…Li et al (2016) and Yang et al (2016) identified six and five pairs of chromosomes of Patinopecten yessoensis by six and eight fosmid clones, respectively. In some plant species, especially in those species with relatively small chromosomes, BAC-FISH had played an important role in chromosome identification and cytogenetic researches (Wang et al, 2007;Wai et al, 2010;Lee et al, 2020;Mendoza et al, 2020). In white campion Silene latifolia, 12 pairs of chromosomes were distinguished by the simultaneous hybridization of five BAC clones and three repetitive sequences on mitotic chromosomes (Lengerova et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

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

Jiang

Xing

et al. 2021

Front. Mar. Sci.

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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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“…The reference genome for this species is the Vic.Pac 3.1, which has been annotated for about 90%, and identifies ~76% of the genome to chromosomes [72,73]. The cytogenetic map currently known for the alpaca consists of 281 genes representative of all chromosomes [72]. So far, no genes have been identified by cytogenetic mapping on the Y-chromosome, except for ten loci on the PAR Yq-ter region (Table 2 and Figure 2) because the CHORI-246 BAC library derives from a female alpaca [74,75].…”

Section: Alpaca Y-chromosome and Parmentioning

confidence: 99%

State of the art on the physical mapping of the Y-chromosome in the Bovidae and comparison with other species — A review

et al. 2022

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The next generation sequencing (NGS) has significantly contributed to clarify the genome structure of many species of zootechnical interest. However, to date, some portions of the genome, especially those linked to a heterogametic nature such as the Y chromosome, are difficult to assemble and many gaps are still present. It is well known that the fluorescence in situ hybridization (FISH) is an excellent tool for identifying genes unequivocably mapped on chromosomes. Therefore, FISH can contribute to the localization of unplaced genome sequences, as well as to correct assembly errors generated by comparative bioinformatics. To this end, it is necessary to have starting points; therefore, in this study, we reviewed the physically mapped genes on the Y chromosome of cattle, buffalo, sheep, goats, pigs, horses and alpacas. A total of 208 loci were currently mapped by FISH. 89 were located in the malespecific region of the Y chromosome (MSY) and 119 were identified in the pseudoautosomal region (PAR). The loci reported in MSY and PAR were respectively: 18 and 25 in BTA, 5 and 7 in BBU, 5 and 24 in OAR, 5 and 19 in CHI, 10 and 16 in SSC, 46 and 18 in ECA. While in VPA only 10 loci are reported in the PAR region.The correct knowledge and assembly of all genome sequences, including those of genes mapped on the Y chromosome, will help to elucidate their biological processes, as well as to discover and exploit potentially epistasis effects useful for selection breeding programs.

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Cytogenetic Mapping of 35 New Markers in the Alpaca (Vicugna pacos)

Cited by 6 publications

References 42 publications

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

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

State of the art on the physical mapping of the Y-chromosome in the Bovidae and comparison with other species — A review

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