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Lai Z, Afriyie G, Cui H, Chen L, Xu Z, Chen Z, Liang Q, Luo J, Dong Z, Shao C, Guo Y, Wang Z. The First High-Quality Chromosome-Level Genome of the Lutjanus erythropterus (Bloch, 1790) Using Single-Tube Long Fragment Reads and Hi-C Technologies. Genome Biol Evol 2023; 15:evad171. [PMID: 37768150 PMCID: PMC10558211 DOI: 10.1093/gbe/evad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/10/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
Lutjanus erythropterus (Bloch, 1790), a Perciformes from the Lutjanidae family, is a commercially important species because of its taste and abundance. Despite the increase in genome resources in recent years, few genome assemblies are available within this fish family for comparative and functional studies. In this study, we determined the chromosomal genome of Crimson snapper using high-throughput Single-Tube Long Fragment Reads sequencing technology and Hi-C data. The final assembly size was 973.04 Mb with contig and scaffold N50 values of 1.51 and 40.65 Mb, respectively. We successfully scaffolded 95.84% of the genome sequence onto 24 chromosomes ranging in length from 19.37 to 49.48 Mb. A total of 22,663 genes and 13,877 gene families were identified in the genome, with 29 gene families being L. erythropterus-specific. A phylogenetic analysis using single-copy gene families showed that L. erythropterus and Larimichthys crocea had the closest genetic relationship with a divergence time of ∼47.7 Ma. This new genomic resource will facilitate comparative genomic studies as well as genetic breeding programs for L. erythropterus.
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Affiliation(s)
- Zhuoxin Lai
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Gyamfua Afriyie
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Haitao Cui
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Lujun Chen
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhenmin Xu
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zizhao Chen
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Quilu Liang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jie Luo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongdian Dong
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Changwei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yusong Guo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong, China
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Recent population expansion in wild gaur (Bos gaurus gaurus) as revealed by microsatellite markers. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00145-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ge H, Lin K, Shen M, Wu S, Wang Y, Zhang Z, Wang Z, Zhang Y, Huang Z, Zhou C, Lin Q, Wu J, Liu L, Hu J, Huang Z, Zheng L. De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C. Mol Ecol Resour 2019; 19:1461-1469. [PMID: 31325912 PMCID: PMC6899872 DOI: 10.1111/1755-0998.13064] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/02/2023]
Abstract
The red‐spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South‐East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome‐level reference genome of E. akaara by taking advantage of long‐read single‐molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi‐C. A red‐spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96‐fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi‐C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA‐seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein‐coding sequences. The high‐quality chromosome‐level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red‐spotted grouper in the future.
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Affiliation(s)
- Hui Ge
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
| | - Kebing Lin
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Mi Shen
- Nextomics Biosciences Institute, Wuhan, China
| | - Shuiqing Wu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
| | - Ziping Zhang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, China
| | - Yong Zhang
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Fujian Normal University, Fuzhou, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Lei Liu
- Nextomics Biosciences Institute, Wuhan, China
| | - Jiang Hu
- Nextomics Biosciences Institute, Wuhan, China
| | - Zhongchi Huang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Leyun Zheng
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
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Affiliation(s)
- Farshid S Ahrestani
- Foundation for Ecological Research, Advocacy and Learning, Auroville Post, Tamil Nadu, India
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De Lorenzi L, Arrighi S, Rossi E, Grignani P, Previderè C, Bonacina S, Cremonesi F, Parma P. XY (SRY-positive) Ovarian Disorder of Sex Development in Cattle. Sex Dev 2018; 12:196-203. [PMID: 29902792 DOI: 10.1159/000489869] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 12/29/2022] Open
Abstract
In mammals, the sex of the embryo depends on the SRY gene. In the presence of at least one intact and functional copy of this genetic factor (XY embryo) undifferentiated gonads will develop as testicles that subsequently determine the male phenotype. When this factor is not present, i.e., in subjects with 2 X chromosomes, an alternative pathway induces the development of ovaries, hence a female phenotype. In this case study, we describe a female cattle affected by a disorder of sex development (DSD). The subject, despite having a chromosomal XY constitution, did not develop testicles but ovaries, although they were underdeveloped. Moreover, genetic analysis highlighted the presence of the SRY gene with a normal coding region in both blood- and tissue-derived DNA. A chimeric condition was excluded in blood by sexing more than 350 cells and by allele profile investigation of 18 microsatellite markers. Array CGH analysis showed the presence of a not yet described 99-kb duplication (BTA18), but its relationship with the phenotype remains to be demonstrated. Gonadal histology demonstrated paired ovaries: the left one containing a large corpus luteum and the right one showing an underdeveloped aspect and very few early follicles. To our knowledge, we describe the first case of XY (SRY+) DSD in cattle with a normal SRY gene coding sequence.
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Du Y, Zou X, Xu Y, Guo X, Li S, Zhang X, Su M, Ma J, Guo S. Microsatellite Loci Analysis Reveals Post-bottleneck Recovery of Genetic Diversity in the Tibetan Antelope. Sci Rep 2016; 6:35501. [PMID: 27739522 PMCID: PMC5064351 DOI: 10.1038/srep35501] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/30/2016] [Indexed: 11/09/2022] Open
Abstract
The Tibetan antelope (chiru, Pantholops hodgsoni) is one of the most endangered mammals native to the Qinghai-Tibetan Plateau. The population size has rapidly declined over the last century due to illegal hunting and habitat damage. In the past 10 years, the population has reportedly been expanding due to conservation efforts. Several lines of evidence suggest that the Tibetan antelope has undergone a demographic bottleneck. However, the consequences of the bottleneck on genetic diversity and the post-bottleneck genetic recovery remain unknown. In this study, we investigate the genetic variation of 15 microsatellite loci from two Tibetan antelope populations sampled in 2003 (Pop2003) and 2013 (Pop2013). A higher level of genetic diversity (NA, 13.286; He, 0.840; PIC, 0.813; I, 2.114) was detected in Pop2013, compared to Pop2003 (NA, 12.929; He, 0.818; PIC, 0.789; I, 2.033). We observe that despite passing through the bottleneck, the Tibetan antelope retains high levels of genetic diversity. Furthermore, our results show significant or near significant increases in genetic diversity (He, PIC and I) in Pop2013 compared with Pop2003, which suggests that protection efforts did not arrive too late for the Tibetan antelope.
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Affiliation(s)
- Yurong Du
- School of Life and Geography Science, Qinghai Normal University, Xining 810008, China
| | - Xiaoyan Zou
- Key Laboratory of Evolution and Adaptation of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810007, China
| | - Yongtao Xu
- School of Life Science, Sichuan University, Chengdu 610064, China
| | - Xinyi Guo
- School of Life Science, Sichuan University, Chengdu 610064, China
| | - Shuang Li
- School of Life and Geography Science, Qinghai Normal University, Xining 810008, China
| | - Xuze Zhang
- School of Chemistry and Chemical Engineering, Qinghai University for Nationalities, Xining 810001, China
| | - Mengyu Su
- School of Life and Geography Science, Qinghai Normal University, Xining 810008, China
| | - Jianbin Ma
- School of Life and Geography Science, Qinghai Normal University, Xining 810008, China
| | - Songchang Guo
- Key Laboratory of Evolution and Adaptation of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810007, China
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Ndiaye NP, Sow A, Dayo GK, Ndiaye S, Sawadogo GJ, Sembène M. Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers. Vet World 2015; 8:994-1005. [PMID: 27047188 PMCID: PMC4774767 DOI: 10.14202/vetworld.2015.994-1005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/09/2015] [Accepted: 07/20/2015] [Indexed: 12/04/2022] Open
Abstract
Aim: In Senegal, uncontrolled cross-breeding of cattle breeds and changes in production systems are assumed to lead to an increase of gene flow between populations. This might constitute a relevant threat to livestock improvement. Therewith, this study was carried out to assess the current genetic diversity and the phylogenetic relationships of the four native Senegalese cattle breeds (Gobra zebu, Maure zebu, Djakoré, and N’Dama). Methods: Genomic DNA was isolated from blood samples of 120 unrelated animals collected from three agro-ecological areas of Senegal according to their phenotypic traits. Genotyping was done using 11 specific highly polymorphic microsatellite makers recommended by Food and Agriculture Organization. The basic measures of genetic variation and phylogenetic trees were computed using bioinformatics’ software. Results: A total of 115 alleles were identified with a number of alleles (Na) at one locus ranging from 6 to 16. All loci were polymorphic with a mean polymorphic information content of 0.76. The mean allelic richness (Rs) lay within the narrow range of 5.14 in N’Dama taurine to 6.10 in Gobra zebu. While, the expected heterozygosity (HE) per breed was high in general with an overall mean of 0.76±0.04. Generally, the heterozygote deficiency (FIS) of 0.073±0.026 was relatively due to inbreeding among these cattle breeds or the occurrence of population substructure. The high values of allelic and gene diversity showed that Senegalese native cattle breeds represented an important reservoir of genetic variation. The genetic distances and clustering trees concluded that the N’Dama cattle were most distinct among the investigated cattle populations. So, the principal component analyses showed qualitatively that there was an intensive genetic admixture between the Gobra zebu and Maure zebu breeds. Conclusions: The broad genetic diversity in Senegalese cattle breeds will allow for greater opportunities for improvement of productivity and adaptation relative to global changes. For the development of sustainable breeding and crossbreeding programs of Senegalese local breeds, effective management is needed towards genetic selection and transhumance to ensure their long-term survival.
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Affiliation(s)
- Ndèye Penda Ndiaye
- Department of Animal Biology, FST (UCAD), Dakar Fann-PO 5005, Laboratory of Endocrinology and Radio-immunology, EISMV, Dakar Fann-PO 5077, Senegal
| | - Adama Sow
- Laboratory of Endocrinology and Radio-immunology, EISMV, Dakar Fann-PO 5077, Senegal
| | | | | | | | - Mbacké Sembène
- Department of Animal Biology, FST (UCAD), Dakar Fann-PO 5005, Laboratory CBGP, IRD, Dakar Bel Air- PO 1386, Senegal
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Panasiewicz G, Zamojska A, Bieniek M, Gizejewski Z, Szafranska B. Persistent Müllerian duct syndrome (PMDS) in the Polish free-ranged bull populations of the European bison (Bison bonasus L.). Anim Reprod Sci 2015; 152:123-36. [DOI: 10.1016/j.anireprosci.2014.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 11/12/2014] [Accepted: 11/19/2014] [Indexed: 11/28/2022]
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Masih P, Luhariya RK, Das R, Gupta A, Mohindra V, Singh RK, Srivastava R, Chauhan UK, Jena JK, Lal KK. Cross-priming of microsatellite loci in subfamily cyprininae (family Cyprinidae): their utility in finding markers for population genetic analysis in three Indian major carps. Mol Biol Rep 2014; 41:5187-97. [PMID: 24792330 DOI: 10.1007/s11033-014-3386-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/22/2014] [Indexed: 11/30/2022]
Abstract
This study is aimed to identify polymorphic microsatellite markers and establish their potential for population genetics studies in three carp (family cyprinidae; subfamily cyprininae) species, Labeo rohita, Catla catla and Cirrhinus mrigala through use of cyprinid primers. These species have high commercial value and knowledge of genetic variation is important for management of farmed and wild populations. We tested 108 microsatellite primers from 11 species belonging to three different cyprinid subfamilies, Cyprininae, Barbinae and Leuciscinae out of which 63 primers (58.33%) successfully amplified orthologous loci in three focal species. Forty-two loci generated from 29 primers were polymorphic in these three carp species. Sequencing of amplified product confirmed the presence of SSRs in these 42 loci and orthologous nature of the loci. To validate potential of these 42 polymorphic loci in determining the genetic variation, we analyzed 486 samples of three focal species collected from Indus, Ganges and Brahmaputra river systems. Results indicated significant genetic variation, with mean number of alleles per locus ranging from 6.80 to 14.40 and observed heterozygosity ranging from 0.50 to 0.74 in the three focal species. Highly significant (P < 0.00001) allelic homogeneity values revealed that the identified loci can be efficiently used in population genetics analysis of these carp species. Further, thirty-two loci from 19 primers were useful for genotyping in more than one species. The data from the present study was compiled with cross-species amplification data from previous results on eight species of subfamily cyprininae to compare cross-transferability of microsatellite loci. It was revealed that out of 226 heterologous loci amplified, 152 loci that originated from 77 loci exhibited polymorphism and 45 primers were of multispecies utility, common for 2-7 species.
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Affiliation(s)
- Prachi Masih
- National Bureau of Fish Genetic Resources (ICAR), Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002, Uttar Pradesh, India
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In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB. BMC Genomics 2013; 14:43. [PMID: 23336431 PMCID: PMC3563513 DOI: 10.1186/1471-2164-14-43] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 01/09/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiation hybrid of buffalo and these reported STR can be used further in final gap plugging and "finishing" expected in de novo genome assembly. QTL and gene mapping needs mining of putative STR from buffalo genome at equal interval on each and every chromosome. Such markers have potential role in improvement of desirable characteristics, such as high milk yields, resistance to diseases, high growth rate. The STR mining from whole genome and development of user friendly database is yet to be done to reap the benefit of whole genome sequence. DESCRIPTION By in silico microsatellite mining of whole genome, we have developed first STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database (http://cabindb.iasri.res.in/buffsatdb/) which is a web based relational database of 910529 microsatellite markers, developed using PHP and MySQL database. Microsatellite markers have been generated using MIcroSAtellite tool. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes, motif type (mono-hexa), repeat motif and repeat kind (simple and composite). The search may be customised by limiting location of STR on chromosome as well as number of markers in that range. This is a novel approach and not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of the selected markers enabling researcher to select markers of choice at desired interval over the chromosome. The unique add-on of degenerate bases further helps in resolving presence of degenerate bases in current buffalo assembly. CONCLUSION Being first buffalo STR database in the world , this would not only pave the way in resolving current assembly problem but shall be of immense use for global community in QTL/gene mapping critically required to increase knowledge in the endeavour to increase buffalo productivity, especially for third world country where rural economy is significantly dependent on buffalo productivity.
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Rosli MKA, Zamzuriada AS, Syed-Shabthar SMF, Mahani MC, Abas-Mazni O, Md-Zain BM. Optimization of PCR conditions to amplify Cyt b, COI and 12S rRNA gene fragments of Malayan gaur (Bos gaurus hubbacki) mtDNA. GENETICS AND MOLECULAR RESEARCH 2011; 10:2554-68. [PMID: 22033937 DOI: 10.4238/2011.october.19.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
PCR has been extensively used for amplification of DNA sequences. We conducted a study to obtain the best amplification conditions for cytochrome b (Cyt b), cytochrome c oxidase I (COI) and 12S rRNA (12S) gene fragments of Malayan gaur mtDNA. DNA from seven Malayan gaur samples were extracted for PCR amplification. Various trials and combinations were tested to determine the best conditions of PCR mixture and profile to obtain the best PCR products for sequencing purposes. Four selected target factors for enhancing PCR, annealing temperature, concentration of primer pairs, amount of Taq polymerase, and PCR cycle duration, were optimized by keeping the amount of DNA template (50 ng/μL) and concentration of PCR buffer (1X), MgCl(2) (2.5 mM) and dNTP mixture (200 μM each) constant. All genes were successfully amplified, giving the correct fragment lengths, as assigned for both forward and reverse primers. The optimal conditions were determined to be: 0.1 μM primers for Cyt b and COI, 0.3 μM primers for 12S, 1 U Taq polymerase for all genes, 30 s of both denaturation and annealing cycles for Cyt b, 1 min of both stages for 12S and COI and annealing temperature of 58.4 ° C for Cyt b, 56.1 ° C for 12S and 51.3 ° C for COI. PCR products obtained under these conditions produced excellent DNA sequences.
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Affiliation(s)
- M K A Rosli
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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Rosli MKA, Zakaria SS, Syed-Shabthar SMF, Zainal ZZ, Shukor MN, Mahani MC, Abas-Mazni O, Md-Zain BM. Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences. GENETICS AND MOLECULAR RESEARCH 2011; 10:482-93. [PMID: 21476194 DOI: 10.4238/vol10-1gmr1002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.
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Affiliation(s)
- M K A Rosli
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
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HUNTER MARGARETKELLOGG, BRODERICK DAMIEN, OVENDEN JENNIFERR, TUCKER KIMBERLYPAUSE, BONDE ROBERTK, MCGUIRE PETERM, LANYON JANETM. Characterization of highly informative cross‐species microsatellite panels for the Australian dugong (
Dugong dugon
) and Florida manatee (
Trichechus manatus latirostris
) including five novel primers. Mol Ecol Resour 2010; 10:368-77. [PMID: 21565032 DOI: 10.1111/j.1755-0998.2009.02761.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- MARGARET KELLOGG HUNTER
- Sirenia Project, Florida Integrated Science Center, U.S. Geological Survey, 2201 NW 40th Terrace, Gainesville, FL 32605, USA
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Box 100245 UFHSC, Gainesville, FL 32610, USA
| | - DAMIEN BRODERICK
- Molecular Fisheries Laboratory, Queensland Department of Primary Industries and Fisheries, Level 3 Ritchie Building, Research Lane, The University of Queensland, St. Lucia, Qld 4072, Australia
| | - JENNIFER R. OVENDEN
- Molecular Fisheries Laboratory, Queensland Department of Primary Industries and Fisheries, Level 3 Ritchie Building, Research Lane, The University of Queensland, St. Lucia, Qld 4072, Australia
| | - KIMBERLY PAUSE TUCKER
- College of Marine Science, University of South Florida, 140 7th Ave S. MSL 119, St. Petersburg, FL 33701, USA
| | - ROBERT K. BONDE
- Sirenia Project, Florida Integrated Science Center, U.S. Geological Survey, 2201 NW 40th Terrace, Gainesville, FL 32605, USA
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Box 100245 UFHSC, Gainesville, FL 32610, USA
| | - PETER M. MCGUIRE
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Box 100245 UFHSC, Gainesville, FL 32610, USA
| | - JANET M. LANYON
- School of Biological Sciences, The University of Queensland, St. Lucia, Qld 4072, Australia
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