AGRIS - 

2018

Novikov, A.A. | Semak, M.S., All-Russia Research and Development Inst. of Animal Breeding, Moscow Region

In the RG the state genetic testing (GT) program for breeding material of agricultural animals has being performed since 2001. The results of generic testing breeding animals were analyzed by the methods of immunogenotypic analysis and DNA testing in dairy breeding, sheep breeding, and horse breeding (data for 2014-2016). There given data on authenticity of origin and occurrence of genetic anomalies. There were tested 1400 cattle heads for authenticity of origin in 2014, 1075 – in 2015, 2738 – in 2016. Inconsistencies were revealed in 3.1% of cases on the average for 3 years. GT was realized most completely in horse breeding (the percentage completion was above 90%) and worst – in dairy breeding (only 60%). The results of GT in 26 regions of the Russian Federation were given. The regions have been revealed where this work is successful and where GT is not performed at all. 4065 cattle heads were tested for 14 types of anomalies in 2014-2016 in the Russian Federation by DNA technologies. The average percent of revealed anomalies was 6%. Practical significance of GT depends on how the results of genetic monitoring are used at farms. The main conditions of effectiveness of genetic monitoring are constancy and regularity of GT by any available method of genetic analysis. | В РФ с 2001 г. выполняется государственная программа генетической экспертизы племенного материала с.-х. животных (ГЭ). Проанализированы результаты генетического тестирования племенных животных методами иммуногенетического и ДНК-анализа в молочном скотоводстве, свиноводстве, овцеводстве, коневодстве (данные за 2014-2016 гг.). Приведены данные по достоверности происхождения и встречаемости генетических аномалий. На достоверность происхождения в 2014 г. проверено 1400 гол. КРС, в 2015 – 1075, в 2016 - 2738. Несоответствия выявлены в 3,1% случаев в среднем за 3 года. В 2016 г. программа ГЭ наиболее полно была реализована в коневодстве (процент выполнения задания свыше 90%) и хуже всего - в молочном скотоводстве (только на 60%). Приведены результаты выполнения ГЭ по 26 областям Российской Федерации. Выявлены регионы, где данная работа идет успешно, и где ГЭ не проводится вообще. Методом ДНК-технологий в Российской Федерации за 2014-2016 гг. на 14 видов аномалий протестировано 4065 гол. КРС. Средний процент выявленных аномалий - 6%. Практическая значимость ГЭ зависит от того, как результаты генетического мониторинга используются в хозяйствах. Основные условия эффективности генетического мониторинга - постоянство и систематичность проведения ГЭ любым из доступных методов генетического анализа.

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Central Scientific Agricultural Library - Russian Federation

2018

Kulikov, I.M., All-Russia Selection and Technological Inst. of Horticulture and Plant Breeding, Moscow (Russian Federation) | Kudryavtsev, A.M., Russian Academy of Agricultural Sciences, Moscow (Russian Federation). The N.I. Vavilov Inst. of Common Genetics | Marchenko, L.A. | Morozova, N.G., All-Russia Selection and Technological Inst. of Horticulture and Plant Breeding, Moscow (Russian Federation) | Boris, K.V. | Trifonova, A.A. | Dedova, L.V., Russian Academy of Agricultural Sciences, Moscow (Russian Federation). The N.I. Vavilov Inst. of Common Genetics

The genetic diversity of 16 apples varieties bred by All-Russian Research Horticultural Institute for Breeding, Cultivation and Nursery has been researched in the Vavilov Institute of General Genetics using microsatellite markers. The DNA of all analyzed apple varieties was isolated from fresh young leaves by the CTAB method. For the analysis, 10 SSR markers were selected: CH02c02b, CH03d01, CH03a04, CH02g04, CH01f03b, CH04e03, CH03d08, CH03d11, CH05g08, CH03d12. Amplification of the SSR-loci selected for the analysis was carried out using reagents manufactured by Dialat Ltd., in the T100 Thermal Cycler (Bio-Rad). As a result, 75 allelic variants were identified at ten of the studied loci. The number of alleles per locus varied from 5 (CH04e03, CH03d11, CH05g08) to 11 (CH03d01, CH03a04), and averaged 7.5 alleles per locus. For each of the microsatellite loci studied, clear and reproducible results of fragment analysis were obtained. On the analyzed 16 apple varieties, 75 alleles at ten studied loci were revealed. For one variety on all microsatellite loci used in the analysis, 17 to 20 alleles were amplified. For all studied varieties, except 'Triumph' variety, at least in one of the 10 examined SSR, loci allelic variants or combinations of allelic variants were marked, and they not were found in other varieties of the sample. Within the varieties 'Legenda', 'Marat Busurin' and 'Mayak Zagor'ya', such specific allelic combinations of allelic variants were revealed in six of the ten analyzed loci. The value of the informative index (PIC) was ranged from 0.49 (CH03d11) to 0.84 (CH03a04) and averaged 0.720. The indicators of the expected (HE) and observed (HO) heterozygosity were varied from 0.54 (CH03d11) and 0.50 (CH04e03) to 0.85 (CH03a04) and 1 (CH02g04, CH01f03b and CH03d12) with an average value of 0.752 (HE) and 0.838 (HO). All the studied SSR loci showed a fairly high level of polymorphism. Data on the allelic composition of the 16 studied apple varieties can be used to identify and certify these varieties. | Приведены результаты применения микросателлитных маркеров для изучения генетического разнообразия 16 сортов яблони селекции Всероссийского селекционно-технологического институт садоводства и питомниководства на базе Института общей генетики им. Н.И. Вавилова. ДНК всех проанализированных сортов яблони выделяли из свежих молодых листьев СТАБ методом. Для анализа были выбраны 10 SSR-маркеров: СН02с02b, CH03d01, CH03a04, CH02g04, CH01f03b, CH04e03, CH03d08, CH03d11, CH05g08, CH03d12. Амплификацию отобранных для анализа SSR-локусов проводили с использованием реактивов производства Диалат Лтд, в амплификаторе T100 Thermal Cycler (Bio-Rad). По каждому из изученных микросателлитных локусов были получены четкие и воспроизводимые результаты фрагментного анализа. В результате были выявлены 75 аллельных вариантов по десяти изученным локусам. Число аллелей на локус варьировало от 5 (CH04e03, CH03d11, CH05g08) до 11 (CH03d01, CH03a04), и в среднем составило 7,5 аллелей на локус. Для одного сорта по всем микросателлитным локусам, использованным в анализе, амплифицировалось от 17 до 20 аллелей. Для всех изученных сортов, кроме сорта Триумф, в хотя бы одном из исследованных 10 SSR-локусов отмечены аллельные варианты или сочетания аллельных вариантов, не выявленные у других сортов выборки. У сортов Легенда, Марат Бусурин и Маяк Загорья такие специфичные аллельные сочетания аллельных вариантов выявлены в шести из десяти проанализированных локусах. Значение показателя информативности (PIC) варьировало от 0,49 (CH03d11) до 0,84 (CH03a04) и в среднем составило 0,720. Показатели ожидаемой (HE) и наблюдаемой (HO) гетерозиготности варьировали от 0,54 (CH03d11) и 0,50 (CH04e03) до 0,85 (CH03a04) и 1 (CH02g04, CH01f03b и CH03d12) при среднем значение 0,752 (HE) и 0,838 (HO). Все изученные SSR-локусы показали достаточно высокий уровень полиморфизма. Данные об аллельном составе 16 изученных сортов яблони могут быть использованы для идентификации и паспортизации данных сортов.

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Central Scientific Agricultural Library - Russian Federation

2018

Kovalev, N.N. | Pozdnyakova, Yu.M. | Leskova, S.E., Far Eastern State Technical Fishery Univ., Vladivostok

Approbation of feed efficiency for Far Eastern trepang of cage culture was carried out using biostimulating components: cholesterol and DNA of salmon milt. Experiment was carried out in 6 groups of animals (feeds №№ 1-6) having starting weight of 50-70 g. Control measurement was realized in 60 and 103 days after beginning the experiment. It has been established that the largest weight gain of trepang (22.4 g) was observed when using feed containing cholesterol at a dosage of 40 g/kg of feed (feed № 2). Formulations containing cholesterol with a dosage of 20 g/kg of feed (feed № 1), DNA of salmon milt at a dosage of 1 g/kg (feed № 3) and feed containing the mix of bioactive substances (feed № 6). Studies of the chemical composition of trepang tissues showed that the greatest effect of experimental feeds resulted in the increase of myofibrillar proteins. Alkali-soluble proteins including collagen were the least influenced by bioactive substances. Accumulation of sarcoplasmic proteins was most active when using high-protein feed (control) and feed № 6: increase by 7.5 and by 7.2 times, respectively. Also, feeds using DNA at dosages of 1 and 5 g/kg (№ 3 and 4), proved to be highly effective, feeding them increased the water-soluble proteins by 6.0 and 6.6 times, respectively. Formulation characterized by high concentration of cholesterol didn't show increasing number of sarcoplasmic proteins. Concentration of hexosamines in trepang tissues rose 2.7 times due to increased cholesterol concentration in feeds. An increase in DNA content in feeds leads to an increase of hexosamine by 1.5 times. The same effect is observed when estimating feeds containing bioactive substances. Experimental data indicate high efficiency of trepang feeds with addition of bioactive substances mentioned above. | Проведены апробация и оценка эффективности кормов для садкового выращивания дальневосточного трепанга с использованием биостимулирующих компонентов: холестерина и ДНК из молок лососевых (МЛ). Эксперимент проводился на 6 группах животных (соответственно, корма №№ 1–6) с начальной массой 50–70 г, контрольные замеры осуществлялись через 60 и 103 дня после начала эксперимента. Установлено, что наибольшие привесы массы тела трепанга (22,4 г) наблюдались при использовании корма, в состав которого был включен холестерин в дозировке 40 г/кг корма (корм № 2). Также эффективными оказались рецептуры кормов с включением холестерина в дозировке 20 г/кг корма (корм № 1), ДНК МЛ в дозировке 1 г/кг (корм № 3) и содержащие оба биологически активных вещества (БАВ) (корм № 6, 20 г/кг холестерина и 5 г/г ДНК МЛ). В ходе исследования химического состава тканей трепанга установлено, что наибольший эффект применения экспериментальных кормов выразился в увеличении количества миофибриллярных белков. Менее всего влиянию БАВ оказались подвержены щелочерастворимые белки, к которым относится коллаген. Накопление саркоплазматических белков наиболее активно происходило при использовании высокобелкового корма (корм-контроль) и корма № 6: увеличение в 7,5 и 7,2 раза соответственно. Также высокоэффективными оказались корма с использованием ДНК в дозировках 1 и 5 г/кг корма (№ 3 и 4), скармливание которых способствовало увеличению водорастворимых белков в 6,0 и 6,6 раз соответственно. Рецептура, отличающаяся высоким содержанием холестерина, практически не приводила к увеличению количества саркоплазматических белков. При увеличении концентрации холестерина в корме количество гексозаминов в тканях трепанга возрастает в 2,7 раз. Увеличение содержания ДНК в корме приводит к увеличению количества гексозаминов в 1,5 раза. Такая тенденция наблюдается и при оценке кормов со смесью БАВ. Сделан вывод о высокой эффективности кормов для трепанга с добавлением указанных БАВ.

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Central Scientific Agricultural Library - Russian Federation

2018

Larkina, T.A., All-Russia Research and Development Inst. of Farm Animal Genetics and Breeding, St. Petersburg

There is an urgent need to find molecular markers for breeding broiler lines to reduce the abdominal fat content. It is to increase the nutritional value of the carcass and reduce the cost of feeding. DNA isolated from 150 broiler liver samples of the Iza Hubbard F-15 cross has been taken as the material to the study. The 35 day-old broilers have been taken from a private farm. DNA has been isolated according to the standard procedure using K proteinase and phenol. Analysis of FABP2 sequence in mutation has showed that the mutation results in recognition of TaqI restriction endonuclease site. Thus, the PCR-RFLP analysis method has been chosen for theoretical simulation of the test system for analyzing polymorphism of FABP2 gene in position -561 at substitution A with C. At the end of the incubation period, the fragments have been electrophoretically separated in a 1.5% agarose gel at 150 V in TBE buffer with the addition of ethidium bromide to a final concentration of 30 ng/ml, and the fragments have been visualized in ultraviolet light. According to the gene test results, the incidence of CC, AC and AA genotypes is the following: (0.42), (0.35) and (0.23), respectively. As for the fat content, Iza Hubbard F-15 cross broilers with heterozygous AS genotype slightly outperform the ones with homozygous genotypes, but these differences are not statistically significant. The medians of fat content in all three genotypes are practically on the same level, which indicates minor differences. Perhaps, to obtain a more meaningful result, it is required to increase the sampling, to include in the research another gene associated fat accumulation, and to study the additive mechanism of the gene action. | Имеется острая необходимость в поиске молекулярных маркеров для селекции родительских линий бройлеров на снижение содержания абдоминального жира, что позволит увеличить пищевую ценность тушки и уменьшить расходы на кормление. Материалом для исследований послужила ДНК, выделенная из 150 образцов печени бройлеров кросса Иза Хаббард Ф-15 в возрасте 35 дней. ДНК выделяли по стандартной методике с использованием протеиназы К и фенола. Анализ последовательности FABP2 в области мутации показал, что мутация приводит к узнаванию сайта рестрикции рестриктазой TaqI. Для теоретического моделирования тест-системы анализа полиморфизма гена FABP2 -561 с заменой A на C был выбран метод ПЦР-ПДРФ анализа. По окончании инкубации проводили электрофоретическое разделение фрагментов в 1,5%-ном агарозном геле при 150В в буфере ТВЕ с добавлением бромистого этидия до конечной концентрации 30 нг/мл и визуализировали фрагменты под ультрафиолетовым светом. По результатам исследования частота встречаемости генотипов составила: СС (0,42), АС (0,35), АА (0,23). Бройлеры кросса "Иза Хаббард Ф-15" с гетерозиготным генотипом АС немного превосходят по содержанию жира особей с гомозиготными генотипами, но эти различия статистически не достоверны. Медианные значения показателя у всех трех генотипов находятся практически на одном уровне, что говорит о незначительных различиях между ними. Возможно, для получения более значимого результата требуется увеличить выборку и добавить в изучение еще один ген, связанный с жиронакоплением, и рассмотреть уже аддитивный механизм работы генов.

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Central Scientific Agricultural Library - Russian Federation

2018

Marzanov, N.S., The L.K. Ehrnst All-Russia Research and Development Inst. of Animal Husbandry, Moscow Region

The researches were carried out during 2013–2017. The material for research was samples of wool bulbs from 24 different age-sex groups of elks living on the territory of the state nature reserve "Sumarokovskiy" (the Kostroma region). DNA on three microsatellite loci of elks (BM6438, CSSM43, BM1225) and 3 ones of cattle (ETH225; TGLA53; CSRM60) was analyzed. It was found that the level of actual heterozygosity varied from 0.375 in the ETH225 locus to 0.985, in the BM1225 locus; while the theoretically calculated index was 0.457 and 0.744, respectively. The greatest number of alleles was found in the BM1225 (n = 8) and CSSM43 (n = 10) loci. The comparison of the actual and theoretical heterozygosity levels showed that in three microsatellite loci (BM6438, CSRM60, ETH225) the heterozygotes were deficient in the studied elk population, which was confirmed by the coefficient data of the of excess (D = 5.7%). For a reliable genetic evaluation of the number of domesticated elks to be obtained the Robertson heterozygosity test and the Robertson homozygosity coefficient were used. The genetic imbalance was observed in 5 of the 6 microsatellite loci. The exception was the TGLA53 locus in which there was no genetic imbalance (xi-square is 2.42, the number of degrees of freedom is 3, P is greater than 0.05). Thus, the above stated data demonstrate the increase of homozygoting of the population, the number of effective alleles decreases, the genetic diversity decreases and thereby, the homogeneity of the studied group of elks under domestication increases. These investigations have shown the necessity of monitoring the allele fund of the elk population under domestication bred not only on the Sumarokovskaya moose farm, but also living in the wild nature of the Kostroma region. | Исследования проводили в течение 2013–2017 гг. Материалом для исследований служили образцы луковиц шерсти от 24 различных половозрастных групп лосей, обитающих на территории государственного природного заказника "Сумароковский" (Костромская обл.). Проанализировано ДНК по трём микросателлитным локусам лосей (BM6438; CSSM43; BM1225) и трём – крупного рогатого скота (ETH225; TGLA53; CSRM60). Установлено, что уровень фактической гетерозиготности варьировал от 0,375 в локусе ETH225 до 0,985 в локусе BM1225, а показатель теоретически рассчитанный составлял 0,457 и 0,744 соответственно. Наибольшее число аллелей было выявлено в локусах BM1225 (n = 8) и CSSM43 (n = 10). Сопоставление фактического и теоретического уровня гетерозиготности показало, что в трёх локусах микросателлитов (BM6438, CSRM60 и ETH225) у изучаемого поголовья лосей отмечался дефицит гетерозигот, что подтверждают данные коэффициента эксцесса (D = 5,7%). Для получения достоверной генетической оценки поголовья одомашниваемых лосей в работе был использован тест гетерозиготности по Робертсону и коэффициент гомозиготности по Робертсону. Нарушение генетического равновесия отмечали у 5 из 6 микросателлитных локусов. Исключением являлся TGLA53 локус, у которого не было отмечено нарушения генного равновесия (сумма хи-квадрат = 2,42; число степеней свободы = 3; Р больше 0,05). Полученные данные свидетельствуют об увеличении огомозигочивания поголовья: уменьшается число эффективных аллелей, снижается генетическое разнообразие, повышается тем самым однородность исследованной группы одомашниваемых лосей. Данные исследования показали необходимость определённого контроля аллелофонда поголовья одомашниваемых лосей, не только разводимых на Сумароковской лосеферме, но и живущих в условиях дикой природы Костромской области.

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Central Scientific Agricultural Library - Russian Federation

2018

Piamonte, R.T.

The abaca bunchy top has been previously identified to be caused by Banana bunchy top virus (BBTV) and Abaca bunchy top virus (ABTV). In this study, the genetic variability of BBTV and ABTV was determined through genomics approach. Virus isolates from a total of nine locations in Bicol, Visayas, and Mindanao were analyzed. The restriction enzyme digestion of rolling circle amplified DNA (RCA-RFLP) has indicated variability between the Bicol isolates, and isolates from Visayas and Mindanao. The DNA- U3 is most variable among the component genomes with eight variations detected by restriction mapping in the virus genomes. Sequence analyses revealed that Bicol isolates are ABTV while Visayas and Mindanao isolates are BBTV. Within species, the ABTV isolates have 99.5% nucleotide identities while BBTV isolates have 93 to 100%, indicating very low genetic variability. Between species, the BBTV and ABTV have 66 to 79% nucleotide identities. Phylogenetic relationship analysis divided the virus isolates into ABTV group in Bicol and BBTV group in Visayas and Mindanao. Some recombination evidences were detected in DNA-U3, DNA-S, DNA-R, and DNA-C of isolates L9-2 (Legaspi), SSS (Surigao del Sur), K13 (Kananga), and B7 (Baybay), respectively. The knowledge generated from this study has important implication in developing, screening and deploying of resistant genotypes to manage abaca bunchy top.

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University Library, University of the Philippines at Los Baños - Philippines

2018

Romero, M.V. | Mamucod, H.F. | Huliganga, R.C. | Corpuz, G.A. | Enriquez, J.O.S. | Millas, R.A. | Tabanao, R.A.

Amylose content (AC) is the most important factor affecting not only cooking and eating quality but also processing behavior of rice. Amylose is synthesized by the granule-bound starch synthase (GBSS) enzyme encoded by the WAXY locus in chromosome 6. The wild type allele, Wxa, is commonly found in cultivars from Indica subspecies while the Wxb allele is commonly distributed in Japonica subspecies. Base substitutions from G T in Wxb allele decrease splicing efficiency which affect the enzyme activity of GBSS and results in an endosperm with lower levels of amylose. This study determined the DNA sequence for WAXY locus for amylose content of 87 traditional rice varieties (TRVs) and validated through the iodine staining method. DNA was extracted from two-week old rice seedlings of TRVs. Polymerase chain reaction was performed in order to detect G/T base substitution and (CT)n repeats in the WAXY locus. Sequence analyses revealed polymorphism in the WAXY locus for AC showing G/T substitution SNP, and variation in (CT)n repeats. The functional nucleotide polymorphisms (FNP), G at the G/T base substitution and (CT) repeats nt 16, for intermediate to low AC were observed in 80 TRVs. A total of 75 TRVs showed similar findings when subjected to amylose analysis using iodine staining method. The difference in the genotypic and phenotypic data for some TRVs can be attributed to environmental factors leading to variation of about 6% in the AC of a certain variety. This study established an excellent match between the results of the iodine staining method for AC determination and DNA sequencing of waxy gene.

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University Library, University of the Philippines at Los Baños - Philippines

2018

Bagunu, E. | Lin, H.C. | Covshoff, S. | Montecillo, F. | Anonuevo, J.J. | Mercado, M.A. | Salazar, P. | Lim, L. | Reyes, J. | Yin, X. | Quick P.

The NADP-malic enzyme (ME) is a key enzyme of the C sub 4 photosynthesis pathway in NADP-ME type C sub 4 plants such as maize. It catalyzes the decarboxylation of malate in the bundle sheath cells to supply CO sub 2 to Rubisco. The full-length cDNA encoding the maize (Zea mays) specific C₄ NADP-malic enzyme was expressed in rice (Oryza sativa L.) under the control of the bundle sheath specific Zoysia japonica PCK (ZjPCK)promoter. The gene was tagged with AcV5 epitope so that it will be detected during the analysis of immunoblotting and immunolocalization. In this study, the T₀ transgenic rice plants were characterized using molecular and biochemical techniques. PCR analysis showed 58 positive plants for the transformed gene but only 16 plants have protein expression based on immunoblotting analysis. Varying copy number of ME gene insertion was also observed in the Southern blot analysis. In the cross-section of transgenic rice leaf, immunolocalization studies using confocal microscope showed that maize NADP-ME was not only localized in bundle sheath cells but also in the mesophyll cells of transgenic rice plants, taken together, transgenic plants expressing the NADP-ME gene will be advanced for further screening to obtain homozygous lines and will later on be used for the gene-pyramiding of C sub 4- photosynthesis related genes to make a C sub 4 Rice Prototype.

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University Library, University of the Philippines at Los Baños - Philippines

2018

Caasi-Lit, M.T. | Dolores, L.M. | del Rosario, E.E. | Pinili, M.S. | Langres, J.A. | Ledesma, E.E. | Calilung, B.J., Jr | Laude, R.A.P. | Lit, I.L., Jr

Insect vectors play a very important role in the spread of plant diseases. The reported insect vectors of phytoplasma in cassava in other countries are mostly planthoppers and leafhoppers and other sucking insects from the Order Hemiptera. In the Philippines, only few studies have reposted insect vectors of witches' broom disease of cassava. Hence, this paper aimed to survey the arthropods associated with cassava infected with phytoplasma disease. Cassava farms in several provinces in the country were visited. Insects were caught using sweep net, with 10 sweeps per replicate and 0 replicates per farmer's field. Samples were sorted and identified, and then classified according to functional guilds, namely: pest (herbivore), pollinator, parasite, predator, transients, and scavengers. Insect samples from phytoplasma-infected cassava were also collected and placed in 70% ethanol. The detection of phytoplasma in insect DNA was performed using nested PCR with primer specific for phytoplasma. Preliminary results in the field survey showed that the common insects associated with cassava were planthoppers, leafhoppers, mealybugs, and scale insects. It is possible that these collected insect pests maybe vectors of cassava phytoplasma disease. However, only mealybugs were collected form infected cassava plants especially those cassava which were already 6-7 months old. PCR analysis showed that some mealybugs were positive for phytoplasma.

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University Library, University of the Philippines at Los Baños - Philippines

2018

Diaz, M.G.Q. | Manalang, A.P. | Berdos, M.L.G. | Anacleto, M.R.U.

Next generation sequencing technology specifically Illumina HiSeq 2500 platform was employed to obtain the microbial community profile of the Manleluag Hyperalkaline Spring in Pangasinan [Philippines]. Sediment samples was collected from location NO [15 deg 42'11002'N (latitude)/120 deg 16'57.41'E (longitude)]. N1 [15 deg 42'17.30'N (latitude)/120 deg 17'0.70'E (longitude)], and N2 [15 deg 42'17.31'N (latitude)/120 deg 17'0.71'E (longitude). For each location three replicates were collected. DNAs were directly isolated from the sediments. Based on DNA quality and amount, five samples were sequenced, three replicates from NO and two DNA quality and amount, five samples were sequenced, three replicates from NO and two replicates for N2. DNA isolated from N1 is very small in amount and is not of good quality. Correlation analysis and Principal Coordinate Analysis (PCoA) of the obtained data showed that the two replicates of N2 were highly similar. For NO, replicates NO-1 and NO-2 were highly similar but their correlation with NO-3 was a lot lower. Because of this observed difference, the succeeding analyses used NO-1 and NO-2 for location O. Two bioinformatics pipelines include quality assessment of reads, assembly by MEGAHIT and taxonomic annotation using DIAMOND and MEGAN. In one of the pipelines, gene prediction using MetaGeneMark and generation of unigenes using CD-HIT and SoapAligner were employed after the metagenome assembly was generated. The second pipeline directly proceeded to taxonomic annotation after the metagenome assembly. Based on both piplelines, the most abundant phylum is Proteobacteria which includes classes Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria and Deltaproteobacteria, Acidobacteria, Delinococcus-Thermus, Planctomycetes, Actinobacteria, Armatimonadetes, and Verrumicrobia. Other abundant clases such as Clostridia, Anaerolineae, Bacteroidia, Solibacteres, and Deinococci also belong to the abundant phyla. The most abundant archaea is phylum Euryarcheota with Methanobacterium. The observed predominating taxa reflect the prevalent metabolic pathways that persist in environments characterized by high pH and exhibit serpentinization. The Manleluag Hyperalkaline Spring is a rich source of microorganisms. The data obtained in this study is very good genomic resource that can be used by the future researches.

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University Library, University of the Philippines at Los Baños - Philippines