Short Communication: RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequences

Pharmawati M, Nurkamila US, Stevanus. 2016. RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequence. Biodiversitas 17: 687-693. In Bali, there are nine species of seagrass identified based on morphological characteristics. Devel...

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Autores principales:	MADE PHARMAWATI, UUL SHOVI NURKAMILA, STEVANUS STEVANUS
Formato:	article
Lenguaje:	EN
Publicado:	MBI & UNS Solo 2016
Materias:	dna fingerprinting key, matk, phylogenetic, rapd, seagrass Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/70983f2b966a4f20a154338167d31625
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spelling	oai:doaj.org-article:70983f2b966a4f20a154338167d316252021-11-14T02:27:09ZShort Communication: RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequences1412-033X2085-472210.13057/biodiv/d170243https://doaj.org/article/70983f2b966a4f20a154338167d316252016-08-01T00:00:00Zhttps://smujo.id/biodiv/article/view/346https://doaj.org/toc/1412-033Xhttps://doaj.org/toc/2085-4722Pharmawati M, Nurkamila US, Stevanus. 2016. RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequence. Biodiversitas 17: 687-693. In Bali, there are nine species of seagrass identified based on morphological characteristics. Development of molecular markers assist identificaton and evolutionary studies of many species including seagrass species. This study aimed to develop a fingerprinting key of nine seagrass species found at Sanur (Sanur Beach and Sindhu Beach), Bali, based on RAPD markers and to analyse their phylogenetic relationships using the matK region. Seagrass samples were collected at low tide and DNA was extracted using CTAB buffer. Six RAPD primers were used in the study. Sequences of matK were analyzed using MEGA 5.2. The phylogenetic tree was constructed by Maximum Likelihood method with 1000 bootstrap replicates. Based on RAPD banding pattern, a DNA fingerprinting key was successfully developed using only one primer â€” OPB12. Phylogenetic analysis of matK sequences grouped seagrass species by genera. There were five clades identified and the tree recognised that Cymodoceaceae was paraphyletic. This result is in disagreement with a previous study using combined rbcL and matK sequences which discussed the monophyly of Cymodoceaceae. Recent published paper using ITS sequence showed that cymodoceaceae might not be monophyletic group. This result supported our finding that Cymodoceaceae is not in the monophyletic group. Combined DNA sequences of chloroplast, nuclear and published paper using ITS sequencing showed that Cymodoceaceae mitochondrial DNA will further resolve phylogeny of seagrass species.MADE PHARMAWATIUUL SHOVI NURKAMILASTEVANUS STEVANUSMBI & UNS Soloarticledna fingerprinting key, matk, phylogenetic, rapd, seagrassBiology (General)QH301-705.5ENBiodiversitas, Vol 17, Iss 2 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	dna fingerprinting key, matk, phylogenetic, rapd, seagrass Biology (General) QH301-705.5
spellingShingle	dna fingerprinting key, matk, phylogenetic, rapd, seagrass Biology (General) QH301-705.5 MADE PHARMAWATI UUL SHOVI NURKAMILA STEVANUS STEVANUS Short Communication: RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequences
description	Pharmawati M, Nurkamila US, Stevanus. 2016. RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequence. Biodiversitas 17: 687-693. In Bali, there are nine species of seagrass identified based on morphological characteristics. Development of molecular markers assist identificaton and evolutionary studies of many species including seagrass species. This study aimed to develop a fingerprinting key of nine seagrass species found at Sanur (Sanur Beach and Sindhu Beach), Bali, based on RAPD markers and to analyse their phylogenetic relationships using the matK region. Seagrass samples were collected at low tide and DNA was extracted using CTAB buffer. Six RAPD primers were used in the study. Sequences of matK were analyzed using MEGA 5.2. The phylogenetic tree was constructed by Maximum Likelihood method with 1000 bootstrap replicates. Based on RAPD banding pattern, a DNA fingerprinting key was successfully developed using only one primer â€” OPB12. Phylogenetic analysis of matK sequences grouped seagrass species by genera. There were five clades identified and the tree recognised that Cymodoceaceae was paraphyletic. This result is in disagreement with a previous study using combined rbcL and matK sequences which discussed the monophyly of Cymodoceaceae. Recent published paper using ITS sequence showed that cymodoceaceae might not be monophyletic group. This result supported our finding that Cymodoceaceae is not in the monophyletic group. Combined DNA sequences of chloroplast, nuclear and published paper using ITS sequencing showed that Cymodoceaceae mitochondrial DNA will further resolve phylogeny of seagrass species.
format	article
author	MADE PHARMAWATI UUL SHOVI NURKAMILA STEVANUS STEVANUS
author_facet	MADE PHARMAWATI UUL SHOVI NURKAMILA STEVANUS STEVANUS
author_sort	MADE PHARMAWATI
title	Short Communication: RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequences
title_short	Short Communication: RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequences
title_full	Short Communication: RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequences
title_fullStr	Short Communication: RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequences
title_full_unstemmed	Short Communication: RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequences
title_sort	short communication: rapd fingerprinting key and phylogenetic of nine seagrass species from sanur coastal water, bali, indonesia using matk sequences
publisher	MBI & UNS Solo
publishDate	2016
url	https://doaj.org/article/70983f2b966a4f20a154338167d31625
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Short Communication: RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequences

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