The ITS1-5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny.

TitleThe ITS1-5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny.
Publication TypeJournal Article
Year of Publication2011
AuthorsHřibová E, Čížková J, Christelová P, Taudien S, de Langhe E, Doležel J
JournalPLoS One
Volume6
Issue3
Paginatione17863
Date Published2011
ISSN1932-6203
KeywordsMusaceae, Phylogeny, Species Specificity
Abstract

Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades--Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes.

DOI10.1371/journal.pone.0017863
Alternate JournalPLoS ONE
PubMed ID21445344
PubMed Central IDPMC3062550
Showing 40 of 60 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
Novaria ITC1329 AAA subgr. Cavendish Unknown ITC
Pahang IRFA ITC0070 acuminata Unknown Unknown ITC
Musa ornata ITC0370 ornata subsp. ornata Unknown ITC
Balbisiana ITC0545 balbisiana Unknown Unknown ITC
Tuu Gia ITC0610 AA Unknown Unknown ITC
Cachaco ITC0643 ABB subgr. Bluggoe Unknown ITC
Long Tavoy ITC0093 acuminata subsp. burmannica Unknown ITC
Calcutta 4 ITC0249 acuminata subsp. burmannicoides India ITC
Pahang ITC0609 acuminata subsp. malaccensis Unknown ITC
Musa textilis ITC1072 textilis subsp. textilis Unknown ITC
Musa mannii ITC1411 Unknown Unknown Unknown ITC
Musa beccarii ITC1070 beccarii subsp. beccarii Unknown ITC
Khae (Phrae) ITC0660 acuminata subsp. siamea Thailand ITC
Malaccensis ITC0250 acuminata subsp. malaccensis Unknown ITC
Balbisiana (10852) ITC0094 balbisiana Unknown Unknown ITC
Cachaco Enano ITC0632 ABB subgr. Bluggoe Unknown ITC
Tavoy ITC0072 acuminata subsp. burmannica Unknown ITC
Pisang Mas ITC0653 AA subgr. Sucrier Malaysia ITC
Tani ITC1120 balbisiana Unknown Unknown ITC
Cameroun ITC0246 balbisiana Unknown Unknown ITC
Kivuvu ITC0157 ABB subgr. Bluggoe Unknown ITC
Dole ITC0767 ABB subgr. Bluggoe Unknown ITC
Tonton Kepa ITC0822 AS Unknown Papua New Guinea ITC
Borneo ITC0253 acuminata subsp. microcarpa Malaysia ITC
Musa acuminata ssp. banksii ITC0896 acuminata subsp. banksii Papua New Guinea ITC
Long Tavoy ITC0283 acuminata subsp. burmannica Unknown ITC
Musa coccinea ITC0287 coccinea subsp. coccinea Unknown ITC
Menei ITC1021 Fe'i Unknown Papua New Guinea ITC
Utafun ITC0913 Fe'i Unknown Papua New Guinea ITC
Musa peekelii ssp. peekelii ITC0917 peekelii subsp. peekelii Papua New Guinea ITC
Obino l'Ewai ITC0109 AAB subgr. Plantain Unknown ITC
Truncata ITC0393 acuminata subsp. truncata Unknown ITC
Musa velutina ITC0638 velutina subsp. velutina Unknown ITC
Honduras ITC0247 balbisiana Unknown Unknown ITC
Asupina ITC1027 Fe'i Unknown Papua New Guinea ITC
Wain ITC0813 Fe'i Unknown Papua New Guinea ITC
Musa jackeyi ITC0588 jackeyi subsp. jackeyi Unknown ITC
Pa (Rayong) ITC0672 acuminata subsp. siamea Thailand ITC
Musa velutina ITC0011 velutina subsp. velutina Unknown ITC
Galeo
ITC0259 AA Unknown Unknown ITC

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