A multilocus molecular phylogeny for the avian genus Liocichla (Passeriformes: Leiothrichidae: Liocichla)

Mays, Herman L; McKay, Bailey D; Tietze, Dieter Thomas; Yao, Cheng-Te; Miller, Lindsey N; Moreland, Kathleen N; Lei, Fumin

doi:10.1186/s40657-015-0025-y

Avian Research

Table 2 Oligonucleotide sequences (5′–3′) used as PCR primers in this study

From: A multilocus molecular phylogeny for the avian genus Liocichla (Passeriformes: Leiothrichidae: Liocichla)

Oligonucleotide name	5′-CS tag + target sequence (5′ → 3′)	Locus description	Location	References
CS1-12630F	ACACTGACGACATGGTTCTACACAGCAGATCCTCAACGTCTC	Magmas-like protein	Autosomal ch: 14	[34]
CS2-12630R	TACGGTAGCAGAGACTTGGTCTCTGCAGGTAGAAGGAGCCTC	Magmas-like protein	Autosomal ch: 14	[34]
CS1-Liocichla_CS12630_F1	ACACTGACGACATGGTTCTACACAAGTGGTCGTAGTTCTGCC	Magmas-like protein	Autosomal ch: 14	This study
CS2-Liocichla_CS12630_R1	TACGGTAGCAGAGACTTGGTCTGAGATCCAGAAGGTAGAGGC	Magmas-like protein	Autosomal ch: 14	This study
CS1-14572F	ACACTGACGACATGGTTCTACACAGTAAAGAAACAGAAGTCC	Phosphotyrosyl phosphatase	Autosomal ch: 1	[34]
CS1-14572R	TACGGTAGCAGAGACTTGGTCTACTGCTGTGTGTTAGACTG	Phosphotyrosyl phosphatase	Autosomal ch: 1	[34]
CS1-Liocichla_CS14572_F1	ACACTGACGACATGGTTCTACAGTCCTCGAGACTCACATTCA	Phosphotyrosyl phosphatase	Autosomal ch: 1	This study
CS2-Liocichla_CS14572_R1	TACGGTAGCAGAGACTTGGTCTGCCATTCCTTCATAAGCTGC	Phosphotyrosyl phosphatase	Autosomal ch: 1	This study
CS1-23361F	ACACTGACGACATGGTTCTACAAAAGCTTATCAGGAGACCTC	Myeloid leukemia factor 2	Autosomal ch: 1	[34]
CS2-23361R	TACGGTAGCAGAGACTTGGTCTTTGATGTAGTCCTGCCTCTC	Myeloid leukemia factor 2	Autosomal ch: 1	[34]
CS1-Liocichla_CS23361_F1	ACACTGACGACATGGTTCTACAAGCCGCTGTCCGAGTCCCTT	Myeloid leukemia factor 2	Autosomal ch: 1	This study
CS2-Liocichla_CS23361_R1	TACGGTAGCAGAGACTTGGTCTCCCGCAGCACTTTGGCTTTGC	Myeloid leukemia factor 2	Autosomal ch: 1	This study
CS1-TGFB2F5	ACACTGACGACATGGTTCTACAGAAGCGTGCTCTAGATGCTG	Transforming growth factor β2	Autosomal ch: 3	[35]
CS2-TGFB2R6	TACGGTAGCAGAGACTTGGTCTAGGCAGCAATTATCCTGCAC	Transforming growth factor β2	Autosomal ch: 3	[35]
CS1-Liocichla_TGF_F1	ACACTGACGACATGGTTCTACATGCACACCCTCATTGTCAGACCCA	Transforming growth factor β2	Autosomal ch: 3	This study
CS2-Liocichla_TGF_R1	TACGGTAGCAGAGACTTGGTCTACAGGCAGGCAAGTCTGAGTCAC	Transforming growth factor β2	Autosomal ch: 3	This study
CS1-FIB5F	ACACTGACGACATGGTTCTACACGCCATACAGAGTATACTGTGACAT	β-fibrinogen intron 5	Autosomal ch: 4	[36]
CS2-FIB5R	TACGGTAGCAGAGACTTGGTCTGCCATCCTGGCGATTCTGAA	β-fibrinogen intron 5	Autosomal ch: 4	[36]
CS1-L5216	ACACTGACGACATGGTTCTACAGGCCCATACCCCGRAAATG	Mitochondrially encoded NADH dehydrogenase 2	Mitochondrial	[38]
CS2-H6313	TACGGTAGCAGAGACTTGGTCTACTCCTRTTTAAGGCTTTGAAGGC	Mitochondrially encoded NADH dehydrogenase 2	Mitochondrial	[38]
CS1-L10755	ACACTGACGACATGGTTCTACAGACTTCCAATCTTTAAAATCTGG	Mitochondrially encoded NADH dehydrogenase 3	Mitochondrial	[39]
CS2-H11151	TACGGTAGCAGAGACTTGGTCTGATTTGTTGAGCCGAAATCAAC	Mitochondrially encoded NADH dehydrogenase 3	Mitochondrial	[39]
CS1-L14851	ACACTGACGACATGGTTCTACACCTACTTAGGATCATTCGCCCT	Mitochondrially encoded cytochrome b	Mitochondrial	[40]
CS2-Hb745	TACGGTAGCAGAGACTTGGTCTTTTCTGGGTCTCCTAGTAGGTT	Mitochondrially encoded cytochrome b	Mitochondrial	[41]
CS1-Liocichla_cytb_F1	ACACTGACGACATGGTTCTACACATATGCCGAAACGTCCA	Mitochondrially encoded cytochrome b	Mitochondrial	This study
CS1-Liocichla_cytb_F2	ACACTGACGACATGGTTCTACACTTTCACATCGGCCGAGG	Mitochondrially encoded cytochrome b	Mitochondrial	This study
CS2-Liocichla_cytb_R1	TACGGTAGCAGAGACTTGGTCTCCTCAGAATGATATTTG	Mitochondrially encoded cytochrome b	Mitochondrial	This study
CS2-Liocichla_cytb_R2	TACGGTAGCAGAGACTTGGTCTGTCATTCTACTAGGG	Mitochondrially encoded cytochrome b	Mitochondrial	This study
CS2-Liocichla_cytb_R3	TACGGTAGCAGAGACTTGGTCTTAGTGGGTTGTTTGATCC	Mitochondrially encoded cytochrome b	Mitochondrial	This study
CS2-Liocichla_cytb_R4	TACGGTAGCAGAGACTTGGTCTGGTGTAGTAGGGGTGGAA	Mitochondrially encoded cytochrome b	Mitochondrial	This study

All oligonucleotides were synthesized by Integrated DNA Technologies (IDT) at the 25 nmole scale and purified by a standard desalting protocol. All oligonucleotides were tagged at the 5′ end with common sequence tags, either CS1 (5′-ACACTGACGACATGGTTCTACA) in the forward direction or CS2 (5′-TACGGTAGCAGAGACTTGGTCT) in the reverse direction. Locations for each locus are based on homology with the chicken (Gallus gallus) genome determined from an NCBI ‘gene’ search of the locus description in the case of transforming growth factor β2 and β-fibrinogen intron 5. For the remainder of the nuclear autosomal loci location was determined from the literature [34]. Internal oligonucleotides designed specifically to match conserved sequences for our samples (Liocichla and outgroups) are prefaced with ‘Liocichla’ in the oligonucleotide name.

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ISSN: 2053-7166

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